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Oct 29

Imaging and controlling electron motion and chemical structural dynamics of biological system in real time and space

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

  • 7 authors
·
Oct 2

Assessing the Sensitivity and Alignment of FOL Closeness Metrics

The recent successful paradigm of solving logical reasoning problems with tool-augmented large language models (LLMs) leverages translation of natural language (NL) statements into First-Order Logic~(FOL) and external theorem provers. However, the correctness of FOL statements, comprising operators and text, often go unverified due to the lack of a reliable evaluation metric for comparing generated and ground-truth FOLs. In this paper, we conduct a comprehensive study on the sensitivity of existing NL-, FOL-, and graph-based metrics to capture differences between a sampled FOL and its corresponding ground-truth. We then measure the alignment between a metric-based ranking of FOL outputs and a strong LLM as-a-judge. To do this, we first apply operator and text-based perturbations to ground-truth FOL statements to assess metric sensitivity. We then evaluate metric robustness by comparing the metrics against LLMs judgment. Our empirical findings highlight a clear oversensitivity in the n-gram metric BLEU for text perturbations. The operator perturbation affects the semantic graph metric Smatch++ for structural changes, and the FOL metric for specific operator changes. We observe a closer alignment between BertScore and LLM judgement, proving the importance of semantic evaluation. Additionally, we show that combining metrics enhances both robustness and sensitivity compared to using individual metrics.

  • 3 authors
·
Jan 15

EAGLE: Efficient Adaptive Geometry-based Learning in Cross-view Understanding

Unsupervised Domain Adaptation has been an efficient approach to transferring the semantic segmentation model across data distributions. Meanwhile, the recent Open-vocabulary Semantic Scene understanding based on large-scale vision language models is effective in open-set settings because it can learn diverse concepts and categories. However, these prior methods fail to generalize across different camera views due to the lack of cross-view geometric modeling. At present, there are limited studies analyzing cross-view learning. To address this problem, we introduce a novel Unsupervised Cross-view Adaptation Learning approach to modeling the geometric structural change across views in Semantic Scene Understanding. First, we introduce a novel Cross-view Geometric Constraint on Unpaired Data to model structural changes in images and segmentation masks across cameras. Second, we present a new Geodesic Flow-based Correlation Metric to efficiently measure the geometric structural changes across camera views. Third, we introduce a novel view-condition prompting mechanism to enhance the view-information modeling of the open-vocabulary segmentation network in cross-view adaptation learning. The experiments on different cross-view adaptation benchmarks have shown the effectiveness of our approach in cross-view modeling, demonstrating that we achieve State-of-the-Art (SOTA) performance compared to prior unsupervised domain adaptation and open-vocabulary semantic segmentation methods.

  • 7 authors
·
Jun 3, 2024

I2V-Adapter: A General Image-to-Video Adapter for Video Diffusion Models

In the rapidly evolving domain of digital content generation, the focus has shifted from text-to-image (T2I) models to more advanced video diffusion models, notably text-to-video (T2V) and image-to-video (I2V). This paper addresses the intricate challenge posed by I2V: converting static images into dynamic, lifelike video sequences while preserving the original image fidelity. Traditional methods typically involve integrating entire images into diffusion processes or using pretrained encoders for cross attention. However, these approaches often necessitate altering the fundamental weights of T2I models, thereby restricting their reusability. We introduce a novel solution, namely I2V-Adapter, designed to overcome such limitations. Our approach preserves the structural integrity of T2I models and their inherent motion modules. The I2V-Adapter operates by processing noised video frames in parallel with the input image, utilizing a lightweight adapter module. This module acts as a bridge, efficiently linking the input to the model's self-attention mechanism, thus maintaining spatial details without requiring structural changes to the T2I model. Moreover, I2V-Adapter requires only a fraction of the parameters of conventional models and ensures compatibility with existing community-driven T2I models and controlling tools. Our experimental results demonstrate I2V-Adapter's capability to produce high-quality video outputs. This performance, coupled with its versatility and reduced need for trainable parameters, represents a substantial advancement in the field of AI-driven video generation, particularly for creative applications.

  • 11 authors
·
Dec 27, 2023 1

Image Editing As Programs with Diffusion Models

While diffusion models have achieved remarkable success in text-to-image generation, they encounter significant challenges with instruction-driven image editing. Our research highlights a key challenge: these models particularly struggle with structurally inconsistent edits that involve substantial layout changes. To mitigate this gap, we introduce Image Editing As Programs (IEAP), a unified image editing framework built upon the Diffusion Transformer (DiT) architecture. At its core, IEAP approaches instructional editing through a reductionist lens, decomposing complex editing instructions into sequences of atomic operations. Each operation is implemented via a lightweight adapter sharing the same DiT backbone and is specialized for a specific type of edit. Programmed by a vision-language model (VLM)-based agent, these operations collaboratively support arbitrary and structurally inconsistent transformations. By modularizing and sequencing edits in this way, IEAP generalizes robustly across a wide range of editing tasks, from simple adjustments to substantial structural changes. Extensive experiments demonstrate that IEAP significantly outperforms state-of-the-art methods on standard benchmarks across various editing scenarios. In these evaluations, our framework delivers superior accuracy and semantic fidelity, particularly for complex, multi-step instructions. Codes are available at https://github.com/YujiaHu1109/IEAP.

