Daily Papers

Spreadsheet table detection is the task of detecting all tables on a given sheet and locating their respective ranges. Automatic table detection is a key enabling technique and an initial step in spreadsheet data intelligence. However, the detection task is challenged by the diversity of table structures and table layouts on the spreadsheet. Considering the analogy between a cell matrix as spreadsheet and a pixel matrix as image, and encouraged by the successful application of Convolutional Neural Networks (CNN) in computer vision, we have developed TableSense, a novel end-to-end framework for spreadsheet table detection. First, we devise an effective cell featurization scheme to better leverage the rich information in each cell; second, we develop an enhanced convolutional neural network model for table detection to meet the domain-specific requirement on precise table boundary detection; third, we propose an effective uncertainty metric to guide an active learning based smart sampling algorithm, which enables the efficient build-up of a training dataset with 22,176 tables on 10,220 sheets with broad coverage of diverse table structures and layouts. Our evaluation shows that TableSense is highly effective with 91.3\% recall and 86.5\% precision in EoB-2 metric, a significant improvement over both the current detection algorithm that are used in commodity spreadsheet tools and state-of-the-art convolutional neural networks in computer vision.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

Generative modeling of single-cell RNA-seq data has shown invaluable potential in community-driven tasks such as trajectory inference, batch effect removal and gene expression generation. However, most recent deep models generating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, ignoring the inherently discrete and over-dispersed nature of single-cell data, which limits downstream applications and hinders the incorporation of robust noise models. Moreover, crucial aspects of deep-learning-based synthetic single-cell generation remain underexplored, such as controllable multi-modal and multi-label generation and its role in the performance enhancement of downstream tasks. This work presents Cell Flow for Generation (CFGen), a flow-based conditional generative model for multi-modal single-cell counts, which explicitly accounts for the discrete nature of the data. Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks such as conditioning on multiple attributes and boosting rare cell type classification via data augmentation. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose a new DL algorithm, Iterative Codebook Feature Learning~(ICFL), and combine it with a pre-processing step that uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical perturbations. The Cell Painting assay is the most popular imaged-based profiling assay wherein six small-molecule dyes label eight cellular compartments and thousands of measurements are made, describing quantitative traits such as size, shape, intensity, and texture within the nucleus, cytoplasm, and whole cell (Cimini et al., 2023). We have created the Cell Painting Gallery, a publicly available collection of Cell Painting datasets, with granular dataset descriptions and access instructions. It is hosted by AWS on the Registry of Open Data (RODA). As of January 2024, the Cell Painting Gallery holds 656 terabytes (TB) of image and associated numerical data. It includes the largest publicly available Cell Painting dataset, in terms of perturbations tested (Joint Undertaking for Morphological Profiling or JUMP (Chandrasekaran et al., 2023)), along with many other canonical datasets using Cell Painting, close derivatives of Cell Painting (such as LipocyteProfiler (Laber et al., 2023) and Pooled Cell Painting (Ramezani et al., 2023)).

Deep learning-based image generation has seen significant advancements with diffusion models, notably improving the quality of generated images. Despite these developments, generating images with unseen characteristics beneficial for downstream tasks has received limited attention. To bridge this gap, we propose Style-Extracting Diffusion Models, featuring two conditioning mechanisms. Specifically, we utilize 1) a style conditioning mechanism which allows to inject style information of previously unseen images during image generation and 2) a content conditioning which can be targeted to a downstream task, e.g., layout for segmentation. We introduce a trainable style encoder to extract style information from images, and an aggregation block that merges style information from multiple style inputs. This architecture enables the generation of images with unseen styles in a zero-shot manner, by leveraging styles from unseen images, resulting in more diverse generations. In this work, we use the image layout as target condition and first show the capability of our method on a natural image dataset as a proof-of-concept. We further demonstrate its versatility in histopathology, where we combine prior knowledge about tissue composition and unannotated data to create diverse synthetic images with known layouts. This allows us to generate additional synthetic data to train a segmentation network in a semi-supervised fashion. We verify the added value of the generated images by showing improved segmentation results and lower performance variability between patients when synthetic images are included during segmentation training. Our code will be made publicly available at [LINK].

Sparse autoencoders (SAEs) emerged as a promising tool for mechanistic interpretability of transformer-based foundation models. Very recently, SAEs were also adopted for the visual domain, enabling the discovery of visual concepts and their patch-wise attribution to tokens in the transformer model. While a growing number of foundation models emerged for medical imaging, tools for explaining their inferences are still lacking. In this work, we show the applicability of SAEs for hematology. We propose CytoSAE, a sparse autoencoder which is trained on over 40,000 peripheral blood single-cell images. CytoSAE generalizes to diverse and out-of-domain datasets, including bone marrow cytology, where it identifies morphologically relevant concepts which we validated with medical experts. Furthermore, we demonstrate scenarios in which CytoSAE can generate patient-specific and disease-specific concepts, enabling the detection of pathognomonic cells and localized cellular abnormalities at the patch level. We quantified the effect of concepts on a patient-level AML subtype classification task and show that CytoSAE concepts reach performance comparable to the state-of-the-art, while offering explainability on the sub-cellular level. Source code and model weights are available at https://github.com/dynamical-inference/cytosae.

Sparse autoencoders (SAEs) have lately been used to uncover interpretable latent features in large language models. Here, we explore their potential for decomposing latent representations in complex and high-dimensional biological data, where the underlying variables are often unknown. On simulated data we show that generative hidden variables can be captured in learned representations in the form of superpositions. The degree to which they are learned depends on the completeness of the representations. Superpositions, however, are not identifiable if these generative variables are unknown. SAEs can to some extent recover these variables, yielding interpretable features. Applied to single-cell multi-omics data, we show that an SAE can uncover key biological processes such as carbon dioxide transport and ion homeostasis, which are crucial for red blood cell differentiation and immune function. Our findings highlight how SAEs can be used in advancing interpretability in biological and other scientific domains.

Over the last five years, deep generative models have gradually been adopted for various tasks in biological research. Notably, image-to-image translation methods showed to be effective in revealing subtle phenotypic cell variations otherwise invisible to the human eye. Current methods to achieve this goal mainly rely on Generative Adversarial Networks (GANs). However, these models are known to suffer from some shortcomings such as training instability and mode collapse. Furthermore, the lack of robustness to invert a real image into the latent of a trained GAN prevents flexible editing of real images. In this work, we propose PhenDiff, an image-to-image translation method based on conditional diffusion models to identify subtle phenotypes in microscopy images. We evaluate this approach on biological datasets against previous work such as CycleGAN. We show that PhenDiff outperforms this baseline in terms of quality and diversity of the generated images. We then apply this method to display invisible phenotypic changes triggered by a rare neurodevelopmental disorder on microscopy images of organoids. Altogether, we demonstrate that PhenDiff is able to perform high quality biological image-to-image translation allowing to spot subtle phenotype variations on a real image.

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

Time-lapse fluorescent microscopy (TLFM) combined with predictive mathematical modelling is a powerful tool to study the inherently dynamic processes of life on the single-cell level. Such experiments are costly, complex and labour intensive. A complimentary approach and a step towards in silico experimentation, is to synthesise the imagery itself. Here, we propose Multi-StyleGAN as a descriptive approach to simulate time-lapse fluorescence microscopy imagery of living cells, based on a past experiment. This novel generative adversarial network synthesises a multi-domain sequence of consecutive timesteps. We showcase Multi-StyleGAN on imagery of multiple live yeast cells in microstructured environments and train on a dataset recorded in our laboratory. The simulation captures underlying biophysical factors and time dependencies, such as cell morphology, growth, physical interactions, as well as the intensity of a fluorescent reporter protein. An immediate application is to generate additional training and validation data for feature extraction algorithms or to aid and expedite development of advanced experimental techniques such as online monitoring or control of cells. Code and dataset is available at https://git.rwth-aachen.de/bcs/projects/tp/multi-stylegan.

Cell instance segmentation is a fundamental task in digital pathology with broad clinical applications. Recently, vision foundation models, which are predominantly based on Vision Transformers (ViTs), have achieved remarkable success in pathology image analysis. However, their improvements in cell instance segmentation remain limited. A key challenge arises from the tokenization process in ViTs, which substantially reduces the spatial resolution of input images, leading to suboptimal segmentation quality, especially for small and densely packed cells. To address this problem, we propose CellVTA (Cell Vision Transformer with Adapter), a novel method that improves the performance of vision foundation models for cell instance segmentation by incorporating a CNN-based adapter module. This adapter extracts high-resolution spatial information from input images and injects it into the ViT through a cross-attention mechanism. Our method preserves the core architecture of ViT, ensuring seamless integration with pretrained foundation models. Extensive experiments show that CellVTA achieves 0.538 mPQ on the CoNIC dataset and 0.506 mPQ on the PanNuke dataset, which significantly outperforms the state-of-the-art cell segmentation methods. Ablation studies confirm the superiority of our approach over other fine-tuning strategies, including decoder-only fine-tuning and full fine-tuning. Our code and models are publicly available at https://github.com/JieZheng-ShanghaiTech/CellVTA.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Realistic hair strand generation is crucial for applications like computer graphics and virtual reality. While diffusion models can generate hairstyles from text or images, these inputs lack precision and user-friendliness. Instead, we propose the first sketch-based strand generation model, which offers finer control while remaining user-friendly. Our framework tackles key challenges, such as modeling complex strand interactions and diverse sketch patterns, through two main innovations: a learnable strand upsampling strategy that encodes 3D strands into multi-scale latent spaces, and a multi-scale adaptive conditioning mechanism using a transformer with diffusion heads to ensure consistency across granularity levels. Experiments on several benchmark datasets show our method outperforms existing approaches in realism and precision. Qualitative results further confirm its effectiveness. Code will be released at [GitHub](https://github.com/fighting-Zhang/StrandDesigner).

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

Histopathology and transcriptomics are fundamental modalities in oncology, encapsulating the morphological and molecular aspects of the disease. Multi-modal self-supervised learning has demonstrated remarkable potential in learning pathological representations by integrating diverse data sources. Conventional multi-modal integration methods primarily emphasize modality alignment, while paying insufficient attention to retaining the modality-specific structures. However, unlike conventional scenarios where multi-modal inputs share highly overlapping features, histopathology and transcriptomics exhibit pronounced heterogeneity, offering orthogonal yet complementary insights. Histopathology provides morphological and spatial context, elucidating tissue architecture and cellular topology, whereas transcriptomics delineates molecular signatures through gene expression patterns. This inherent disparity introduces a major challenge in aligning them while maintaining modality-specific fidelity. To address these challenges, we present MIRROR, a novel multi-modal representation learning method designed to foster both modality alignment and retention. MIRROR employs dedicated encoders to extract comprehensive features for each modality, which is further complemented by a modality alignment module to achieve seamless integration between phenotype patterns and molecular profiles. Furthermore, a modality retention module safeguards unique attributes from each modality, while a style clustering module mitigates redundancy and enhances disease-relevant information by modeling and aligning consistent pathological signatures within a clustering space. Extensive evaluations on TCGA cohorts for cancer subtyping and survival analysis highlight MIRROR's superior performance, demonstrating its effectiveness in constructing comprehensive oncological feature representations and benefiting the cancer diagnosis.

Segmenting cells and tracking their motion over time is a common task in biomedical applications. However, predicting accurate instance-wise segmentation and cell motions from microscopy imagery remains a challenging task. Using microstructured environments for analyzing single cells in a constant flow of media adds additional complexity. While large-scale labeled microscopy datasets are available, we are not aware of any large-scale dataset, including both cells and microstructures. In this paper, we introduce the trapped yeast cell (TYC) dataset, a novel dataset for understanding instance-level semantics and motions of cells in microstructures. We release 105 dense annotated high-resolution brightfield microscopy images, including about 19k instance masks. We also release 261 curated video clips composed of 1293 high-resolution microscopy images to facilitate unsupervised understanding of cell motions and morphology. TYC offers ten times more instance annotations than the previously largest dataset, including cells and microstructures. Our effort also exceeds previous attempts in terms of microstructure variability, resolution, complexity, and capturing device (microscopy) variability. We facilitate a unified comparison on our novel dataset by introducing a standardized evaluation strategy. TYC and evaluation code are publicly available under CC BY 4.0 license.

Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spanning 6 different gene panels and 54 donors. We systematically evaluated state-of-the-art image and gene expression encoders across multiple pretraining strategies and assessed their effectiveness on two downstream tasks: gene mutation classification and gene expression prediction. Our benchmark demonstrates that gene expression encoders are the primary determinant of strong representational alignment, and that gene models pretrained on spatial transcriptomics data outperform both those trained without spatial data and simple baseline approaches. However, downstream task evaluation reveals a striking contradiction: while contrastive pretraining consistently improves gene mutation classification performance, it degrades direct gene expression prediction compared to baseline encoders trained without cross-modal objectives. We identify batch effects as a key factor that interferes with effective cross-modal alignment. Our findings highlight the critical need for batch-robust multimodal learning approaches in spatial transcriptomics. To accelerate progress in this direction, we release HESCAPE, providing standardized datasets, evaluation protocols, and benchmarking tools for the community

Deep features are a cornerstone of computer vision research, capturing image semantics and enabling the community to solve downstream tasks even in the zero- or few-shot regime. However, these features often lack the spatial resolution to directly perform dense prediction tasks like segmentation and depth prediction because models aggressively pool information over large areas. In this work, we introduce FeatUp, a task- and model-agnostic framework to restore lost spatial information in deep features. We introduce two variants of FeatUp: one that guides features with high-resolution signal in a single forward pass, and one that fits an implicit model to a single image to reconstruct features at any resolution. Both approaches use a multi-view consistency loss with deep analogies to NeRFs. Our features retain their original semantics and can be swapped into existing applications to yield resolution and performance gains even without re-training. We show that FeatUp significantly outperforms other feature upsampling and image super-resolution approaches in class activation map generation, transfer learning for segmentation and depth prediction, and end-to-end training for semantic segmentation.

In standard hospital blood tests, the traditional process requires doctors to manually isolate leukocytes from microscopic images of patients' blood using microscopes. These isolated leukocytes are then categorized via automatic leukocyte classifiers to determine the proportion and volume of different types of leukocytes present in the blood samples, aiding disease diagnosis. This methodology is not only time-consuming and labor-intensive, but it also has a high propensity for errors due to factors such as image quality and environmental conditions, which could potentially lead to incorrect subsequent classifications and misdiagnosis. To address these issues, this paper proposes an innovative method of leukocyte detection: the Multi-level Feature Fusion and Deformable Self-attention DETR (MFDS-DETR). To tackle the issue of leukocyte scale disparity, we designed the High-level Screening-feature Fusion Pyramid (HS-FPN), enabling multi-level fusion. This model uses high-level features as weights to filter low-level feature information via a channel attention module and then merges the screened information with the high-level features, thus enhancing the model's feature expression capability. Further, we address the issue of leukocyte feature scarcity by incorporating a multi-scale deformable self-attention module in the encoder and using the self-attention and cross-deformable attention mechanisms in the decoder, which aids in the extraction of the global features of the leukocyte feature maps. The effectiveness, superiority, and generalizability of the proposed MFDS-DETR method are confirmed through comparisons with other cutting-edge leukocyte detection models using the private WBCDD, public LISC and BCCD datasets. Our source code and private WBCCD dataset are available at https://github.com/JustlfC03/MFDS-DETR.

Optimal transport (OT) theory focuses, among all maps T:R^drightarrow R^d that can morph a probability measure onto another, on those that are the ``thriftiest'', i.e. such that the averaged cost c(x, T(x)) between x and its image T(x) be as small as possible. Many computational approaches have been proposed to estimate such Monge maps when c is the ell_2^2 distance, e.g., using entropic maps [Pooladian'22], or neural networks [Makkuva'20, Korotin'20]. We propose a new model for transport maps, built on a family of translation invariant costs c(x, y):=h(x-y), where h:=1{2}|cdot|_2^2+tau and tau is a regularizer. We propose a generalization of the entropic map suitable for h, and highlight a surprising link tying it with the Bregman centroids of the divergence D_h generated by h, and the proximal operator of tau. We show that choosing a sparsity-inducing norm for tau results in maps that apply Occam's razor to transport, in the sense that the displacement vectors Delta(x):= T(x)-x they induce are sparse, with a sparsity pattern that varies depending on x. We showcase the ability of our method to estimate meaningful OT maps for high-dimensional single-cell transcription data, in the 34000-d space of gene counts for cells, without using dimensionality reduction, thus retaining the ability to interpret all displacements at the gene level.

Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments. While deep learning approaches have proven useful for general cell segmentation tasks, existing segmentation tools for the yeast-microstructure setting rely on traditional machine learning approaches. Here we present convolutional neural networks trained for multiclass segmenting of individual yeast cells and discerning these from cell-similar microstructures. We give an overview of the datasets recorded for training, validating and testing the networks, as well as a typical use-case. We showcase the method's contribution to segmenting yeast in microstructured environments with a typical synthetic biology application in mind. The models achieve robust segmentation results, outperforming the previous state-of-the-art in both accuracy and speed. The combination of fast and accurate segmentation is not only beneficial for a posteriori data processing, it also makes online monitoring of thousands of trapped cells or closed-loop optimal experimental design feasible from an image processing perspective.

Text-to-Image models such as Stable Diffusion have shown impressive image generation synthesis, thanks to the utilization of large-scale datasets. However, these datasets may contain sexually explicit, copyrighted, or undesirable content, which allows the model to directly generate them. Given that retraining these large models on individual concept deletion requests is infeasible, fine-tuning algorithms have been developed to tackle concept erasing in diffusion models. While these algorithms yield good concept erasure, they all present one of the following issues: 1) the corrupted feature space yields synthesis of disintegrated objects, 2) the initially synthesized content undergoes a divergence in both spatial structure and semantics in the generated images, and 3) sub-optimal training updates heighten the model's susceptibility to utility harm. These issues severely degrade the original utility of generative models. In this work, we present a new approach that solves all of these challenges. We take inspiration from the concept of classifier guidance and propose a surgical update on the classifier guidance term while constraining the drift of the unconditional score term. Furthermore, our algorithm empowers the user to select an alternative to the erasing concept, allowing for more controllability. Our experimental results show that our algorithm not only erases the target concept effectively but also preserves the model's generation capability.

During their formative years, radiology trainees are required to interpret hundreds of mammograms per month, with the objective of becoming apt at discerning the subtle patterns differentiating benign from malignant lesions. Unfortunately, medico-legal and technical hurdles make it difficult to access and query medical images for training. In this paper we train a generative adversarial network (GAN) to synthesize 512 x 512 high-resolution mammograms. The resulting model leads to the unsupervised separation of high-level features (e.g. the standard mammography views and the nature of the breast lesions), with stochastic variation in the generated images (e.g. breast adipose tissue, calcification), enabling user-controlled global and local attribute-editing of the synthesized images. We demonstrate the model's ability to generate anatomically and medically relevant mammograms by achieving an average AUC of 0.54 in a double-blind study on four expert mammography radiologists to distinguish between generated and real images, ascribing to the high visual quality of the synthesized and edited mammograms, and to their potential use in advancing and facilitating medical education.

Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significant obstacle to understanding biophysical processes such as cell adhesion and migration. Here, we develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. Strikingly, experimental images of a single focal adhesion protein, such as zyxin, are sufficient to predict forces and generalize to unseen biological regimes. This protein field alone contains enough information to yield accurate predictions even if forces themselves are generated by many interacting proteins. We next develop two approaches - one explicitly constrained by physics, the other more agnostic - that help construct data-driven continuum models of cellular forces using this single focal adhesion field. Both strategies consistently reveal that cellular forces are encoded by two different length scales in adhesion protein distributions. Beyond adherent cell mechanics, our work serves as a case study for how to integrate neural networks in the construction of predictive phenomenological models in cell biology, even when little knowledge of the underlying microscopic mechanisms exist.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

Hematoxylin and Eosin (H&E) staining is widely regarded as the standard in pathology for diagnosing diseases and tracking tumor recurrence. While H&E staining shows tissue structures, it lacks the ability to reveal specific proteins that are associated with disease severity and treatment response. Immunohistochemical (IHC) stains use antibodies to highlight the expression of these proteins on their respective cell types, improving diagnostic accuracy, and assisting with drug selection for treatment. Despite their value, IHC stains require additional time and resources, limiting their utilization in some clinical settings. Recent advances in deep learning have positioned Image-to-Image (I2I) translation as a computational, cost-effective alternative for IHC. I2I generates high fidelity stain transformations digitally, potentially replacing manual staining in IHC. Diffusion models, the current state of the art in image generation and conditional tasks, are particularly well suited for virtual IHC due to their ability to produce high quality images and resilience to mode collapse. However, these models require extensive and diverse datasets (often millions of samples) to achieve a robust performance, a challenge in virtual staining applications where only thousands of samples are typically available. Inspired by the success of multitask deep learning models in scenarios with limited data, we introduce STAINDIFFUSER, a novel multitask diffusion architecture tailored to virtual staining that achieves convergence with smaller datasets. STAINDIFFUSER simultaneously trains two diffusion processes: (a) generating cell specific IHC stains from H&E images and (b) performing H&E based cell segmentation, utilizing coarse segmentation labels exclusively during training. STAINDIFFUSER generates high-quality virtual stains for two markers, outperforming over twenty I2I baselines.

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

Deep learning models have emerged as a powerful tool for various medical applications. However, their success depends on large, high-quality datasets that are challenging to obtain due to privacy concerns and costly annotation. Generative models, such as diffusion models, offer a potential solution by synthesizing medical images, but their practical adoption is hindered by long inference times. In this paper, we propose the use of an optimal transport flow matching approach to accelerate image generation. By introducing a straighter mapping between the source and target distribution, our method significantly reduces inference time while preserving and further enhancing the quality of the outputs. Furthermore, this approach is highly adaptable, supporting various medical imaging modalities, conditioning mechanisms (such as class labels and masks), and different spatial dimensions, including 2D and 3D. Beyond image generation, it can also be applied to related tasks such as image enhancement. Our results demonstrate the efficiency and versatility of this framework, making it a promising advancement for medical imaging applications. Code with checkpoints and a synthetic dataset (beneficial for classification and segmentation) is now available on: https://github.com/milad1378yz/MOTFM.

Domain generalization is critical for real-world applications of machine learning to microscopy images, including histopathology and fluorescence imaging. Artifacts in these modalities arise through a complex combination of factors relating to tissue collection and laboratory processing, as well as factors intrinsic to patient samples. In fluorescence imaging, these artifacts stem from variations across experimental batches. The complexity and subtlety of these artifacts make the enumeration of data domains intractable. Therefore, augmentation-based methods of domain generalization that require domain identifiers and manual fine-tuning are inadequate in this setting. To overcome this challenge, we introduce ContriMix, a domain generalization technique that learns to generate synthetic images by disentangling and permuting the biological content ("content") and technical variations ("attributes") in microscopy images. ContriMix does not rely on domain identifiers or handcrafted augmentations and makes no assumptions about the input characteristics of images. We assess the performance of ContriMix on two pathology datasets dealing with patch classification and Whole Slide Image label prediction tasks respectively (Camelyon17-WILDS and RCC subtyping), and one fluorescence microscopy dataset (RxRx1-WILDS). Without any access to domain identifiers at train or test time, ContriMix performs similar or better than current state-of-the-art methods in all these datasets, motivating its usage for microscopy image analysis in real-world settings where domain information is hard to come by. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

Given a single in-the-wild human photo, it remains a challenging task to reconstruct a high-fidelity 3D human model. Existing methods face difficulties including a) the varying body proportions captured by in-the-wild human images; b) diverse personal belongings within the shot; and c) ambiguities in human postures and inconsistency in human textures. In addition, the scarcity of high-quality human data intensifies the challenge. To address these problems, we propose a Generalizable image-to-3D huMAN reconstruction framework, dubbed GeneMAN, building upon a comprehensive multi-source collection of high-quality human data, including 3D scans, multi-view videos, single photos, and our generated synthetic human data. GeneMAN encompasses three key modules. 1) Without relying on parametric human models (e.g., SMPL), GeneMAN first trains a human-specific text-to-image diffusion model and a view-conditioned diffusion model, serving as GeneMAN 2D human prior and 3D human prior for reconstruction, respectively. 2) With the help of the pretrained human prior models, the Geometry Initialization-&-Sculpting pipeline is leveraged to recover high-quality 3D human geometry given a single image. 3) To achieve high-fidelity 3D human textures, GeneMAN employs the Multi-Space Texture Refinement pipeline, consecutively refining textures in the latent and the pixel spaces. Extensive experimental results demonstrate that GeneMAN could generate high-quality 3D human models from a single image input, outperforming prior state-of-the-art methods. Notably, GeneMAN could reveal much better generalizability in dealing with in-the-wild images, often yielding high-quality 3D human models in natural poses with common items, regardless of the body proportions in the input images.

Multiplex immunofluorescence and immunohistochemistry benefit patients by allowing cancer pathologists to identify several proteins expressed on the surface of cells, enabling cell classification, better understanding of the tumour micro-environment, more accurate diagnoses, prognoses, and tailored immunotherapy based on the immune status of individual patients. However, they are expensive and time consuming processes which require complex staining and imaging techniques by expert technicians. Hoechst staining is much cheaper and easier to perform, but is not typically used in this case as it binds to DNA rather than to the proteins targeted by immunofluorescent techniques, and it was not previously thought possible to differentiate cells expressing these proteins based only on DNA morphology. In this work we show otherwise, training a deep convolutional neural network to identify cells expressing three proteins (T lymphocyte markers CD3 and CD8, and the B lymphocyte marker CD20) with greater than 90% precision and recall, from Hoechst 33342 stained tissue only. Our model learns previously unknown morphological features associated with expression of these proteins which can be used to accurately differentiate lymphocyte subtypes for use in key prognostic metrics such as assessment of immune cell infiltration,and thereby predict and improve patient outcomes without the need for costly multiplex immunofluorescence.

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

Large diffusion-based Text-to-Image (T2I) models have shown impressive generative powers for text-to-image generation as well as spatially conditioned image generation. For most applications, we can train the model end-toend with paired data to obtain photorealistic generation quality. However, to add an additional task, one often needs to retrain the model from scratch using paired data across all modalities to retain good generation performance. In this paper, we tackle this issue and propose a novel strategy to scale a generative model across new tasks with minimal compute. During our experiments, we discovered that the variance maps of intermediate feature maps of diffusion models capture the intensity of conditioning. Utilizing this prior information, we propose MaxFusion, an efficient strategy to scale up text-to-image generation models to accommodate new modality conditions. Specifically, we combine aligned features of multiple models, hence bringing a compositional effect. Our fusion strategy can be integrated into off-the-shelf models to enhance their generative prowess.

To synthesize high-fidelity samples, diffusion models typically require auxiliary data to guide the generation process. However, it is impractical to procure the painstaking patch-level annotation effort required in specialized domains like histopathology and satellite imagery; it is often performed by domain experts and involves hundreds of millions of patches. Modern-day self-supervised learning (SSL) representations encode rich semantic and visual information. In this paper, we posit that such representations are expressive enough to act as proxies to fine-grained human labels. We introduce a novel approach that trains diffusion models conditioned on embeddings from SSL. Our diffusion models successfully project these features back to high-quality histopathology and remote sensing images. In addition, we construct larger images by assembling spatially consistent patches inferred from SSL embeddings, preserving long-range dependencies. Augmenting real data by generating variations of real images improves downstream classifier accuracy for patch-level and larger, image-scale classification tasks. Our models are effective even on datasets not encountered during training, demonstrating their robustness and generalizability. Generating images from learned embeddings is agnostic to the source of the embeddings. The SSL embeddings used to generate a large image can either be extracted from a reference image, or sampled from an auxiliary model conditioned on any related modality (e.g. class labels, text, genomic data). As proof of concept, we introduce the text-to-large image synthesis paradigm where we successfully synthesize large pathology and satellite images out of text descriptions.

Immunohistochemical (IHC) staining highlights the molecular information critical to diagnostics in tissue samples. However, compared to H&E staining, IHC staining can be much more expensive in terms of both labor and the laboratory equipment required. This motivates recent research that demonstrates that the correlations between the morphological information present in the H&E-stained slides and the molecular information in the IHC-stained slides can be used for H&E-to-IHC stain translation. However, due to a lack of pixel-perfect H&E-IHC groundtruth pairs, most existing methods have resorted to relying on expert annotations. To remedy this situation, we present a new loss function, Adaptive Supervised PatchNCE (ASP), to directly deal with the input to target inconsistencies in a proposed H&E-to-IHC image-to-image translation framework. The ASP loss is built upon a patch-based contrastive learning criterion, named Supervised PatchNCE (SP), and augments it further with weight scheduling to mitigate the negative impact of noisy supervision. Lastly, we introduce the Multi-IHC Stain Translation (MIST) dataset, which contains aligned H&E-IHC patches for 4 different IHC stains critical to breast cancer diagnosis. In our experiment, we demonstrate that our proposed method outperforms existing image-to-image translation methods for stain translation to multiple IHC stains. All of our code and datasets are available at https://github.com/lifangda01/AdaptiveSupervisedPatchNCE.

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how self-supervised deep learning approaches scale when training larger models on larger microscopy datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised baselines. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 93-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised baseline at inferring known biological relationships curated from public databases. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.

Extracting single-cell information from microscopy data requires accurate instance-wise segmentations. Obtaining pixel-wise segmentations from microscopy imagery remains a challenging task, especially with the added complexity of microstructured environments. This paper presents a novel dataset for segmenting yeast cells in microstructures. We offer pixel-wise instance segmentation labels for both cells and trap microstructures. In total, we release 493 densely annotated microscopy images. To facilitate a unified comparison between novel segmentation algorithms, we propose a standardized evaluation strategy for our dataset. The aim of the dataset and evaluation strategy is to facilitate the development of new cell segmentation approaches. The dataset is publicly available at https://christophreich1996.github.io/yeast_in_microstructures_dataset/ .

Earlier diagnosis of Leukemia can save thousands of lives annually. The prognosis of leukemia is challenging without the morphological information of White Blood Cells (WBC) and relies on the accessibility of expensive microscopes and the availability of hematologists to analyze Peripheral Blood Samples (PBS). Deep Learning based methods can be employed to assist hematologists. However, these algorithms require a large amount of labeled data, which is not readily available. To overcome this limitation, we have acquired a realistic, generalized, and large dataset. To collect this comprehensive dataset for real-world applications, two microscopes from two different cost spectrums (high-cost HCM and low-cost LCM) are used for dataset capturing at three magnifications (100x, 40x, 10x) through different sensors (high-end camera for HCM, middle-level camera for LCM and mobile-phone camera for both). The high-sensor camera is 47 times more expensive than the middle-level camera and HCM is 17 times more expensive than LCM. In this collection, using HCM at high resolution (100x), experienced hematologists annotated 10.3k WBC types (14) and artifacts, having 55k morphological labels (Cell Size, Nuclear Chromatin, Nuclear Shape, etc.) from 2.4k images of several PBS leukemia patients. Later on, these annotations are transferred to other 2 magnifications of HCM, and 3 magnifications of LCM, and on each camera captured images. Along with the LeukemiaAttri dataset, we provide baselines over multiple object detectors and Unsupervised Domain Adaptation (UDA) strategies, along with morphological information-based attribute prediction. The dataset will be publicly available after publication to facilitate the research in this direction.

Generating high-resolution, photo-realistic images has been a long-standing goal in machine learning. Recently, Nguyen et al. (2016) showed one interesting way to synthesize novel images by performing gradient ascent in the latent space of a generator network to maximize the activations of one or multiple neurons in a separate classifier network. In this paper we extend this method by introducing an additional prior on the latent code, improving both sample quality and sample diversity, leading to a state-of-the-art generative model that produces high quality images at higher resolutions (227x227) than previous generative models, and does so for all 1000 ImageNet categories. In addition, we provide a unified probabilistic interpretation of related activation maximization methods and call the general class of models "Plug and Play Generative Networks". PPGNs are composed of 1) a generator network G that is capable of drawing a wide range of image types and 2) a replaceable "condition" network C that tells the generator what to draw. We demonstrate the generation of images conditioned on a class (when C is an ImageNet or MIT Places classification network) and also conditioned on a caption (when C is an image captioning network). Our method also improves the state of the art of Multifaceted Feature Visualization, which generates the set of synthetic inputs that activate a neuron in order to better understand how deep neural networks operate. Finally, we show that our model performs reasonably well at the task of image inpainting. While image models are used in this paper, the approach is modality-agnostic and can be applied to many types of data.

Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight cellular components in the images. We propose a new approach, StainFuser, which treats this problem as a style transfer task using a novel Conditional Latent Diffusion architecture, eliminating the need for handcrafted color components. With this method, we curate SPI-2M the largest stain normalization dataset to date of over 2 million histology images with neural style transfer for high-quality transformations. Trained on this data, StainFuser outperforms current state-of-the-art GAN and handcrafted methods in terms of the quality of normalized images. Additionally, compared to existing approaches, it improves the performance of nuclei instance segmentation and classification models when used as a test time augmentation method on the challenging CoNIC dataset. Finally, we apply StainFuser on multi-gigapixel Whole Slide Images (WSIs) and demonstrate improved performance in terms of computational efficiency, image quality and consistency across tiles over current methods.

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

Text-to-image diffusion generative models can generate high quality images at the cost of tedious prompt engineering. Controllability can be improved by introducing layout conditioning, however existing methods lack layout editing ability and fine-grained control over object attributes. The concept of multi-layer generation holds great potential to address these limitations, however generating image instances concurrently to scene composition limits control over fine-grained object attributes, relative positioning in 3D space and scene manipulation abilities. In this work, we propose a novel multi-stage generation paradigm that is designed for fine-grained control, flexibility and interactivity. To ensure control over instance attributes, we devise a novel training paradigm to adapt a diffusion model to generate isolated scene components as RGBA images with transparency information. To build complex images, we employ these pre-generated instances and introduce a multi-layer composite generation process that smoothly assembles components in realistic scenes. Our experiments show that our RGBA diffusion model is capable of generating diverse and high quality instances with precise control over object attributes. Through multi-layer composition, we demonstrate that our approach allows to build and manipulate images from highly complex prompts with fine-grained control over object appearance and location, granting a higher degree of control than competing methods.

Tumor synthesis can generate examples that AI often misses or over-detects, improving AI performance by training on these challenging cases. However, existing synthesis methods, which are typically unconditional -- generating images from random variables -- or conditioned only by tumor shapes, lack controllability over specific tumor characteristics such as texture, heterogeneity, boundaries, and pathology type. As a result, the generated tumors may be overly similar or duplicates of existing training data, failing to effectively address AI's weaknesses. We propose a new text-driven tumor synthesis approach, termed TextoMorph, that provides textual control over tumor characteristics. This is particularly beneficial for examples that confuse the AI the most, such as early tumor detection (increasing Sensitivity by +8.5%), tumor segmentation for precise radiotherapy (increasing DSC by +6.3%), and classification between benign and malignant tumors (improving Sensitivity by +8.2%). By incorporating text mined from radiology reports into the synthesis process, we increase the variability and controllability of the synthetic tumors to target AI's failure cases more precisely. Moreover, TextoMorph uses contrastive learning across different texts and CT scans, significantly reducing dependence on scarce image-report pairs (only 141 pairs used in this study) by leveraging a large corpus of 34,035 radiology reports. Finally, we have developed rigorous tests to evaluate synthetic tumors, including Text-Driven Visual Turing Test and Radiomics Pattern Analysis, showing that our synthetic tumors is realistic and diverse in texture, heterogeneity, boundaries, and pathology.

Recent advances in text-to-image (T2I) diffusion models have significantly improved the quality of generated images. However, providing efficient control over individual subjects, particularly the attributes characterizing them, remains a key challenge. While existing methods have introduced mechanisms to modulate attribute expression, they typically provide either detailed, object-specific localization of such a modification or full-scale fine-grained, nuanced control of attributes. No current approach offers both simultaneously, resulting in a gap when trying to achieve precise continuous and subject-specific attribute modulation in image generation. In this work, we demonstrate that token-level directions exist within commonly used CLIP text embeddings that enable fine-grained, subject-specific control of high-level attributes in T2I models. We introduce two methods to identify these directions: a simple, optimization-free technique and a learning-based approach that utilizes the T2I model to characterize semantic concepts more specifically. Our methods allow the augmentation of the prompt text input, enabling fine-grained control over multiple attributes of individual subjects simultaneously, without requiring any modifications to the diffusion model itself. This approach offers a unified solution that fills the gap between global and localized control, providing competitive flexibility and precision in text-guided image generation. Project page: https://compvis.github.io/attribute-control. Code is available at https://github.com/CompVis/attribute-control.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Inverse problems aim to determine parameters from observations, a crucial task in engineering and science. Lately, generative models, especially diffusion models, have gained popularity in this area for their ability to produce realistic solutions and their good mathematical properties. Despite their success, an important drawback of diffusion models is their sensitivity to the choice of variance schedule, which controls the dynamics of the diffusion process. Fine-tuning this schedule for specific applications is crucial but time-costly and does not guarantee an optimal result. We propose a novel approach for learning the schedule as part of the training process. Our method supports probabilistic conditioning on data, provides high-quality solutions, and is flexible, proving able to adapt to different applications with minimum overhead. This approach is tested in two unrelated inverse problems: super-resolution microscopy and quantitative phase imaging, yielding comparable or superior results to previous methods and fine-tuned diffusion models. We conclude that fine-tuning the schedule by experimentation should be avoided because it can be learned during training in a stable way that yields better results.

Recent advances in text-to-image generation with diffusion models present transformative capabilities in image quality. However, user controllability of the generated image, and fast adaptation to new tasks still remains an open challenge, currently mostly addressed by costly and long re-training and fine-tuning or ad-hoc adaptations to specific image generation tasks. In this work, we present MultiDiffusion, a unified framework that enables versatile and controllable image generation, using a pre-trained text-to-image diffusion model, without any further training or finetuning. At the center of our approach is a new generation process, based on an optimization task that binds together multiple diffusion generation processes with a shared set of parameters or constraints. We show that MultiDiffusion can be readily applied to generate high quality and diverse images that adhere to user-provided controls, such as desired aspect ratio (e.g., panorama), and spatial guiding signals, ranging from tight segmentation masks to bounding boxes. Project webpage: https://multidiffusion.github.io

In controllable generation tasks, flexibly manipulating the generated images to attain a desired appearance or structure based on a single input image cue remains a critical and longstanding challenge. Achieving this requires the effective decoupling of key attributes within the input image data, aiming to get representations accurately. Previous research has predominantly concentrated on disentangling image attributes within feature space. However, the complex distribution present in real-world data often makes the application of such decoupling algorithms to other datasets challenging. Moreover, the granularity of control over feature encoding frequently fails to meet specific task requirements. Upon scrutinizing the characteristics of various generative models, we have observed that the input sensitivity and dynamic evolution properties of the diffusion model can be effectively fused with the explicit decomposition operation in pixel space. This integration enables the image processing operations performed in pixel space for a specific feature distribution of the input image, and can achieve the desired control effect in the generated results. Therefore, we propose FilterPrompt, an approach to enhance the model control effect. It can be universally applied to any diffusion model, allowing users to adjust the representation of specific image features in accordance with task requirements, thereby facilitating more precise and controllable generation outcomes. In particular, our designed experiments demonstrate that the FilterPrompt optimizes feature correlation, mitigates content conflicts during the generation process, and enhances the model's control capability.

Current controls over diffusion models (e.g., through text or ControlNet) for image generation fall short in recognizing abstract, continuous attributes like illumination direction or non-rigid shape change. In this paper, we present an approach for allowing users of text-to-image models to have fine-grained control of several attributes in an image. We do this by engineering special sets of input tokens that can be transformed in a continuous manner -- we call them Continuous 3D Words. These attributes can, for example, be represented as sliders and applied jointly with text prompts for fine-grained control over image generation. Given only a single mesh and a rendering engine, we show that our approach can be adopted to provide continuous user control over several 3D-aware attributes, including time-of-day illumination, bird wing orientation, dollyzoom effect, and object poses. Our method is capable of conditioning image creation with multiple Continuous 3D Words and text descriptions simultaneously while adding no overhead to the generative process. Project Page: https://ttchengab.github.io/continuous_3d_words

Structured illumination microscopy (SIM) is an optical super-resolution technique that enables live-cell imaging beyond the diffraction limit. Reconstruction of SIM data is prone to artefacts, which becomes problematic when imaging highly dynamic samples because previous methods rely on the assumption that samples are static. We propose a new transformer-based reconstruction method, VSR-SIM, that uses shifted 3-dimensional window multi-head attention in addition to channel attention mechanism to tackle the problem of video super-resolution (VSR) in SIM. The attention mechanisms are found to capture motion in sequences without the need for common motion estimation techniques such as optical flow. We take an approach to training the network that relies solely on simulated data using videos of natural scenery with a model for SIM image formation. We demonstrate a use case enabled by VSR-SIM referred to as rolling SIM imaging, which increases temporal resolution in SIM by a factor of 9. Our method can be applied to any SIM setup enabling precise recordings of dynamic processes in biomedical research with high temporal resolution.

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

Cytology is essential for cancer diagnostics and screening due to its minimally invasive nature. However, the development of robust deep learning models for digital cytology is challenging due to the heterogeneity in staining and preparation methods of samples, differences across organs, and the limited availability of large, diverse, annotated datasets. Developing a task-specific model for every cytology application is impractical and non-cytology-specific foundation models struggle to generalize to tasks in this domain where the emphasis is on cell morphology. To address these challenges, we introduce CytoFM, the first cytology self-supervised foundation model. Using iBOT, a self-supervised Vision Transformer (ViT) training framework incorporating masked image modeling and self-distillation, we pretrain CytoFM on a diverse collection of cytology datasets to learn robust, transferable representations. We evaluate CytoFM on multiple downstream cytology tasks, including breast cancer classification and cell type identification, using an attention-based multiple instance learning framework. Our results demonstrate that CytoFM performs better on two out of three downstream tasks than existing foundation models pretrained on histopathology (UNI) or natural images (iBOT-Imagenet). Visualizations of learned representations demonstrate our model is able to attend to cytologically relevant features. Despite a small pre-training dataset, CytoFM's promising results highlight the ability of task-agnostic pre-training approaches to learn robust and generalizable features from cytology data.

We present HAAR, a new strand-based generative model for 3D human hairstyles. Specifically, based on textual inputs, HAAR produces 3D hairstyles that could be used as production-level assets in modern computer graphics engines. Current AI-based generative models take advantage of powerful 2D priors to reconstruct 3D content in the form of point clouds, meshes, or volumetric functions. However, by using the 2D priors, they are intrinsically limited to only recovering the visual parts. Highly occluded hair structures can not be reconstructed with those methods, and they only model the ''outer shell'', which is not ready to be used in physics-based rendering or simulation pipelines. In contrast, we propose a first text-guided generative method that uses 3D hair strands as an underlying representation. Leveraging 2D visual question-answering (VQA) systems, we automatically annotate synthetic hair models that are generated from a small set of artist-created hairstyles. This allows us to train a latent diffusion model that operates in a common hairstyle UV space. In qualitative and quantitative studies, we demonstrate the capabilities of the proposed model and compare it to existing hairstyle generation approaches.

We propose a learning-based method to recover normals, specularity, and roughness from a single diffuse image of a material, using microgeometry appearance as our primary cue. Previous methods that work on single images tend to produce over-smooth outputs with artifacts, operate at limited resolution, or train one model per class with little room for generalization. Previous methods that work on single images tend to produce over-smooth outputs with artifacts, operate at limited resolution, or train one model per class with little room for generalization. In contrast, in this work, we propose a novel capture approach that leverages a generative network with attention and a U-Net discriminator, which shows outstanding performance integrating global information at reduced computational complexity. We showcase the performance of our method with a real dataset of digitized textile materials and show that a commodity flatbed scanner can produce the type of diffuse illumination required as input to our method. Additionally, because the problem might be illposed -more than a single diffuse image might be needed to disambiguate the specular reflection- or because the training dataset is not representative enough of the real distribution, we propose a novel framework to quantify the model's confidence about its prediction at test time. Our method is the first one to deal with the problem of modeling uncertainty in material digitization, increasing the trustworthiness of the process and enabling more intelligent strategies for dataset creation, as we demonstrate with an active learning experiment.

Cell instance segmentation (CIS) is crucial for identifying individual cell morphologies in histopathological images, providing valuable insights for biological and medical research. While unsupervised CIS (UCIS) models aim to reduce the heavy reliance on labor-intensive image annotations, they fail to accurately capture cell boundaries, causing missed detections and poor performance. Recognizing the absence of error-free instances as a key limitation, we present COIN (COnfidence score-guided INstance distillation), a novel annotation-free framework with three key steps: (1) Increasing the sensitivity for the presence of error-free instances via unsupervised semantic segmentation with optimal transport, leveraging its ability to discriminate spatially minor instances, (2) Instance-level confidence scoring to measure the consistency between model prediction and refined mask and identify highly confident instances, offering an alternative to ground truth annotations, and (3) Progressive expansion of confidence with recursive self-distillation. Extensive experiments across six datasets show COIN outperforming existing UCIS methods, even surpassing semi- and weakly-supervised approaches across all metrics on the MoNuSeg and TNBC datasets. The code is available at https://github.com/shjo-april/COIN.

Generative models hold promise for revolutionizing medical education, robot-assisted surgery, and data augmentation for medical AI development. Diffusion models can now generate realistic images from text prompts, while recent advancements have demonstrated their ability to create diverse, high-quality videos. However, these models often struggle with generating accurate representations of medical procedures and detailed anatomical structures. This paper introduces Bora, the first spatio-temporal diffusion probabilistic model designed for text-guided biomedical video generation. Bora leverages Transformer architecture and is pre-trained on general-purpose video generation tasks. It is fine-tuned through model alignment and instruction tuning using a newly established medical video corpus, which includes paired text-video data from various biomedical fields. To the best of our knowledge, this is the first attempt to establish such a comprehensive annotated biomedical video dataset. Bora is capable of generating high-quality video data across four distinct biomedical domains, adhering to medical expert standards and demonstrating consistency and diversity. This generalist video generative model holds significant potential for enhancing medical consultation and decision-making, particularly in resource-limited settings. Additionally, Bora could pave the way for immersive medical training and procedure planning. Extensive experiments on distinct medical modalities such as endoscopy, ultrasound, MRI, and cell tracking validate the effectiveness of our model in understanding biomedical instructions and its superior performance across subjects compared to state-of-the-art generation models.

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.

Mitotic figures are classified into typical and atypical variants, with atypical counts correlating strongly with tumor aggressiveness. Accurate differentiation is therefore essential for patient prognostication and resource allocation, yet remains challenging even for expert pathologists. Here, we leveraged Pathology Foundation Models (PFMs) pre-trained on large histopathology datasets and applied parameter-efficient fine-tuning via low-rank adaptation. In addition, we incorporated ConvNeXt V2, a state-of-the-art convolutional neural network architecture, to complement PFMs. During training, we employed a fisheye transform to emphasize mitoses and Fourier Domain Adaptation using ImageNet target images. Finally, we ensembled multiple PFMs to integrate complementary morphological insights, achieving competitive balanced accuracy on the Preliminary Evaluation Phase dataset.

Personalizing generative models offers a way to guide image generation with user-provided references. Current personalization methods can invert an object or concept into the textual conditioning space and compose new natural sentences for text-to-image diffusion models. However, representing and editing specific visual attributes such as material, style, and layout remains a challenge, leading to a lack of disentanglement and editability. To address this problem, we propose a novel approach that leverages the step-by-step generation process of diffusion models, which generate images from low to high frequency information, providing a new perspective on representing, generating, and editing images. We develop the Prompt Spectrum Space P*, an expanded textual conditioning space, and a new image representation method called \sysname. ProSpect represents an image as a collection of inverted textual token embeddings encoded from per-stage prompts, where each prompt corresponds to a specific generation stage (i.e., a group of consecutive steps) of the diffusion model. Experimental results demonstrate that P* and ProSpect offer better disentanglement and controllability compared to existing methods. We apply ProSpect in various personalized attribute-aware image generation applications, such as image-guided or text-driven manipulations of materials, style, and layout, achieving previously unattainable results from a single image input without fine-tuning the diffusion models. Our source code is available athttps://github.com/zyxElsa/ProSpect.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

Recently, diffusion models have made significant strides in synthesizing realistic 2D human images based on provided text prompts. Building upon this, researchers have extended 2D text-to-image diffusion models into the 3D domain for generating human textures (UV Maps). However, some important problems about UV Map Generative models are still not solved, i.e., how to generate personalized texture maps for any given face image, and how to define and evaluate the quality of these generated texture maps. To solve the above problems, we introduce a novel method, UVMap-ID, which is a controllable and personalized UV Map generative model. Unlike traditional large-scale training methods in 2D, we propose to fine-tune a pre-trained text-to-image diffusion model which is integrated with a face fusion module for achieving ID-driven customized generation. To support the finetuning strategy, we introduce a small-scale attribute-balanced training dataset, including high-quality textures with labeled text and Face ID. Additionally, we introduce some metrics to evaluate the multiple aspects of the textures. Finally, both quantitative and qualitative analyses demonstrate the effectiveness of our method in controllable and personalized UV Map generation. Code is publicly available via https://github.com/twowwj/UVMap-ID.