  • 5 authors
·
Jun 4 2

dyGRASS: Dynamic Spectral Graph Sparsification via Localized Random Walks on GPUs

This work presents dyGRASS, an efficient dynamic algorithm for spectral sparsification of large undirected graphs that undergo streaming edge insertions and deletions. At its core, dyGRASS employs a random-walk-based method to efficiently estimate node-to-node distances in both the original graph (for decremental update) and its sparsifier (for incremental update). For incremental updates, dyGRASS enables the identification of spectrally critical edges among the updates to capture the latest structural changes. For decremental updates, dyGRASS facilitates the recovery of important edges from the original graph back into the sparsifier. To further enhance computational efficiency, dyGRASS employs a GPU-based non-backtracking random walk scheme that allows multiple walkers to operate simultaneously across various target updates. This parallelization significantly improves both the performance and scalability of the proposed dyGRASS framework. Our comprehensive experimental evaluations reveal that dyGRASS achieves approximately a 10x speedup compared to the state-of-the-art incremental sparsification (inGRASS) algorithm while eliminating the setup overhead and improving solution quality in incremental spectral sparsification tasks. Moreover, dyGRASS delivers high efficiency and superior solution quality for fully dynamic graph sparsification, accommodating both edge insertions and deletions across a diverse range of graph instances originating from integrated circuit simulations, finite element analysis, and social networks.

  • 3 authors
·
May 5

Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.

  • 4 authors
·
Oct 25, 2022

Multi-Layer Deep xVA: Structural Credit Models, Measure Changes and Convergence Analysis

We propose a structural default model for portfolio-wide valuation adjustments (xVAs) and represent it as a system of coupled backward stochastic differential equations. The framework is divided into four layers, each capturing a key component: (i) clean values, (ii) initial margin and Collateral Valuation Adjustment (ColVA), (iii) Credit/Debit Valuation Adjustments (CVA/DVA) together with Margin Valuation Adjustment (MVA), and (iv) Funding Valuation Adjustment (FVA). Because these layers depend on one another through collateral and default effects, a naive Monte Carlo approach would require deeply nested simulations, making the problem computationally intractable. To address this challenge, we use an iterative deep BSDE approach, handling each layer sequentially so that earlier outputs serve as inputs to the subsequent layers. Initial margin is computed via deep quantile regression to reflect margin requirements over the Margin Period of Risk. We also adopt a change-of-measure method that highlights rare but significant defaults of the bank or counterparty, ensuring that these events are accurately captured in the training process. We further extend Han and Long's (2020) a posteriori error analysis to BSDEs on bounded domains. Due to the random exit from the domain, we obtain an order of convergence of O(h^{1/4-epsilon}) rather than the usual O(h^{1/2}). Numerical experiments illustrate that this method drastically reduces computational demands and successfully scales to high-dimensional, non-symmetric portfolios. The results confirm its effectiveness and accuracy, offering a practical alternative to nested Monte Carlo simulations in multi-counterparty xVA analyses.

  • 2 authors
·
Feb 20

Structural Text Segmentation of Legal Documents

The growing complexity of legal cases has lead to an increasing interest in legal information retrieval systems that can effectively satisfy user-specific information needs. However, such downstream systems typically require documents to be properly formatted and segmented, which is often done with relatively simple pre-processing steps, disregarding topical coherence of segments. Systems generally rely on representations of individual sentences or paragraphs, which may lack crucial context, or document-level representations, which are too long for meaningful search results. To address this issue, we propose a segmentation system that can predict topical coherence of sequential text segments spanning several paragraphs, effectively segmenting a document and providing a more balanced representation for downstream applications. We build our model on top of popular transformer networks and formulate structural text segmentation as topical change detection, by performing a series of independent classifications that allow for efficient fine-tuning on task-specific data. We crawl a novel dataset consisting of roughly 74,000 online Terms-of-Service documents, including hierarchical topic annotations, which we use for training. Results show that our proposed system significantly outperforms baselines, and adapts well to structural peculiarities of legal documents. We release both data and trained models to the research community for future work.https://github.com/dennlinger/TopicalChange

  • 4 authors
·
Dec 7, 2020

AgentPack: A Dataset of Code Changes, Co-Authored by Agents and Humans

Fine-tuning large language models for code editing has typically relied on mining commits and pull requests. The working hypothesis has been that commit messages describe human intent in natural language, and patches to code describe the changes that implement that intent. However, much of the previously collected data is noisy: commit messages are terse, human-written commits commingle several unrelated edits, and many commits come from simple, rule-based bots. The recent adoption of software engineering agents changes this landscape. Code changes co-authored by humans and agents tend to be more narrowly scoped and focused on clearer goals. Their commit messages, generated by LLMs, articulate intent and rationale in much greater detail. Moreover, when these changes land in public repositories, they are implicitly filtered by humans: maintainers discard low-quality commits to their projects. We present AgentPack, a corpus of 1.3M code edits co-authored by Claude Code, OpenAI Codex, and Cursor Agent across public GitHub projects up to mid-August 2025. We describe the identification and curation pipeline, quantify adoption trends of these agents, and analyze the structural properties of the edits. Finally, we show that models fine-tuned on AgentPack can outperform models trained on prior human-only commit corpora, highlighting the potential of using public data from software engineering agents to train future code-editing models.