We address the task of generating 3D hair geometry from a single image, which is challenging due to the diversity of hairstyles and the lack of paired image-to-3D hair data. Previous methods are primarily trained on synthetic data and cope with the limited amount of such data by using low-dimensional intermediate representations, such as guide strands and scalp-level embeddings, that require post-processing to decode, upsample, and add realism. These approaches fail to reconstruct detailed hair, struggle with curly hair, or are limited to handling only a few hairstyles. To overcome these limitations, we propose DiffLocks, a novel framework that enables detailed reconstruction of a wide variety of hairstyles directly from a single image. First, we address the lack of 3D hair data by automating the creation of the largest synthetic hair dataset to date, containing 40K hairstyles. Second, we leverage the synthetic hair dataset to learn an image-conditioned diffusion-transfomer model that generates accurate 3D strands from a single frontal image. By using a pretrained image backbone, our method generalizes to in-the-wild images despite being trained only on synthetic data. Our diffusion model predicts a scalp texture map in which any point in the map contains the latent code for an individual hair strand. These codes are directly decoded to 3D strands without post-processing techniques. Representing individual strands, instead of guide strands, enables the transformer to model the detailed spatial structure of complex hairstyles. With this, DiffLocks can recover highly curled hair, like afro hairstyles, from a single image for the first time. Data and code is available at https://radualexandru.github.io/difflocks/

Recent text-to-image diffusion models are able to learn and synthesize images containing novel, personalized concepts (e.g., their own pets or specific items) with just a few examples for training. This paper tackles two interconnected issues within this realm of personalizing text-to-image diffusion models. First, current personalization techniques fail to reliably extend to multiple concepts -- we hypothesize this to be due to the mismatch between complex scenes and simple text descriptions in the pre-training dataset (e.g., LAION). Second, given an image containing multiple personalized concepts, there lacks a holistic metric that evaluates performance on not just the degree of resemblance of personalized concepts, but also whether all concepts are present in the image and whether the image accurately reflects the overall text description. To address these issues, we introduce Gen4Gen, a semi-automated dataset creation pipeline utilizing generative models to combine personalized concepts into complex compositions along with text-descriptions. Using this, we create a dataset called MyCanvas, that can be used to benchmark the task of multi-concept personalization. In addition, we design a comprehensive metric comprising two scores (CP-CLIP and TI-CLIP) for better quantifying the performance of multi-concept, personalized text-to-image diffusion methods. We provide a simple baseline built on top of Custom Diffusion with empirical prompting strategies for future researchers to evaluate on MyCanvas. We show that by improving data quality and prompting strategies, we can significantly increase multi-concept personalized image generation quality, without requiring any modifications to model architecture or training algorithms.

Image-to-image translation (I2I) methods allow the generation of artificial images that share the content of the original image but have a different style. With the advances in Generative Adversarial Networks (GANs)-based methods, I2I methods enabled the generation of artificial images that are indistinguishable from natural images. Recently, I2I methods were also employed in histopathology for generating artificial images of in silico stained tissues from a different type of staining. We refer to this process as stain transfer. The number of I2I variants is constantly increasing, which makes a well justified choice of the most suitable I2I methods for stain transfer challenging. In our work, we compare twelve stain transfer approaches, three of which are based on traditional and nine on GAN-based image processing methods. The analysis relies on complementary quantitative measures for the quality of image translation, the assessment of the suitability for deep learning-based tissue grading, and the visual evaluation by pathologists. Our study highlights the strengths and weaknesses of the stain transfer approaches, thereby allowing a rational choice of the underlying I2I algorithms. Code, data, and trained models for stain transfer between H&E and Masson's Trichrome staining will be made available online.

The traditional image inpainting task aims to restore corrupted regions by referencing surrounding background and foreground. However, the object erasure task, which is in increasing demand, aims to erase objects and generate harmonious background. Previous GAN-based inpainting methods struggle with intricate texture generation. Emerging diffusion model-based algorithms, such as Stable Diffusion Inpainting, exhibit the capability to generate novel content, but they often produce incongruent results at the locations of the erased objects and require high-quality text prompt inputs. To address these challenges, we introduce MagicEraser, a diffusion model-based framework tailored for the object erasure task. It consists of two phases: content initialization and controllable generation. In the latter phase, we develop two plug-and-play modules called prompt tuning and semantics-aware attention refocus. Additionally, we propose a data construction strategy that generates training data specially suitable for this task. MagicEraser achieves fine and effective control of content generation while mitigating undesired artifacts. Experimental results highlight a valuable advancement of our approach in the object erasure task.

Despite recent successes in hair acquisition that fits a high-dimensional hair model to a specific input subject, generative hair models, which establish general embedding spaces for encoding, editing, and sampling diverse hairstyles, are way less explored. In this paper, we present GroomGen, the first generative model designed for hair geometry composed of highly-detailed dense strands. Our approach is motivated by two key ideas. First, we construct hair latent spaces covering both individual strands and hairstyles. The latent spaces are compact, expressive, and well-constrained for high-quality and diverse sampling. Second, we adopt a hierarchical hair representation that parameterizes a complete hair model to three levels: single strands, sparse guide hairs, and complete dense hairs. This representation is critical to the compactness of latent spaces, the robustness of training, and the efficiency of inference. Based on this hierarchical latent representation, our proposed pipeline consists of a strand-VAE and a hairstyle-VAE that encode an individual strand and a set of guide hairs to their respective latent spaces, and a hybrid densification step that populates sparse guide hairs to a dense hair model. GroomGen not only enables novel hairstyle sampling and plausible hairstyle interpolation, but also supports interactive editing of complex hairstyles, or can serve as strong data-driven prior for hairstyle reconstruction from images. We demonstrate the superiority of our approach with qualitative examples of diverse sampled hairstyles and quantitative evaluation of generation quality regarding every single component and the entire pipeline.

Fluorescence labeling is the standard approach to reveal cellular structures and other subcellular constituents for microscopy images. However, this invasive procedure may perturb or even kill the cells and the procedure itself is highly time-consuming and complex. Recently, in silico labeling has emerged as a promising alternative, aiming to use machine learning models to directly predict the fluorescently labeled images from label-free microscopy. In this paper, we propose a deep learning-based in silico labeling method for the Light My Cells challenge. Built upon pix2pix, our proposed method can be trained using the partially labeled datasets with an adaptive loss. Moreover, we explore the effectiveness of several training strategies to handle different input modalities, such as training them together or separately. The results show that our method achieves promising performance for in silico labeling. Our code is available at https://github.com/MedICL-VU/LightMyCells.

3D cellular image segmentation methods are commonly divided into non-2D-based and 2D-based approaches, the latter reconstructing 3D shapes from the segmentation results of 2D layers. However, errors in 2D results often propagate, leading to oversegmentations in the final 3D results. To tackle this issue, we introduce an interpretable geometric framework that addresses the oversegmentations by correcting the 2D segmentation results based on geometric information from adjacent layers. Leveraging both geometric (layer-to-layer, 2D) and topological (3D shape) features, we use binary classification to determine whether neighboring cells should be stitched. We develop a pre-trained classifier on public plant cell datasets and validate its performance on animal cell datasets, confirming its effectiveness in correcting oversegmentations under the transfer learning setting. Furthermore, we demonstrate that our framework can be extended to correcting oversegmentation on non-2D-based methods. A clear pipeline is provided for end-users to build the pre-trained model to any labeled dataset.

Accurately predicting immunotherapy response in Non-Small Cell Lung Cancer (NSCLC) remains a critical unmet need. Existing radiomics and deep learning-based predictive models rely primarily on pre-treatment imaging to predict categorical response outcomes, limiting their ability to capture the complex morphological and textural transformations induced by immunotherapy. This study introduces ImmunoDiff, an anatomy-aware diffusion model designed to synthesize post-treatment CT scans from baseline imaging while incorporating clinically relevant constraints. The proposed framework integrates anatomical priors, specifically lobar and vascular structures, to enhance fidelity in CT synthesis. Additionally, we introduce a novel cbi-Adapter, a conditioning module that ensures pairwise-consistent multimodal integration of imaging and clinical data embeddings, to refine the generative process. Additionally, a clinical variable conditioning mechanism is introduced, leveraging demographic data, blood-based biomarkers, and PD-L1 expression to refine the generative process. Evaluations on an in-house NSCLC cohort treated with immune checkpoint inhibitors demonstrate a 21.24% improvement in balanced accuracy for response prediction and a 0.03 increase in c-index for survival prediction. Code will be released soon.

Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset that comprises Cell Painting features for 11,000 genes and 3,600 compounds along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E), a U-Net-inspired architecture that integrates state-of-the-art ViT foundation models as encoders to predict mIF signals from H&E images. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available ORION dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on two independent datasets. MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.88 for Pan-CK, 0.57 for CD3e, 0.56 for SMA, 0.36 for CD68, and 0.30 for CD20, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that our model effectively captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.

Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (e.g., foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.

In this paper, we present Diffusion-4K, a novel framework for direct ultra-high-resolution image synthesis using text-to-image diffusion models. The core advancements include: (1) Aesthetic-4K Benchmark: addressing the absence of a publicly available 4K image synthesis dataset, we construct Aesthetic-4K, a comprehensive benchmark for ultra-high-resolution image generation. We curated a high-quality 4K dataset with carefully selected images and captions generated by GPT-4o. Additionally, we introduce GLCM Score and Compression Ratio metrics to evaluate fine details, combined with holistic measures such as FID, Aesthetics and CLIPScore for a comprehensive assessment of ultra-high-resolution images. (2) Wavelet-based Fine-tuning: we propose a wavelet-based fine-tuning approach for direct training with photorealistic 4K images, applicable to various latent diffusion models, demonstrating its effectiveness in synthesizing highly detailed 4K images. Consequently, Diffusion-4K achieves impressive performance in high-quality image synthesis and text prompt adherence, especially when powered by modern large-scale diffusion models (e.g., SD3-2B and Flux-12B). Extensive experimental results from our benchmark demonstrate the superiority of Diffusion-4K in ultra-high-resolution image synthesis.

Large text-to-image diffusion models have impressive capabilities in generating photorealistic images from text prompts. How to effectively guide or control these powerful models to perform different downstream tasks becomes an important open problem. To tackle this challenge, we introduce a principled finetuning method -- Orthogonal Finetuning (OFT), for adapting text-to-image diffusion models to downstream tasks. Unlike existing methods, OFT can provably preserve hyperspherical energy which characterizes the pairwise neuron relationship on the unit hypersphere. We find that this property is crucial for preserving the semantic generation ability of text-to-image diffusion models. To improve finetuning stability, we further propose Constrained Orthogonal Finetuning (COFT) which imposes an additional radius constraint to the hypersphere. Specifically, we consider two important finetuning text-to-image tasks: subject-driven generation where the goal is to generate subject-specific images given a few images of a subject and a text prompt, and controllable generation where the goal is to enable the model to take in additional control signals. We empirically show that our OFT framework outperforms existing methods in generation quality and convergence speed.

Advancements in text-to-image diffusion models have led to significant progress in fast 3D content creation. One common approach is to generate a set of multi-view images of an object, and then reconstruct it into a 3D model. However, this approach bypasses the use of a native 3D representation of the object and is hence prone to geometric artifacts and limited in controllability and manipulation capabilities. An alternative approach involves native 3D generative models that directly produce 3D representations. These models, however, are typically limited in their resolution, resulting in lower quality 3D objects. In this work, we bridge the quality gap between methods that directly generate 3D representations and ones that reconstruct 3D objects from multi-view images. We introduce a multi-view to multi-view diffusion model called Sharp-It, which takes a 3D consistent set of multi-view images rendered from a low-quality object and enriches its geometric details and texture. The diffusion model operates on the multi-view set in parallel, in the sense that it shares features across the generated views. A high-quality 3D model can then be reconstructed from the enriched multi-view set. By leveraging the advantages of both 2D and 3D approaches, our method offers an efficient and controllable method for high-quality 3D content creation. We demonstrate that Sharp-It enables various 3D applications, such as fast synthesis, editing, and controlled generation, while attaining high-quality assets.

The advancement of diffusion models has pushed the boundary of text-to-3D object generation. While it is straightforward to composite objects into a scene with reasonable geometry, it is nontrivial to texture such a scene perfectly due to style inconsistency and occlusions between objects. To tackle these problems, we propose a coarse-to-fine 3D scene texturing framework, referred to as RoomTex, to generate high-fidelity and style-consistent textures for untextured compositional scene meshes. In the coarse stage, RoomTex first unwraps the scene mesh to a panoramic depth map and leverages ControlNet to generate a room panorama, which is regarded as the coarse reference to ensure the global texture consistency. In the fine stage, based on the panoramic image and perspective depth maps, RoomTex will refine and texture every single object in the room iteratively along a series of selected camera views, until this object is completely painted. Moreover, we propose to maintain superior alignment between RGB and depth spaces via subtle edge detection methods. Extensive experiments show our method is capable of generating high-quality and diverse room textures, and more importantly, supporting interactive fine-grained texture control and flexible scene editing thanks to our inpainting-based framework and compositional mesh input. Our project page is available at https://qwang666.github.io/RoomTex/.

While generative models produce high-quality images of concepts learned from a large-scale database, a user often wishes to synthesize instantiations of their own concepts (for example, their family, pets, or items). Can we teach a model to quickly acquire a new concept, given a few examples? Furthermore, can we compose multiple new concepts together? We propose Custom Diffusion, an efficient method for augmenting existing text-to-image models. We find that only optimizing a few parameters in the text-to-image conditioning mechanism is sufficiently powerful to represent new concepts while enabling fast tuning (~6 minutes). Additionally, we can jointly train for multiple concepts or combine multiple fine-tuned models into one via closed-form constrained optimization. Our fine-tuned model generates variations of multiple, new concepts and seamlessly composes them with existing concepts in novel settings. Our method outperforms several baselines and concurrent works, regarding both qualitative and quantitative evaluations, while being memory and computationally efficient.

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks. Despite the promising performance, there are still several challenges. First, prior works have resorted to either vision-only or image-caption data, disregarding pathology reports with more clinically authentic information from pathologists and gene expression profiles which respectively offer distinct knowledge for versatile clinical applications. Second, the current progress in pathology FMs predominantly concentrates on the patch level, where the restricted context of patch-level pretraining fails to capture whole-slide patterns. Even recent slide-level FMs still struggle to provide whole-slide context for patch representation. In this study, for the first time, we develop a pathology foundation model incorporating three levels of modalities: pathology slides, pathology reports, and gene expression data, which resulted in 26,169 slide-level modality pairs from 10,275 patients across 32 cancer types, amounting to over 116 million pathological patch images. To leverage these data for CPath, we propose a novel whole-slide pretraining paradigm that injects the multimodal whole-slide context into the patch representation, called Multimodal Self-TAught PRetraining (mSTAR). The proposed paradigm revolutionizes the pretraining workflow for CPath, enabling the pathology FM to acquire the whole-slide context. To the best of our knowledge, this is the first attempt to incorporate three modalities at the whole-slide context for enhancing pathology FMs. To systematically evaluate the capabilities of mSTAR, we built the largest spectrum of oncological benchmark, spanning 7 categories of oncological applications in 15 types of 97 practical oncological tasks.

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

Despite recent advances in large-scale text-to-image generative models, manipulating real images with these models remains a challenging problem. The main limitations of existing editing methods are that they either fail to perform with consistent quality on a wide range of image edits or require time-consuming hyperparameter tuning or fine-tuning of the diffusion model to preserve the image-specific appearance of the input image. We propose a novel approach that is built upon a modified diffusion sampling process via the guidance mechanism. In this work, we explore the self-guidance technique to preserve the overall structure of the input image and its local regions appearance that should not be edited. In particular, we explicitly introduce layout-preserving energy functions that are aimed to save local and global structures of the source image. Additionally, we propose a noise rescaling mechanism that allows to preserve noise distribution by balancing the norms of classifier-free guidance and our proposed guiders during generation. Such a guiding approach does not require fine-tuning the diffusion model and exact inversion process. As a result, the proposed method provides a fast and high-quality editing mechanism. In our experiments, we show through human evaluation and quantitative analysis that the proposed method allows to produce desired editing which is more preferable by humans and also achieves a better trade-off between editing quality and preservation of the original image. Our code is available at https://github.com/FusionBrainLab/Guide-and-Rescale.

Following the remarkable success of diffusion models on image generation, recent works have also demonstrated their impressive ability to address a number of inverse problems in an unsupervised way, by properly constraining the sampling process based on a conditioning input. Motivated by this, in this paper, we present the first approach to use diffusion models as a prior for highly accurate 3D facial BRDF reconstruction from a single image. We start by leveraging a high-quality UV dataset of facial reflectance (diffuse and specular albedo and normals), which we render under varying illumination settings to simulate natural RGB textures and, then, train an unconditional diffusion model on concatenated pairs of rendered textures and reflectance components. At test time, we fit a 3D morphable model to the given image and unwrap the face in a partial UV texture. By sampling from the diffusion model, while retaining the observed texture part intact, the model inpaints not only the self-occluded areas but also the unknown reflectance components, in a single sequence of denoising steps. In contrast to existing methods, we directly acquire the observed texture from the input image, thus, resulting in more faithful and consistent reflectance estimation. Through a series of qualitative and quantitative comparisons, we demonstrate superior performance in both texture completion as well as reflectance reconstruction tasks.

As humans, we aspire to create media content that is both freely willed and readily controlled. Thanks to the prominent development of generative techniques, we now can easily utilize 2D diffusion methods to synthesize images controlled by raw sketch or designated human poses, and even progressively edit/regenerate local regions with masked inpainting. However, similar workflows in 3D modeling tasks are still unavailable due to the lack of controllability and efficiency in 3D generation. In this paper, we present a novel controllable and interactive 3D assets modeling framework, named Coin3D. Coin3D allows users to control the 3D generation using a coarse geometry proxy assembled from basic shapes, and introduces an interactive generation workflow to support seamless local part editing while delivering responsive 3D object previewing within a few seconds. To this end, we develop several techniques, including the 3D adapter that applies volumetric coarse shape control to the diffusion model, proxy-bounded editing strategy for precise part editing, progressive volume cache to support responsive preview, and volume-SDS to ensure consistent mesh reconstruction. Extensive experiments of interactive generation and editing on diverse shape proxies demonstrate that our method achieves superior controllability and flexibility in the 3D assets generation task.

Originating from the diffusion phenomenon in physics that describes particle movement, the diffusion generative models inherit the characteristics of stochastic random walk in the data space along the denoising trajectory. However, the intrinsic mutual interference among image regions contradicts the need for practical downstream application scenarios where the preservation of low-level pixel information from given conditioning is desired (e.g., customization tasks like personalized generation and inpainting based on a user-provided single image). In this work, we investigate the diffusion (physics) in diffusion (machine learning) properties and propose our Cyclic One-Way Diffusion (COW) method to control the direction of diffusion phenomenon given a pre-trained frozen diffusion model for versatile customization application scenarios, where the low-level pixel information from the conditioning needs to be preserved. Notably, unlike most current methods that incorporate additional conditions by fine-tuning the base text-to-image diffusion model or learning auxiliary networks, our method provides a novel perspective to understand the task needs and is applicable to a wider range of customization scenarios in a learning-free manner. Extensive experiment results show that our proposed COW can achieve more flexible customization based on strict visual conditions in different application settings. Project page: https://wangruoyu02.github.io/cow.github.io/.

Cell detection, segmentation and classification are essential for analyzing tumor microenvironments (TME) on hematoxylin and eosin (H&E) slides. Existing methods suffer from poor performance on understudied cell types (rare or not present in public datasets) and limited cross-domain generalization. To address these shortcomings, we introduce HistoPLUS, a state-of-the-art model for cell analysis, trained on a novel curated pan-cancer dataset of 108,722 nuclei covering 13 cell types. In external validation across 4 independent cohorts, HistoPLUS outperforms current state-of-the-art models in detection quality by 5.2% and overall F1 classification score by 23.7%, while using 5x fewer parameters. Notably, HistoPLUS unlocks the study of 7 understudied cell types and brings significant improvements on 8 of 13 cell types. Moreover, we show that HistoPLUS robustly transfers to two oncology indications unseen during training. To support broader TME biomarker research, we release the model weights and inference code at https://github.com/owkin/histoplus/.

Due to the three-dimensional nature of CT- or MR-scans, generative modeling of medical images is a particularly challenging task. Existing approaches mostly apply patch-wise, slice-wise, or cascaded generation techniques to fit the high-dimensional data into the limited GPU memory. However, these approaches may introduce artifacts and potentially restrict the model's applicability for certain downstream tasks. This work presents WDM, a wavelet-based medical image synthesis framework that applies a diffusion model on wavelet decomposed images. The presented approach is a simple yet effective way of scaling diffusion models to high resolutions and can be trained on a single 40 GB GPU. Experimental results on BraTS and LIDC-IDRI unconditional image generation at a resolution of 128 times 128 times 128 show state-of-the-art image fidelity (FID) and sample diversity (MS-SSIM) scores compared to GANs, Diffusion Models, and Latent Diffusion Models. Our proposed method is the only one capable of generating high-quality images at a resolution of 256 times 256 times 256.

Significant progress has been made in training large generative models for natural language and images. Yet, the advancement of 3D generative models is hindered by their substantial resource demands for training, along with inefficient, non-compact, and less expressive representations. This paper introduces Make-A-Shape, a new 3D generative model designed for efficient training on a vast scale, capable of utilizing 10 millions publicly-available shapes. Technical-wise, we first innovate a wavelet-tree representation to compactly encode shapes by formulating the subband coefficient filtering scheme to efficiently exploit coefficient relations. We then make the representation generatable by a diffusion model by devising the subband coefficients packing scheme to layout the representation in a low-resolution grid. Further, we derive the subband adaptive training strategy to train our model to effectively learn to generate coarse and detail wavelet coefficients. Last, we extend our framework to be controlled by additional input conditions to enable it to generate shapes from assorted modalities, e.g., single/multi-view images, point clouds, and low-resolution voxels. In our extensive set of experiments, we demonstrate various applications, such as unconditional generation, shape completion, and conditional generation on a wide range of modalities. Our approach not only surpasses the state of the art in delivering high-quality results but also efficiently generates shapes within a few seconds, often achieving this in just 2 seconds for most conditions.

The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods. The code is available at https://github.com/KrishnaswamyLab/DiffKillR.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

In recent years, deep learning models have been extensively applied to biological data across various modalities. Discriminative deep learning models have excelled at classifying images into categories (e.g., healthy versus diseased, treated versus untreated). However, these models are often perceived as black boxes due to their complexity and lack of interpretability, limiting their application in real-world biological contexts. In biological research, explainability is essential: understanding classifier decisions and identifying subtle differences between conditions are critical for elucidating the effects of treatments, disease progression, and biological processes. To address this challenge, we propose DiffEx, a method for generating visually interpretable attributes to explain classifiers and identify microscopic cellular variations between different conditions. We demonstrate the effectiveness of DiffEx in explaining classifiers trained on natural and biological images. Furthermore, we use DiffEx to uncover phenotypic differences within microscopy datasets. By offering insights into cellular variations through classifier explanations, DiffEx has the potential to advance the understanding of diseases and aid drug discovery by identifying novel biomarkers.

Multimodal pathology-genomic analysis is critical for cancer survival prediction. However, existing approaches predominantly integrate formalin-fixed paraffin-embedded (FFPE) slides with genomic data, while neglecting the availability of other preservation slides, such as Fresh Froze (FF) slides. Moreover, as the high-resolution spatial nature of pathology data tends to dominate the cross-modality fusion process, it hinders effective multimodal fusion and leads to modality imbalance challenges between pathology and genomics. These methods also typically require complete data modalities, limiting their clinical applicability with incomplete modalities, such as missing either pathology or genomic data. In this paper, we propose a multimodal survival prediction framework that leverages hypergraph learning to effectively integrate multi-WSI information and cross-modality interactions between pathology slides and genomics data while addressing modality imbalance. In addition, we introduce a memory mechanism that stores previously learned paired pathology-genomic features and dynamically compensates for incomplete modalities. Experiments on five TCGA datasets demonstrate that our model outperforms advanced methods by over 2.3% in C-Index. Under incomplete modality scenarios, our approach surpasses pathology-only (3.3%) and gene-only models (7.9%). Code: https://github.com/MCPathology/M2Surv

The controllable generation of diffusion models aims to steer the model to generate samples that optimize some given objective functions. It is desirable for a variety of applications including image generation, molecule generation, and DNA/sequence generation. Reinforcement Learning (RL) based fine-tuning of the base model is a popular approach but it can overfit the reward function while requiring significant resources. We frame controllable generation as a problem of finding a distribution that optimizes a KL-regularized objective function. We present SLCD -- Supervised Learning based Controllable Diffusion, which iteratively generates online data and trains a small classifier to guide the generation of the diffusion model. Similar to the standard classifier-guided diffusion, SLCD's key computation primitive is classification and does not involve any complex concepts from RL or control. Via a reduction to no-regret online learning analysis, we show that under KL divergence, the output from SLCD provably converges to the optimal solution of the KL-regularized objective. Further, we empirically demonstrate that SLCD can generate high quality samples with nearly the same inference time as the base model in both image generation with continuous diffusion and biological sequence generation with discrete diffusion. Our code is available at https://github.com/Owen-Oertell/slcd

There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .

Recent surge in large-scale generative models has spurred the development of vast fields in computer vision. In particular, text-to-image diffusion models have garnered widespread adoption across diverse domain due to their potential for high-fidelity image generation. Nonetheless, existing large-scale diffusion models are confined to generate images of up to 1K resolution, which is far from meeting the demands of contemporary commercial applications. Directly sampling higher-resolution images often yields results marred by artifacts such as object repetition and distorted shapes. Addressing the aforementioned issues typically necessitates training or fine-tuning models on higher resolution datasets. However, this undertaking poses a formidable challenge due to the difficulty in collecting large-scale high-resolution contents and substantial computational resources. While several preceding works have proposed alternatives, they often fail to produce convincing results. In this work, we probe the generative ability of diffusion models at higher resolution beyond its original capability and propose a novel progressive approach that fully utilizes generated low-resolution image to guide the generation of higher resolution image. Our method obviates the need for additional training or fine-tuning which significantly lowers the burden of computational costs. Extensive experiments and results validate the efficiency and efficacy of our method. Project page: https://yhyun225.github.io/DiffuseHigh/

Objective: While recent advances in text-conditioned generative models have enabled the synthesis of realistic medical images, progress has been largely confined to 2D modalities such as chest X-rays. Extending text-to-image generation to volumetric Computed Tomography (CT) remains a significant challenge, due to its high dimensionality, anatomical complexity, and the absence of robust frameworks that align vision-language data in 3D medical imaging. Methods: We introduce a novel architecture for Text-to-CT generation that combines a latent diffusion model with a 3D contrastive vision-language pretraining scheme. Our approach leverages a dual-encoder CLIP-style model trained on paired CT volumes and radiology reports to establish a shared embedding space, which serves as the conditioning input for generation. CT volumes are compressed into a low-dimensional latent space via a pretrained volumetric VAE, enabling efficient 3D denoising diffusion without requiring external super-resolution stages. Results: We evaluate our method on the CT-RATE dataset and conduct a comprehensive assessment of image fidelity, clinical relevance, and semantic alignment. Our model achieves competitive performance across all tasks, significantly outperforming prior baselines for text-to-CT generation. Moreover, we demonstrate that CT scans synthesized by our framework can effectively augment real data, improving downstream diagnostic performance. Conclusion: Our results show that modality-specific vision-language alignment is a key component for high-quality 3D medical image generation. By integrating contrastive pretraining and volumetric diffusion, our method offers a scalable and controllable solution for synthesizing clinically meaningful CT volumes from text, paving the way for new applications in data augmentation, medical education, and automated clinical simulation.

Photo-realistic and controllable 3D avatars are crucial for various applications such as virtual and mixed reality (VR/MR), telepresence, gaming, and film production. Traditional methods for avatar creation often involve time-consuming scanning and reconstruction processes for each avatar, which limits their scalability. Furthermore, these methods do not offer the flexibility to sample new identities or modify existing ones. On the other hand, by learning a strong prior from data, generative models provide a promising alternative to traditional reconstruction methods, easing the time constraints for both data capture and processing. Additionally, generative methods enable downstream applications beyond reconstruction, such as editing and stylization. Nonetheless, the research on generative 3D avatars is still in its infancy, and therefore current methods still have limitations such as creating static avatars, lacking photo-realism, having incomplete facial details, or having limited drivability. To address this, we propose a text-conditioned generative model that can generate photo-realistic facial avatars of diverse identities, with more complete details like hair, eyes and mouth interior, and which can be driven through a powerful non-parametric latent expression space. Specifically, we integrate the generative and editing capabilities of latent diffusion models with a strong prior model for avatar expression driving. Our model can generate and control high-fidelity avatars, even those out-of-distribution. We also highlight its potential for downstream applications, including avatar editing and single-shot avatar reconstruction.

Recently, several works tackled the video editing task fostered by the success of large-scale text-to-image generative models. However, most of these methods holistically edit the frame using the text, exploiting the prior given by foundation diffusion models and focusing on improving the temporal consistency across frames. In this work, we introduce a framework that is object-centric and is designed to control both the object's appearance and, notably, to execute precise and explicit structural modifications on the object. We build our framework on a pre-trained image-conditioned diffusion model, integrate layers to handle the temporal dimension, and propose training strategies and architectural modifications to enable shape control. We evaluate our method on the image-driven video editing task showing similar performance to the state-of-the-art, and showcasing novel shape-editing capabilities. Further details, code and examples are available on our project page: https://helia95.github.io/vase-website/

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

Solar activity is one of the main drivers of variability in our solar system and the key source of space weather phenomena that affect Earth and near Earth space. The extensive record of high resolution extreme ultraviolet (EUV) observations from the Solar Dynamics Observatory (SDO) offers an unprecedented, very large dataset of solar images. In this work, we make use of this comprehensive dataset to investigate capabilities of current state-of-the-art generative models to accurately capture the data distribution behind the observed solar activity states. Starting from StyleGAN-based methods, we uncover severe deficits of this model family in handling fine-scale details of solar images when training on high resolution samples, contrary to training on natural face images. When switching to the diffusion based generative model family, we observe strong improvements of fine-scale detail generation. For the GAN family, we are able to achieve similar improvements in fine-scale generation when turning to ProjectedGANs, which uses multi-scale discriminators with a pre-trained frozen feature extractor. We conduct ablation studies to clarify mechanisms responsible for proper fine-scale handling. Using distributed training on supercomputers, we are able to train generative models for up to 1024x1024 resolution that produce high quality samples indistinguishable to human experts, as suggested by the evaluation we conduct. We make all code, models and workflows used in this study publicly available at https://github.com/SLAMPAI/generative-models-for-highres-solar-images.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Multi-subject personalized image generation aims to synthesize customized images containing multiple specified subjects without requiring test-time optimization. However, achieving fine-grained independent control over multiple subjects remains challenging due to difficulties in preserving subject fidelity and preventing cross-subject attribute leakage. We present FocusDPO, a framework that adaptively identifies focus regions based on dynamic semantic correspondence and supervision image complexity. During training, our method progressively adjusts these focal areas across noise timesteps, implementing a weighted strategy that rewards information-rich patches while penalizing regions with low prediction confidence. The framework dynamically adjusts focus allocation during the DPO process according to the semantic complexity of reference images and establishes robust correspondence mappings between generated and reference subjects. Extensive experiments demonstrate that our method substantially enhances the performance of existing pre-trained personalized generation models, achieving state-of-the-art results on both single-subject and multi-subject personalized image synthesis benchmarks. Our method effectively mitigates attribute leakage while preserving superior subject fidelity across diverse generation scenarios, advancing the frontier of controllable multi-subject image synthesis.

Recently, we have seen a surge of personalization methods for text-to-image (T2I) diffusion models to learn a concept using a few images. Existing approaches, when used for face personalization, suffer to achieve convincing inversion with identity preservation and rely on semantic text-based editing of the generated face. However, a more fine-grained control is desired for facial attribute editing, which is challenging to achieve solely with text prompts. In contrast, StyleGAN models learn a rich face prior and enable smooth control towards fine-grained attribute editing by latent manipulation. This work uses the disentangled W+ space of StyleGANs to condition the T2I model. This approach allows us to precisely manipulate facial attributes, such as smoothly introducing a smile, while preserving the existing coarse text-based control inherent in T2I models. To enable conditioning of the T2I model on the W+ space, we train a latent mapper to translate latent codes from W+ to the token embedding space of the T2I model. The proposed approach excels in the precise inversion of face images with attribute preservation and facilitates continuous control for fine-grained attribute editing. Furthermore, our approach can be readily extended to generate compositions involving multiple individuals. We perform extensive experiments to validate our method for face personalization and fine-grained attribute editing.

The inherent generative power of denoising diffusion models makes them well-suited for image restoration tasks where the objective is to find the optimal high-quality image within the generative space that closely resembles the input image. We propose a method to adapt a pretrained diffusion model for image restoration by simply adding noise to the input image to be restored and then denoise. Our method is based on the observation that the space of a generative model needs to be constrained. We impose this constraint by finetuning the generative model with a set of anchor images that capture the characteristics of the input image. With the constrained space, we can then leverage the sampling strategy used for generation to do image restoration. We evaluate against previous methods and show superior performances on multiple real-world restoration datasets in preserving identity and image quality. We also demonstrate an important and practical application on personalized restoration, where we use a personal album as the anchor images to constrain the generative space. This approach allows us to produce results that accurately preserve high-frequency details, which previous works are unable to do. Project webpage: https://gen2res.github.io.

Medical image segmentation has recently demonstrated impressive progress with deep neural networks, yet the heterogeneous modalities and scarcity of mask annotations limit the development of segmentation models on unannotated modalities. This paper investigates a new paradigm for leveraging generative models in medical applications: controllably synthesizing data for unannotated modalities, without requiring registered data pairs. Specifically, we make the following contributions in this paper: (i) we collect and curate a large-scale radiology image-text dataset, MedGen-1M, comprising modality labels, attributes, region, and organ information, along with a subset of organ mask annotations, to support research in controllable medical image generation; (ii) we propose a diffusion-based data engine, termed MRGen, which enables generation conditioned on text prompts and masks, synthesizing MR images for diverse modalities lacking mask annotations, to train segmentation models on unannotated modalities; (iii) we conduct extensive experiments across various modalities, illustrating that our data engine can effectively synthesize training samples and extend MRI segmentation towards unannotated modalities.

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the W_2 distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale Spatial Transcriptomics Foundation Model. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

This paper presents a 3D generative model that uses diffusion models to automatically generate 3D digital avatars represented as neural radiance fields. A significant challenge in generating such avatars is that the memory and processing costs in 3D are prohibitive for producing the rich details required for high-quality avatars. To tackle this problem we propose the roll-out diffusion network (Rodin), which represents a neural radiance field as multiple 2D feature maps and rolls out these maps into a single 2D feature plane within which we perform 3D-aware diffusion. The Rodin model brings the much-needed computational efficiency while preserving the integrity of diffusion in 3D by using 3D-aware convolution that attends to projected features in the 2D feature plane according to their original relationship in 3D. We also use latent conditioning to orchestrate the feature generation for global coherence, leading to high-fidelity avatars and enabling their semantic editing based on text prompts. Finally, we use hierarchical synthesis to further enhance details. The 3D avatars generated by our model compare favorably with those produced by existing generative techniques. We can generate highly detailed avatars with realistic hairstyles and facial hair like beards. We also demonstrate 3D avatar generation from image or text as well as text-guided editability.

Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible for live-cell imaging. However, the reconstruction of SIM images is often slow and prone to artefacts. Here we propose a versatile reconstruction method, ML-SIM, which makes use of machine learning. The model is an end-to-end deep residual neural network that is trained on a simulated data set to be free of common SIM artefacts. ML-SIM is thus robust to noise and irregularities in the illumination patterns of the raw SIM input frames. The reconstruction method is widely applicable and does not require the acquisition of experimental training data. Since the training data are generated from simulations of the SIM process on images from generic libraries the method can be efficiently adapted to specific experimental SIM implementations. The reconstruction quality enabled by our method is compared with traditional SIM reconstruction methods, and we demonstrate advantages in terms of noise, reconstruction fidelity and contrast for both simulated and experimental inputs. In addition, reconstruction of one SIM frame typically only takes ~100ms to perform on PCs with modern Nvidia graphics cards, making the technique compatible with real-time imaging. The full implementation and the trained networks are available at http://ML-SIM.com.

Three-dimensional microscopy is often limited by anisotropic spatial resolution, resulting in lower axial resolution than lateral resolution. Current State-of-The-Art (SoTA) isotropic reconstruction methods utilizing deep neural networks can achieve impressive super-resolution performance in fixed imaging settings. However, their generality in practical use is limited by degraded performance caused by artifacts and blurring when facing unseen anisotropic factors. To address these issues, we propose DiffuseIR, an unsupervised method for isotropic reconstruction based on diffusion models. First, we pre-train a diffusion model to learn the structural distribution of biological tissue from lateral microscopic images, resulting in generating naturally high-resolution images. Then we use low-axial-resolution microscopy images to condition the generation process of the diffusion model and generate high-axial-resolution reconstruction results. Since the diffusion model learns the universal structural distribution of biological tissues, which is independent of the axial resolution, DiffuseIR can reconstruct authentic images with unseen low-axial resolutions into a high-axial resolution without requiring re-training. The proposed DiffuseIR achieves SoTA performance in experiments on EM data and can even compete with supervised methods.

This paper introduces a pioneering 3D volumetric encoder designed for text-to-3D generation. To scale up the training data for the diffusion model, a lightweight network is developed to efficiently acquire feature volumes from multi-view images. The 3D volumes are then trained on a diffusion model for text-to-3D generation using a 3D U-Net. This research further addresses the challenges of inaccurate object captions and high-dimensional feature volumes. The proposed model, trained on the public Objaverse dataset, demonstrates promising outcomes in producing diverse and recognizable samples from text prompts. Notably, it empowers finer control over object part characteristics through textual cues, fostering model creativity by seamlessly combining multiple concepts within a single object. This research significantly contributes to the progress of 3D generation by introducing an efficient, flexible, and scalable representation methodology. Code is available at https://github.com/tzco/VolumeDiffusion.

Text-conditioned image generation models are a prevalent use of AI image synthesis, yet intuitively controlling output guided by an artist remains challenging. Current methods require multiple images and textual prompts for each object to specify them as concepts to generate a single customized image. On the other hand, our work, \verb|DiffMorph|, introduces a novel approach that synthesizes images that mix concepts without the use of textual prompts. Our work integrates a sketch-to-image module to incorporate user sketches as input. \verb|DiffMorph| takes an initial image with conditioning artist-drawn sketches to generate a morphed image. We employ a pre-trained text-to-image diffusion model and fine-tune it to reconstruct each image faithfully. We seamlessly merge images and concepts from sketches into a cohesive composition. The image generation capability of our work is demonstrated through our results and a comparison of these with prompt-based image generation.

The prevalent use of commercial and open-source diffusion models (DMs) for text-to-image generation prompts risk mitigation to prevent undesired behaviors. Existing concept erasing methods in academia are all based on full parameter or specification-based fine-tuning, from which we observe the following issues: 1) Generation alternation towards erosion: Parameter drift during target elimination causes alternations and potential deformations across all generations, even eroding other concepts at varying degrees, which is more evident with multi-concept erased; 2) Transfer inability & deployment inefficiency: Previous model-specific erasure impedes the flexible combination of concepts and the training-free transfer towards other models, resulting in linear cost growth as the deployment scenarios increase. To achieve non-invasive, precise, customizable, and transferable elimination, we ground our erasing framework on one-dimensional adapters to erase multiple concepts from most DMs at once across versatile erasing applications. The concept-SemiPermeable structure is injected as a Membrane (SPM) into any DM to learn targeted erasing, and meantime the alteration and erosion phenomenon is effectively mitigated via a novel Latent Anchoring fine-tuning strategy. Once obtained, SPMs can be flexibly combined and plug-and-play for other DMs without specific re-tuning, enabling timely and efficient adaptation to diverse scenarios. During generation, our Facilitated Transport mechanism dynamically regulates the permeability of each SPM to respond to different input prompts, further minimizing the impact on other concepts. Quantitative and qualitative results across ~40 concepts, 7 DMs and 4 erasing applications have demonstrated the superior erasing of SPM. Our code and pre-tuned SPMs will be available on the project page https://lyumengyao.github.io/projects/spm.

Recent advances in generative diffusion models have enabled the previously unfeasible capability of generating 3D assets from a single input image or a text prompt. In this work, we aim to enhance the quality and functionality of these models for the task of creating controllable, photorealistic human avatars. We achieve this by integrating a 3D morphable model into the state-of-the-art multiview-consistent diffusion approach. We demonstrate that accurate conditioning of a generative pipeline on the articulated 3D model enhances the baseline model performance on the task of novel view synthesis from a single image. More importantly, this integration facilitates a seamless and accurate incorporation of facial expression and body pose control into the generation process. To the best of our knowledge, our proposed framework is the first diffusion model to enable the creation of fully 3D-consistent, animatable, and photorealistic human avatars from a single image of an unseen subject; extensive quantitative and qualitative evaluations demonstrate the advantages of our approach over existing state-of-the-art avatar creation models on both novel view and novel expression synthesis tasks.

This paper addresses complex challenges in histopathological image analysis through three key contributions. Firstly, it introduces a fast patch selection method, FPS, for whole-slide image (WSI) analysis, significantly reducing computational cost while maintaining accuracy. Secondly, it presents PathDino, a lightweight histopathology feature extractor with a minimal configuration of five Transformer blocks and only 9 million parameters, markedly fewer than alternatives. Thirdly, it introduces a rotation-agnostic representation learning paradigm using self-supervised learning, effectively mitigating overfitting. We also show that our compact model outperforms existing state-of-the-art histopathology-specific vision transformers on 12 diverse datasets, including both internal datasets spanning four sites (breast, liver, skin, and colorectal) and seven public datasets (PANDA, CAMELYON16, BRACS, DigestPath, Kather, PanNuke, and WSSS4LUAD). Notably, even with a training dataset of 6 million histopathology patches from The Cancer Genome Atlas (TCGA), our approach demonstrates an average 8.5% improvement in patch-level majority vote performance. These contributions provide a robust framework for enhancing image analysis in digital pathology, rigorously validated through extensive evaluation. Project Page: https://rhazeslab.github.io/PathDino-Page/

Prior work using Masked Autoencoders (MAEs) typically relies on random patch masking based on the assumption that images have significant redundancies across different channels, allowing for the reconstruction of masked content using cross-channel correlations. However, this assumption does not hold in Multi-Channel Imaging (MCI), where channels may provide complementary information with minimal feature overlap. Thus, these MAEs primarily learn local structures within individual channels from patch reconstruction, failing to fully leverage cross-channel interactions and limiting their MCI effectiveness. In this paper, we present ChA-MAEViT, an MAE-based method that enhances feature learning across MCI channels via four key strategies: (1) dynamic channel-patch masking, which compels the model to reconstruct missing channels in addition to masked patches, thereby enhancing cross-channel dependencies and improving robustness to varying channel configurations; (2) memory tokens, which serve as long-term memory aids to promote information sharing across channels, addressing the challenges of reconstructing structurally diverse channels; (3) hybrid token fusion module, which merges fine-grained patch tokens with a global class token to capture richer representations; and (4) Channel-Aware Decoder, a lightweight decoder utilizes channel tokens to effectively reconstruct image patches. Experiments on satellite and microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, show that ChA-MAEViT significantly outperforms state-of-the-art MCI-ViTs by 3.0-21.5%, highlighting the importance of cross-channel interactions in MCI. Our code is publicly available at https://github.com/chaudatascience/cha_mae_vit.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Recent developments in the field of diffusion models have demonstrated an exceptional capacity to generate high-quality prompt-conditioned image edits. Nevertheless, previous approaches have primarily relied on textual prompts for image editing, which tend to be less effective when making precise edits to specific objects or fine-grained regions within a scene containing single/multiple objects. We introduce a novel framework for zero-shot localized multi-object editing through a multi-diffusion process to overcome this challenge. This framework empowers users to perform various operations on objects within an image, such as adding, replacing, or editing many objects in a complex scene in one pass. Our approach leverages foreground masks and corresponding simple text prompts that exert localized influences on the target regions resulting in high-fidelity image editing. A combination of cross-attention and background preservation losses within the latent space ensures that the characteristics of the object being edited are preserved while simultaneously achieving a high-quality, seamless reconstruction of the background with fewer artifacts compared to the current methods. We also curate and release a dataset dedicated to multi-object editing, named LoMOE-Bench. Our experiments against existing state-of-the-art methods demonstrate the improved effectiveness of our approach in terms of both image editing quality and inference speed.

We introduce YOSO, a novel generative model designed for rapid, scalable, and high-fidelity one-step image synthesis. This is achieved by integrating the diffusion process with GANs. Specifically, we smooth the distribution by the denoising generator itself, performing self-cooperative learning. We show that our method can serve as a one-step generation model training from scratch with competitive performance. Moreover, we show that our method can be extended to finetune pre-trained text-to-image diffusion for high-quality one-step text-to-image synthesis even with LoRA fine-tuning. In particular, we provide the first diffusion transformer that can generate images in one step trained on 512 resolution, with the capability of adapting to 1024 resolution without explicit training. Our code is provided at https://github.com/Luo-Yihong/YOSO.

With the recent development of generative models, Text-to-3D generations have also seen significant growth. Nonetheless, achieving precise control over 3D generation continues to be an arduous task, as using text to control often leads to missing objects and imprecise locations. Contemporary strategies for enhancing controllability in 3D generation often entail the introduction of additional parameters, such as customized diffusion models. This often induces hardness in adapting to different diffusion models or creating distinct objects. In this paper, we present LucidDreaming as an effective pipeline capable of fine-grained control over 3D generation. It requires only minimal input of 3D bounding boxes, which can be deduced from a simple text prompt using a Large Language Model. Specifically, we propose clipped ray sampling to separately render and optimize objects with user specifications. We also introduce object-centric density blob bias, fostering the separation of generated objects. With individual rendering and optimizing of objects, our method excels not only in controlled content generation from scratch but also within the pre-trained NeRF scenes. In such scenarios, existing generative approaches often disrupt the integrity of the original scene, and current editing methods struggle to synthesize new content in empty spaces. We show that our method exhibits remarkable adaptability across a spectrum of mainstream Score Distillation Sampling-based 3D generation frameworks, and achieves superior alignment of 3D content when compared to baseline approaches. We also provide a dataset of prompts with 3D bounding boxes, benchmarking 3D spatial controllability.

While diffusion models have gained prominence in image synthesis, their generative pre-training has been shown to yield discriminative representations, paving the way towards unified visual generation and understanding. However, two key questions remain: 1) Can these representations be leveraged to improve the training of diffusion models themselves, rather than solely benefiting downstream tasks? 2) Can the feature quality be enhanced to rival or even surpass modern self-supervised learners, without compromising generative capability? This work addresses these questions by introducing self-conditioning, a straightforward yet effective mechanism that internally leverages the rich semantics inherent in denoising network to guide its own decoding layers, forming a tighter bottleneck that condenses high-level semantics to improve generation. Results are compelling: our method boosts both generation FID and recognition accuracy with 1% computational overhead and generalizes across diverse diffusion architectures. Crucially, self-conditioning facilitates an effective integration of discriminative techniques, such as contrastive self-distillation, directly into diffusion models without sacrificing generation quality. Extensive experiments on pixel-space and latent-space datasets show that in linear evaluations, our enhanced diffusion models, particularly UViT and DiT, serve as strong representation learners, surpassing various self-supervised models.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Benefiting from the rapid development of 2D diffusion models, 3D content creation has made significant progress recently. One promising solution involves the fine-tuning of pre-trained 2D diffusion models to harness their capacity for producing multi-view images, which are then lifted into accurate 3D models via methods like fast-NeRFs or large reconstruction models. However, as inconsistency still exists and limited generated resolution, the generation results of such methods still lack intricate textures and complex geometries. To solve this problem, we propose Magic-Boost, a multi-view conditioned diffusion model that significantly refines coarse generative results through a brief period of SDS optimization (sim15min). Compared to the previous text or single image based diffusion models, Magic-Boost exhibits a robust capability to generate images with high consistency from pseudo synthesized multi-view images. It provides precise SDS guidance that well aligns with the identity of the input images, enriching the local detail in both geometry and texture of the initial generative results. Extensive experiments show Magic-Boost greatly enhances the coarse inputs and generates high-quality 3D assets with rich geometric and textural details. (Project Page: https://magic-research.github.io/magic-boost/)

Zero-shot and prompt-based technologies capitalized on using frequently occurring images to transform visual reasoning tasks, which explains why such technologies struggle with valuable yet scarce scientific image sets. In this work, we propose Zenesis, a comprehensive no-code interactive platform designed to minimize barriers posed by data readiness for scientific images. We develop lightweight multi-modal adaptation techniques that enable zero-shot operation on raw scientific data, along with human-in-the-loop refinement and heuristic-based temporal enhancement options. We demonstrate the performance of our approach through comprehensive comparison and validation on challenging Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) data of catalyst-loaded membranes. Zenesis significantly outperforms baseline methods, achieving an average accuracy of 0.947, an Intersection over Union (IOU) of 0.858, and a Dice score of 0.923 for amorphous catalyst samples and accuracy of 0.987, an IOU of 0.857, and a Dice score of 0.923 for crystalline samples. These results mark a substantial improvement over traditional methods like Otsu thresholding and even advanced models like Segment Anything Model (SAM) when used in isolation. Our results demonstrate that Zenesis is a powerful tool for scientific applications, particularly in fields where high-quality annotated datasets are unavailable, accelerating accurate analysis of experimental imaging.

Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate the performance of state-of-the-art deep learning architectures to segment nuclei in fluorescence images of various tissue origins and sample preparation types without post-processing. We compare architectures that operate on pixel to pixel translation and an architecture that operates on object detection and subsequent locally applied segmentation. In addition, we propose a novel strategy to create artificial images to extend the training set. We evaluate the influence of ground truth annotation quality, image scale and segmentation complexity on segmentation performance. Results show that three out of four deep learning architectures (U-Net, U-Net with ResNet34 backbone, Mask R-CNN) can segment fluorescent nuclear images on most of the sample preparation types and tissue origins with satisfactory segmentation performance. Mask R-CNN, an architecture designed to address instance aware segmentation tasks, outperforms other architectures. Equal nuclear mean size, consistent nuclear annotations and the use of artificially generated images result in overall acceptable precision and recall across different tissues and sample preparation types.

Image editing using diffusion models has witnessed extremely fast-paced growth recently. There are various ways in which previous works enable controlling and editing images. Some works use high-level conditioning such as text, while others use low-level conditioning. Nevertheless, most of them lack fine-grained control over the properties of the different objects present in the image, i.e. object-level image editing. In this work, we consider an image as a composition of multiple objects, each defined by various properties. Out of these properties, we identify structure and appearance as the most intuitive to understand and useful for editing purposes. We propose Structure-and-Appearance Paired Diffusion model (PAIR-Diffusion), which is trained using structure and appearance information explicitly extracted from the images. The proposed model enables users to inject a reference image's appearance into the input image at both the object and global levels. Additionally, PAIR-Diffusion allows editing the structure while maintaining the style of individual components of the image unchanged. We extensively evaluate our method on LSUN datasets and the CelebA-HQ face dataset, and we demonstrate fine-grained control over both structure and appearance at the object level. We also applied the method to Stable Diffusion to edit any real image at the object level.

In this study, we delve into the generation of high-resolution images from pre-trained diffusion models, addressing persistent challenges, such as repetitive patterns and structural distortions, that emerge when models are applied beyond their trained resolutions. To address this issue, we introduce an innovative, training-free approach FouriScale from the perspective of frequency domain analysis. We replace the original convolutional layers in pre-trained diffusion models by incorporating a dilation technique along with a low-pass operation, intending to achieve structural consistency and scale consistency across resolutions, respectively. Further enhanced by a padding-then-crop strategy, our method can flexibly handle text-to-image generation of various aspect ratios. By using the FouriScale as guidance, our method successfully balances the structural integrity and fidelity of generated images, achieving an astonishing capacity of arbitrary-size, high-resolution, and high-quality generation. With its simplicity and compatibility, our method can provide valuable insights for future explorations into the synthesis of ultra-high-resolution images. The code will be released at https://github.com/LeonHLJ/FouriScale.

Benefiting from large-scale pre-trained text-to-image (T2I) generative models, impressive progress has been achieved in customized image generation, which aims to generate user-specified concepts. Existing approaches have extensively focused on single-concept customization and still encounter challenges when it comes to complex scenarios that involve combining multiple concepts. These approaches often require retraining/fine-tuning using a few images, leading to time-consuming training processes and impeding their swift implementation. Furthermore, the reliance on multiple images to represent a singular concept increases the difficulty of customization. To this end, we propose FreeCustom, a novel tuning-free method to generate customized images of multi-concept composition based on reference concepts, using only one image per concept as input. Specifically, we introduce a new multi-reference self-attention (MRSA) mechanism and a weighted mask strategy that enables the generated image to access and focus more on the reference concepts. In addition, MRSA leverages our key finding that input concepts are better preserved when providing images with context interactions. Experiments show that our method's produced images are consistent with the given concepts and better aligned with the input text. Our method outperforms or performs on par with other training-based methods in terms of multi-concept composition and single-concept customization, but is simpler. Codes can be found at https://github.com/aim-uofa/FreeCustom.

Material reconstruction from a photograph is a key component of 3D content creation democratization. We propose to formulate this ill-posed problem as a controlled synthesis one, leveraging the recent progress in generative deep networks. We present ControlMat, a method which, given a single photograph with uncontrolled illumination as input, conditions a diffusion model to generate plausible, tileable, high-resolution physically-based digital materials. We carefully analyze the behavior of diffusion models for multi-channel outputs, adapt the sampling process to fuse multi-scale information and introduce rolled diffusion to enable both tileability and patched diffusion for high-resolution outputs. Our generative approach further permits exploration of a variety of materials which could correspond to the input image, mitigating the unknown lighting conditions. We show that our approach outperforms recent inference and latent-space-optimization methods, and carefully validate our diffusion process design choices. Supplemental materials and additional details are available at: https://gvecchio.com/controlmat/.

Conditioning image generation facilitates seamless editing and the creation of photorealistic images. However, conditioning on noisy or Out-of-Distribution (OoD) images poses significant challenges, particularly in balancing fidelity to the input and realism of the output. We introduce Confident Ordinary Differential Editing (CODE), a novel approach for image synthesis that effectively handles OoD guidance images. Utilizing a diffusion model as a generative prior, CODE enhances images through score-based updates along the probability-flow Ordinary Differential Equation (ODE) trajectory. This method requires no task-specific training, no handcrafted modules, and no assumptions regarding the corruptions affecting the conditioning image. Our method is compatible with any diffusion model. Positioned at the intersection of conditional image generation and blind image restoration, CODE operates in a fully blind manner, relying solely on a pre-trained generative model. Our method introduces an alternative approach to blind restoration: instead of targeting a specific ground truth image based on assumptions about the underlying corruption, CODE aims to increase the likelihood of the input image while maintaining fidelity. This results in the most probable in-distribution image around the input. Our contributions are twofold. First, CODE introduces a novel editing method based on ODE, providing enhanced control, realism, and fidelity compared to its SDE-based counterpart. Second, we introduce a confidence interval-based clipping method, which improves CODE's effectiveness by allowing it to disregard certain pixels or information, thus enhancing the restoration process in a blind manner. Experimental results demonstrate CODE's effectiveness over existing methods, particularly in scenarios involving severe degradation or OoD inputs.

Retouching is an essential task in post-manipulation of raw photographs. Generative editing, guided by text or strokes, provides a new tool accessible to users but can easily change the identity of the original objects in unacceptable and unpredictable ways. In contrast, although traditional procedural edits, as commonly supported by photoediting tools (e.g., Gimp, Lightroom), are conservative, they are still preferred by professionals. Unfortunately, professional quality retouching involves many individual procedural editing operations that is challenging to plan for most novices. In this paper, we ask if a multimodal large language model (MLLM) can be taught to critique raw photographs, suggest suitable remedies, and finally realize them with a given set of pre-authored procedural image operations. We demonstrate that MLLMs can be first made aware of the underlying image processing operations, by training them to solve specially designed visual puzzles. Subsequently, such an operation-aware MLLM can both plan and propose edit sequences. To facilitate training, given a set of expert-edited photos, we synthesize a reasoning dataset by procedurally manipulating the expert edits and then grounding a pretrained LLM on the visual adjustments, to synthesize reasoning for finetuning. The proposed retouching operations are, by construction, understandable by the users, preserve object details and resolution, and can be optionally overridden. We evaluate our setup on a variety of test examples and show advantages, in terms of explainability and identity preservation, over existing generative and other procedural alternatives. Code, data, models, and supplementary results can be found via our project website at https://monetgpt.github.io.

Human brains respond to semantic features of presented stimuli with different neurons. It is then curious whether modern deep neural networks admit a similar behavior pattern. Specifically, this paper finds a small cluster of neurons in a diffusion model corresponding to a particular subject. We call those neurons the concept neurons. They can be identified by statistics of network gradients to a stimulation connected with the given subject. The concept neurons demonstrate magnetic properties in interpreting and manipulating generation results. Shutting them can directly yield the related subject contextualized in different scenes. Concatenating multiple clusters of concept neurons can vividly generate all related concepts in a single image. A few steps of further fine-tuning can enhance the multi-concept capability, which may be the first to manage to generate up to four different subjects in a single image. For large-scale applications, the concept neurons are environmentally friendly as we only need to store a sparse cluster of int index instead of dense float32 values of the parameters, which reduces storage consumption by 90\% compared with previous subject-driven generation methods. Extensive qualitative and quantitative studies on diverse scenarios show the superiority of our method in interpreting and manipulating diffusion models.

Diffusion models have revolutionized image generation, yet several challenges restrict their application to large-image domains, such as digital pathology and satellite imagery. Given that it is infeasible to directly train a model on 'whole' images from domains with potential gigapixel sizes, diffusion-based generative methods have focused on synthesizing small, fixed-size patches extracted from these images. However, generating small patches has limited applicability since patch-based models fail to capture the global structures and wider context of large images, which can be crucial for synthesizing (semantically) accurate samples. To overcome this limitation, we present ZoomLDM, a diffusion model tailored for generating images across multiple scales. Central to our approach is a novel magnification-aware conditioning mechanism that utilizes self-supervised learning (SSL) embeddings and allows the diffusion model to synthesize images at different 'zoom' levels, i.e., fixed-size patches extracted from large images at varying scales. ZoomLDM synthesizes coherent histopathology images that remain contextually accurate and detailed at different zoom levels, achieving state-of-the-art image generation quality across all scales and excelling in the data-scarce setting of generating thumbnails of entire large images. The multi-scale nature of ZoomLDM unlocks additional capabilities in large image generation, enabling computationally tractable and globally coherent image synthesis up to 4096 times 4096 pixels and 4times super-resolution. Additionally, multi-scale features extracted from ZoomLDM are highly effective in multiple instance learning experiments.

We present a method to create interpretable concept sliders that enable precise control over attributes in image generations from diffusion models. Our approach identifies a low-rank parameter direction corresponding to one concept while minimizing interference with other attributes. A slider is created using a small set of prompts or sample images; thus slider directions can be created for either textual or visual concepts. Concept Sliders are plug-and-play: they can be composed efficiently and continuously modulated, enabling precise control over image generation. In quantitative experiments comparing to previous editing techniques, our sliders exhibit stronger targeted edits with lower interference. We showcase sliders for weather, age, styles, and expressions, as well as slider compositions. We show how sliders can transfer latents from StyleGAN for intuitive editing of visual concepts for which textual description is difficult. We also find that our method can help address persistent quality issues in Stable Diffusion XL including repair of object deformations and fixing distorted hands. Our code, data, and trained sliders are available at https://sliders.baulab.info/

The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H&E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.

Creating photorealistic materials for light transport algorithms requires carefully fine-tuning a set of material properties to achieve a desired artistic effect. This is typically a lengthy process that involves a trained artist with specialized knowledge. In this work, we present a technique that aims to empower novice and intermediate-level users to synthesize high-quality photorealistic materials by only requiring basic image processing knowledge. In the proposed workflow, the user starts with an input image and applies a few intuitive transforms (e.g., colorization, image inpainting) within a 2D image editor of their choice, and in the next step, our technique produces a photorealistic result that approximates this target image. Our method combines the advantages of a neural network-augmented optimizer and an encoder neural network to produce high-quality output results within 30 seconds. We also demonstrate that it is resilient against poorly-edited target images and propose a simple extension to predict image sequences with a strict time budget of 1-2 seconds per image.

Breast cancer is a significant health concern affecting millions of women worldwide. Accurate survival risk stratification plays a crucial role in guiding personalised treatment decisions and improving patient outcomes. Here we present BioFusionNet, a deep learning framework that fuses image-derived features with genetic and clinical data to achieve a holistic patient profile and perform survival risk stratification of ER+ breast cancer patients. We employ multiple self-supervised feature extractors, namely DINO and MoCoV3, pretrained on histopathology patches to capture detailed histopathological image features. We then utilise a variational autoencoder (VAE) to fuse these features, and harness the latent space of the VAE to feed into a self-attention network, generating patient-level features. Next, we develop a co-dual-cross-attention mechanism to combine the histopathological features with genetic data, enabling the model to capture the interplay between them. Additionally, clinical data is incorporated using a feed-forward network (FFN), further enhancing predictive performance and achieving comprehensive multimodal feature integration. Furthermore, we introduce a weighted Cox loss function, specifically designed to handle imbalanced survival data, which is a common challenge in the field. The proposed model achieves a mean concordance index (C-index) of 0.77 and a time-dependent area under the curve (AUC) of 0.84, outperforming state-of-the-art methods. It predicts risk (high versus low) with prognostic significance for overall survival (OS) in univariate analysis (HR=2.99, 95% CI: 1.88--4.78, p<0.005), and maintains independent significance in multivariate analysis incorporating standard clinicopathological variables (HR=2.91, 95% CI: 1.80--4.68, p<0.005). The proposed method not only improves model performance but also addresses a critical gap in handling imbalanced data.

Multi-modality image fusion aims to combine different modalities to produce fused images that retain the complementary features of each modality, such as functional highlights and texture details. To leverage strong generative priors and address challenges such as unstable training and lack of interpretability for GAN-based generative methods, we propose a novel fusion algorithm based on the denoising diffusion probabilistic model (DDPM). The fusion task is formulated as a conditional generation problem under the DDPM sampling framework, which is further divided into an unconditional generation subproblem and a maximum likelihood subproblem. The latter is modeled in a hierarchical Bayesian manner with latent variables and inferred by the expectation-maximization (EM) algorithm. By integrating the inference solution into the diffusion sampling iteration, our method can generate high-quality fused images with natural image generative priors and cross-modality information from source images. Note that all we required is an unconditional pre-trained generative model, and no fine-tuning is needed. Our extensive experiments indicate that our approach yields promising fusion results in infrared-visible image fusion and medical image fusion. The code is available at https://github.com/Zhaozixiang1228/MMIF-DDFM.

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

Text-guided diffusion models have revolutionized generative tasks by producing high-fidelity content from text descriptions. They have also enabled an editing paradigm where concepts can be replaced through text conditioning (e.g., a dog to a tiger). In this work, we explore a novel approach: instead of replacing a concept, can we enhance or suppress the concept itself? Through an empirical study, we identify a trend where concepts can be decomposed in text-guided diffusion models. Leveraging this insight, we introduce ScalingConcept, a simple yet effective method to scale decomposed concepts up or down in real input without introducing new elements. To systematically evaluate our approach, we present the WeakConcept-10 dataset, where concepts are imperfect and need to be enhanced. More importantly, ScalingConcept enables a variety of novel zero-shot applications across image and audio domains, including tasks such as canonical pose generation and generative sound highlighting or removal.

We propose a method to control material attributes of objects like roughness, metallic, albedo, and transparency in real images. Our method capitalizes on the generative prior of text-to-image models known for photorealism, employing a scalar value and instructions to alter low-level material properties. Addressing the lack of datasets with controlled material attributes, we generated an object-centric synthetic dataset with physically-based materials. Fine-tuning a modified pre-trained text-to-image model on this synthetic dataset enables us to edit material properties in real-world images while preserving all other attributes. We show the potential application of our model to material edited NeRFs.

Recent interactive matting methods have shown satisfactory performance in capturing the primary regions of objects, but they fall short in extracting fine-grained details in edge regions. Diffusion models trained on billions of image-text pairs, demonstrate exceptional capability in modeling highly complex data distributions and synthesizing realistic texture details, while exhibiting robust text-driven interaction capabilities, making them an attractive solution for interactive matting. To this end, we propose SDMatte, a diffusion-driven interactive matting model, with three key contributions. First, we exploit the powerful priors of diffusion models and transform the text-driven interaction capability into visual prompt-driven interaction capability to enable interactive matting. Second, we integrate coordinate embeddings of visual prompts and opacity embeddings of target objects into U-Net, enhancing SDMatte's sensitivity to spatial position information and opacity information. Third, we propose a masked self-attention mechanism that enables the model to focus on areas specified by visual prompts, leading to better performance. Extensive experiments on multiple datasets demonstrate the superior performance of our method, validating its effectiveness in interactive matting. Our code and model are available at https://github.com/vivoCameraResearch/SDMatte.

Text-guided 3D face synthesis has achieved remarkable results by leveraging text-to-image (T2I) diffusion models. However, most existing works focus solely on the direct generation, ignoring the editing, restricting them from synthesizing customized 3D faces through iterative adjustments. In this paper, we propose a unified text-guided framework from face generation to editing. In the generation stage, we propose a geometry-texture decoupled generation to mitigate the loss of geometric details caused by coupling. Besides, decoupling enables us to utilize the generated geometry as a condition for texture generation, yielding highly geometry-texture aligned results. We further employ a fine-tuned texture diffusion model to enhance texture quality in both RGB and YUV space. In the editing stage, we first employ a pre-trained diffusion model to update facial geometry or texture based on the texts. To enable sequential editing, we introduce a UV domain consistency preservation regularization, preventing unintentional changes to irrelevant facial attributes. Besides, we propose a self-guided consistency weight strategy to improve editing efficacy while preserving consistency. Through comprehensive experiments, we showcase our method's superiority in face synthesis. Project page: https://faceg2e.github.io/.

Existing facial appearance capture methods can reconstruct plausible facial reflectance from smartphone-recorded videos. However, the reconstruction quality is still far behind the ones based on studio recordings. This paper fills the gap by developing a novel daily-used solution with a co-located smartphone and flashlight video capture setting in a dim room. To enhance the quality, our key observation is to solve facial reflectance maps within the data distribution of studio-scanned ones. Specifically, we first learn a diffusion prior over the Light Stage scans and then steer it to produce the reflectance map that best matches the captured images. We propose to train the diffusion prior at the patch level to improve generalization ability and training stability, as current Light Stage datasets are in ultra-high resolution but limited in data size. Tailored to this prior, we propose a patch-level posterior sampling technique to sample seamless full-resolution reflectance maps from this patch-level diffusion model. Experiments demonstrate our method closes the quality gap between low-cost and studio recordings by a large margin, opening the door for everyday users to clone themselves to the digital world. Our code will be released at https://github.com/yxuhan/DoRA.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

In this work we develop 3D Paintbrush, a technique for automatically texturing local semantic regions on meshes via text descriptions. Our method is designed to operate directly on meshes, producing texture maps which seamlessly integrate into standard graphics pipelines. We opt to simultaneously produce a localization map (to specify the edit region) and a texture map which conforms to it. This synergistic approach improves the quality of both the localization and the stylization. To enhance the details and resolution of the textured area, we leverage multiple stages of a cascaded diffusion model to supervise our local editing technique with generative priors learned from images at different resolutions. Our technique, referred to as Cascaded Score Distillation (CSD), simultaneously distills scores at multiple resolutions in a cascaded fashion, enabling control over both the granularity and global understanding of the supervision. We demonstrate the effectiveness of 3D Paintbrush to locally texture a variety of shapes within different semantic regions. Project page: https://threedle.github.io/3d-paintbrush

The advancement of makeup transfer, editing, and image encoding has demonstrated their effectiveness and superior quality. However, existing makeup works primarily focus on low-dimensional features such as color distributions and patterns, limiting their versatillity across a wide range of makeup applications. Futhermore, existing high-dimensional latent encoding methods mainly target global features such as structure and style, and are less effective for tasks that require detailed attention to local color and pattern features of makeup. To overcome these limitations, we propose BeautyBank, a novel makeup encoder that disentangles pattern features of bare and makeup faces. Our method encodes makeup features into a high-dimensional space, preserving essential details necessary for makeup reconstruction and broadening the scope of potential makeup research applications. We also propose a Progressive Makeup Tuning (PMT) strategy, specifically designed to enhance the preservation of detailed makeup features while preventing the inclusion of irrelevant attributes. We further explore novel makeup applications, including facial image generation with makeup injection and makeup similarity measure. Extensive empirical experiments validate that our method offers superior task adaptability and holds significant potential for widespread application in various makeup-related fields. Furthermore, to address the lack of large-scale, high-quality paired makeup datasets in the field, we constructed the Bare-Makeup Synthesis Dataset (BMS), comprising 324,000 pairs of 512x512 pixel images of bare and makeup-enhanced faces.

Model customization introduces new concepts to existing text-to-image models, enabling the generation of the new concept in novel contexts. However, such methods lack accurate camera view control w.r.t the object, and users must resort to prompt engineering (e.g., adding "top-view") to achieve coarse view control. In this work, we introduce a new task -- enabling explicit control of camera viewpoint for model customization. This allows us to modify object properties amongst various background scenes via text prompts, all while incorporating the target camera pose as additional control. This new task presents significant challenges in merging a 3D representation from the multi-view images of the new concept with a general, 2D text-to-image model. To bridge this gap, we propose to condition the 2D diffusion process on rendered, view-dependent features of the new object. During training, we jointly adapt the 2D diffusion modules and 3D feature predictions to reconstruct the object's appearance and geometry while reducing overfitting to the input multi-view images. Our method outperforms existing image editing and model personalization baselines in preserving the custom object's identity while following the input text prompt and the object's camera pose.

Personalized text-to-image generation using diffusion models has recently been proposed and attracted lots of attention. Given a handful of images containing a novel concept (e.g., a unique toy), we aim to tune the generative model to capture fine visual details of the novel concept and generate photorealistic images following a text condition. We present a plug-in method, named ViCo, for fast and lightweight personalized generation. Specifically, we propose an image attention module to condition the diffusion process on the patch-wise visual semantics. We introduce an attention-based object mask that comes almost at no cost from the attention module. In addition, we design a simple regularization based on the intrinsic properties of text-image attention maps to alleviate the common overfitting degradation. Unlike many existing models, our method does not finetune any parameters of the original diffusion model. This allows more flexible and transferable model deployment. With only light parameter training (~6% of the diffusion U-Net), our method achieves comparable or even better performance than all state-of-the-art models both qualitatively and quantitatively.

Medical imaging often contains critical fine-grained features, such as tumors or hemorrhages, crucial for diagnosis yet potentially too subtle for detection with conventional methods. In this paper, we introduce DIA, dissolving is amplifying. DIA is a fine-grained anomaly detection framework for medical images. First, we introduce dissolving transformations. We employ diffusion with a generative diffusion model as a dedicated feature-aware denoiser. Applying diffusion to medical images in a certain manner can remove or diminish fine-grained discriminative features. Second, we introduce an amplifying framework based on contrastive learning to learn a semantically meaningful representation of medical images in a self-supervised manner, with a focus on fine-grained features. The amplifying framework contrasts additional pairs of images with and without dissolving transformations applied and thereby emphasizes the dissolved fine-grained features. DIA significantly improves the medical anomaly detection performance with around 18.40\% AUC boost against the baseline method and achieves an overall SOTA against other benchmark methods. Our code is available at https://github.com/shijianjian/DIA.git.

In this work, we focus on synthesizing high-quality textures on 3D meshes. We present Point-UV diffusion, a coarse-to-fine pipeline that marries the denoising diffusion model with UV mapping to generate 3D consistent and high-quality texture images in UV space. We start with introducing a point diffusion model to synthesize low-frequency texture components with our tailored style guidance to tackle the biased color distribution. The derived coarse texture offers global consistency and serves as a condition for the subsequent UV diffusion stage, aiding in regularizing the model to generate a 3D consistent UV texture image. Then, a UV diffusion model with hybrid conditions is developed to enhance the texture fidelity in the 2D UV space. Our method can process meshes of any genus, generating diversified, geometry-compatible, and high-fidelity textures. Code is available at https://cvmi-lab.github.io/Point-UV-Diffusion

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

Given a small number of images of a subject, personalized image generation techniques can fine-tune large pre-trained text-to-image diffusion models to generate images of the subject in novel contexts, conditioned on text prompts. In doing so, a trade-off is made between prompt fidelity, subject fidelity and diversity. As the pre-trained model is fine-tuned, earlier checkpoints synthesize images with low subject fidelity but high prompt fidelity and diversity. In contrast, later checkpoints generate images with low prompt fidelity and diversity but high subject fidelity. This inherent trade-off limits the prompt fidelity, subject fidelity and diversity of generated images. In this work, we propose DreamBlend to combine the prompt fidelity from earlier checkpoints and the subject fidelity from later checkpoints during inference. We perform a cross attention guided image synthesis from a later checkpoint, guided by an image generated by an earlier checkpoint, for the same prompt. This enables generation of images with better subject fidelity, prompt fidelity and diversity on challenging prompts, outperforming state-of-the-art fine-tuning methods.

Over the last years, many face analysis tasks have accomplished astounding performance, with applications including face generation and 3D face reconstruction from a single "in-the-wild" image. Nevertheless, to the best of our knowledge, there is no method which can produce render-ready high-resolution 3D faces from "in-the-wild" images and this can be attributed to the: (a) scarcity of available data for training, and (b) lack of robust methodologies that can successfully be applied on very high-resolution data. In this work, we introduce the first method that is able to reconstruct photorealistic render-ready 3D facial geometry and BRDF from a single "in-the-wild" image. We capture a large dataset of facial shape and reflectance, which we have made public. We define a fast facial photorealistic differentiable rendering methodology with accurate facial skin diffuse and specular reflection, self-occlusion and subsurface scattering approximation. With this, we train a network that disentangles the facial diffuse and specular BRDF components from a shape and texture with baked illumination, reconstructed with a state-of-the-art 3DMM fitting method. Our method outperforms the existing arts by a significant margin and reconstructs high-resolution 3D faces from a single low-resolution image, that can be rendered in various applications, and bridge the uncanny valley.

This paper introduces an innovative approach for image matting that redefines the traditional regression-based task as a generative modeling challenge. Our method harnesses the capabilities of latent diffusion models, enriched with extensive pre-trained knowledge, to regularize the matting process. We present novel architectural innovations that empower our model to produce mattes with superior resolution and detail. The proposed method is versatile and can perform both guidance-free and guidance-based image matting, accommodating a variety of additional cues. Our comprehensive evaluation across three benchmark datasets demonstrates the superior performance of our approach, both quantitatively and qualitatively. The results not only reflect our method's robust effectiveness but also highlight its ability to generate visually compelling mattes that approach photorealistic quality. The project page for this paper is available at https://lightchaserx.github.io/matting-by-generation/

Recent large-scale generative models learned on big data are capable of synthesizing incredible images yet suffer from limited controllability. This work offers a new generation paradigm that allows flexible control of the output image, such as spatial layout and palette, while maintaining the synthesis quality and model creativity. With compositionality as the core idea, we first decompose an image into representative factors, and then train a diffusion model with all these factors as the conditions to recompose the input. At the inference stage, the rich intermediate representations work as composable elements, leading to a huge design space (i.e., exponentially proportional to the number of decomposed factors) for customizable content creation. It is noteworthy that our approach, which we call Composer, supports various levels of conditions, such as text description as the global information, depth map and sketch as the local guidance, color histogram for low-level details, etc. Besides improving controllability, we confirm that Composer serves as a general framework and facilitates a wide range of classical generative tasks without retraining. Code and models will be made available.

Learning the underlying dynamics of single cells from snapshot data has gained increasing attention in scientific and machine learning research. The destructive measurement technique and cell proliferation/death result in unpaired and unbalanced data between snapshots, making the learning of the underlying dynamics challenging. In this paper, we propose joint Velocity-Growth Flow Matching (VGFM), a novel paradigm that jointly learns state transition and mass growth of single-cell populations via flow matching. VGFM builds an ideal single-cell dynamics containing velocity of state and growth of mass, driven by a presented two-period dynamic understanding of the static semi-relaxed optimal transport, a mathematical tool that seeks the coupling between unpaired and unbalanced data. To enable practical usage, we approximate the ideal dynamics using neural networks, forming our joint velocity and growth matching framework. A distribution fitting loss is also employed in VGFM to further improve the fitting performance for snapshot data. Extensive experimental results on both synthetic and real datasets demonstrate that VGFM can capture the underlying biological dynamics accounting for mass and state variations over time, outperforming existing approaches for single-cell dynamics modeling.

Recent advancements in open-world 3D object generation have been remarkable, with image-to-3D methods offering superior fine-grained control over their text-to-3D counterparts. However, most existing models fall short in simultaneously providing rapid generation speeds and high fidelity to input images - two features essential for practical applications. In this paper, we present One-2-3-45++, an innovative method that transforms a single image into a detailed 3D textured mesh in approximately one minute. Our approach aims to fully harness the extensive knowledge embedded in 2D diffusion models and priors from valuable yet limited 3D data. This is achieved by initially finetuning a 2D diffusion model for consistent multi-view image generation, followed by elevating these images to 3D with the aid of multi-view conditioned 3D native diffusion models. Extensive experimental evaluations demonstrate that our method can produce high-quality, diverse 3D assets that closely mirror the original input image. Our project webpage: https://sudo-ai-3d.github.io/One2345plus_page.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Recent advancements in diffusion-based generative image editing have sparked a profound revolution, reshaping the landscape of image outpainting and inpainting tasks. Despite these strides, the field grapples with inherent challenges, including: i) inferior quality; ii) poor consistency; iii) insufficient instrcution adherence; iv) suboptimal generation efficiency. To address these obstacles, we present ByteEdit, an innovative feedback learning framework meticulously designed to Boost, Comply, and Accelerate Generative Image Editing tasks. ByteEdit seamlessly integrates image reward models dedicated to enhancing aesthetics and image-text alignment, while also introducing a dense, pixel-level reward model tailored to foster coherence in the output. Furthermore, we propose a pioneering adversarial and progressive feedback learning strategy to expedite the model's inference speed. Through extensive large-scale user evaluations, we demonstrate that ByteEdit surpasses leading generative image editing products, including Adobe, Canva, and MeiTu, in both generation quality and consistency. ByteEdit-Outpainting exhibits a remarkable enhancement of 388% and 135% in quality and consistency, respectively, when compared to the baseline model. Experiments also verfied that our acceleration models maintains excellent performance results in terms of quality and consistency.

We present 3DGH, an unconditional generative model for 3D human heads with composable hair and face components. Unlike previous work that entangles the modeling of hair and face, we propose to separate them using a novel data representation with template-based 3D Gaussian Splatting, in which deformable hair geometry is introduced to capture the geometric variations across different hairstyles. Based on this data representation, we design a 3D GAN-based architecture with dual generators and employ a cross-attention mechanism to model the inherent correlation between hair and face. The model is trained on synthetic renderings using carefully designed objectives to stabilize training and facilitate hair-face separation. We conduct extensive experiments to validate the design choice of 3DGH, and evaluate it both qualitatively and quantitatively by comparing with several state-of-the-art 3D GAN methods, demonstrating its effectiveness in unconditional full-head image synthesis and composable 3D hairstyle editing. More details will be available on our project page: https://c-he.github.io/projects/3dgh/.

Diffusion models excel in generating images that closely resemble their training data but are also susceptible to data memorization, raising privacy, ethical, and legal concerns, particularly in sensitive domains such as medical imaging. We hypothesize that this memorization stems from the overparameterization of deep models and propose that regularizing model capacity during fine-tuning can mitigate this issue. Firstly, we empirically show that regulating the model capacity via Parameter-efficient fine-tuning (PEFT) mitigates memorization to some extent, however, it further requires the identification of the exact parameter subsets to be fine-tuned for high-quality generation. To identify these subsets, we introduce a bi-level optimization framework, MemControl, that automates parameter selection using memorization and generation quality metrics as rewards during fine-tuning. The parameter subsets discovered through MemControl achieve a superior tradeoff between generation quality and memorization. For the task of medical image generation, our approach outperforms existing state-of-the-art memorization mitigation strategies by fine-tuning as few as 0.019% of model parameters. Moreover, we demonstrate that the discovered parameter subsets are transferable to non-medical domains. Our framework is scalable to large datasets, agnostic to reward functions, and can be integrated with existing approaches for further memorization mitigation. To the best of our knowledge, this is the first study to empirically evaluate memorization in medical images and propose a targeted yet universal mitigation strategy. The code is available at https://github.com/Raman1121/Diffusion_Memorization_HPO.

Creating fine-retouched portrait images is tedious and time-consuming even for professional artists. There exist automatic retouching methods, but they either suffer from over-smoothing artifacts or lack generalization ability. To address such issues, we present StyleRetoucher, a novel automatic portrait image retouching framework, leveraging StyleGAN's generation and generalization ability to improve an input portrait image's skin condition while preserving its facial details. Harnessing the priors of pretrained StyleGAN, our method shows superior robustness: a). performing stably with fewer training samples and b). generalizing well on the out-domain data. Moreover, by blending the spatial features of the input image and intermediate features of the StyleGAN layers, our method preserves the input characteristics to the largest extent. We further propose a novel blemish-aware feature selection mechanism to effectively identify and remove the skin blemishes, improving the image skin condition. Qualitative and quantitative evaluations validate the great generalization capability of our method. Further experiments show StyleRetoucher's superior performance to the alternative solutions in the image retouching task. We also conduct a user perceptive study to confirm the superior retouching performance of our method over the existing state-of-the-art alternatives.

The recent progress in diffusion-based text-to-image generation models has significantly expanded generative capabilities via conditioning the text descriptions. However, since relying solely on text prompts is still restrictive for fine-grained customization, we aim to extend the boundaries of conditional generation to incorporate diverse types of modalities, e.g., sketch, box, and style embedding, simultaneously. We thus design a multimodal text-to-image diffusion model, coined as DiffBlender, that achieves the aforementioned goal in a single model by training only a few small hypernetworks. DiffBlender facilitates a convenient scaling of input modalities, without altering the parameters of an existing large-scale generative model to retain its well-established knowledge. Furthermore, our study sets new standards for multimodal generation by conducting quantitative and qualitative comparisons with existing approaches. By diversifying the channels of conditioning modalities, DiffBlender faithfully reflects the provided information or, in its absence, creates imaginative generation.

We propose a probabilistic shape completion method extended to the continuous geometry of large-scale 3D scenes. Real-world scans of 3D scenes suffer from a considerable amount of missing data cluttered with unsegmented objects. The problem of shape completion is inherently ill-posed, and high-quality result requires scalable solutions that consider multiple possible outcomes. We employ the Generative Cellular Automata that learns the multi-modal distribution and transform the formulation to process large-scale continuous geometry. The local continuous shape is incrementally generated as a sparse voxel embedding, which contains the latent code for each occupied cell. We formally derive that our training objective for the sparse voxel embedding maximizes the variational lower bound of the complete shape distribution and therefore our progressive generation constitutes a valid generative model. Experiments show that our model successfully generates diverse plausible scenes faithful to the input, especially when the input suffers from a significant amount of missing data. We also demonstrate that our approach outperforms deterministic models even in less ambiguous cases with a small amount of missing data, which infers that probabilistic formulation is crucial for high-quality geometry completion on input scans exhibiting any levels of completeness.