  • 5 authors
·
Sep 26

CSIM: A Copula-based similarity index sensitive to local changes for Image quality assessment

Image similarity metrics play an important role in computer vision applications, as they are used in image processing, computer vision and machine learning. Furthermore, those metrics enable tasks such as image retrieval, object recognition and quality assessment, essential in fields like healthcare, astronomy and surveillance. Existing metrics, such as PSNR, MSE, SSIM, ISSM and FSIM, often face limitations in terms of either speed, complexity or sensitivity to small changes in images. To address these challenges, a novel image similarity metric, namely CSIM, that combines real-time while being sensitive to subtle image variations is investigated in this paper. The novel metric uses Gaussian Copula from probability theory to transform an image into vectors of pixel distribution associated to local image patches. These vectors contain, in addition to intensities and pixel positions, information on the dependencies between pixel values, capturing the structural relationships within the image. By leveraging the properties of Copulas, CSIM effectively models the joint distribution of pixel intensities, enabling a more nuanced comparison of image patches making it more sensitive to local changes compared to other metrics. Experimental results demonstrate that CSIM outperforms existing similarity metrics in various image distortion scenarios, including noise, compression artifacts and blur. The metric's ability to detect subtle differences makes it suitable for applications requiring high precision, such as medical imaging, where the detection of minor anomalies can be of a high importance. The results obtained in this work can be reproduced from this Github repository: https://github.com/safouaneelg/copulasimilarity.

  • 4 authors
·
Oct 2, 2024

LDL: Line Distance Functions for Panoramic Localization

We introduce LDL, a fast and robust algorithm that localizes a panorama to a 3D map using line segments. LDL focuses on the sparse structural information of lines in the scene, which is robust to illumination changes and can potentially enable efficient computation. While previous line-based localization approaches tend to sacrifice accuracy or computation time, our method effectively observes the holistic distribution of lines within panoramic images and 3D maps. Specifically, LDL matches the distribution of lines with 2D and 3D line distance functions, which are further decomposed along principal directions of lines to increase the expressiveness. The distance functions provide coarse pose estimates by comparing the distributional information, where the poses are further optimized using conventional local feature matching. As our pipeline solely leverages line geometry and local features, it does not require costly additional training of line-specific features or correspondence matching. Nevertheless, our method demonstrates robust performance on challenging scenarios including object layout changes, illumination shifts, and large-scale scenes, while exhibiting fast pose search terminating within a matter of milliseconds. We thus expect our method to serve as a practical solution for line-based localization, and complement the well-established point-based paradigm. The code for LDL is available through the following link: https://github.com/82magnolia/panoramic-localization.

  • 4 authors
·
Aug 26, 2023

Sketch3DVE: Sketch-based 3D-Aware Scene Video Editing

Recent video editing methods achieve attractive results in style transfer or appearance modification. However, editing the structural content of 3D scenes in videos remains challenging, particularly when dealing with significant viewpoint changes, such as large camera rotations or zooms. Key challenges include generating novel view content that remains consistent with the original video, preserving unedited regions, and translating sparse 2D inputs into realistic 3D video outputs. To address these issues, we propose Sketch3DVE, a sketch-based 3D-aware video editing method to enable detailed local manipulation of videos with significant viewpoint changes. To solve the challenge posed by sparse inputs, we employ image editing methods to generate edited results for the first frame, which are then propagated to the remaining frames of the video. We utilize sketching as an interaction tool for precise geometry control, while other mask-based image editing methods are also supported. To handle viewpoint changes, we perform a detailed analysis and manipulation of the 3D information in the video. Specifically, we utilize a dense stereo method to estimate a point cloud and the camera parameters of the input video. We then propose a point cloud editing approach that uses depth maps to represent the 3D geometry of newly edited components, aligning them effectively with the original 3D scene. To seamlessly merge the newly edited content with the original video while preserving the features of unedited regions, we introduce a 3D-aware mask propagation strategy and employ a video diffusion model to produce realistic edited videos. Extensive experiments demonstrate the superiority of Sketch3DVE in video editing. Homepage and code: http://http://geometrylearning.com/Sketch3DVE/

  • 5 authors
·
Aug 19 2

Object Detectors in the Open Environment: Challenges, Solutions, and Outlook

With the emergence of foundation models, deep learning-based object detectors have shown practical usability in closed set scenarios. However, for real-world tasks, object detectors often operate in open environments, where crucial factors (e.g., data distribution, objective) that influence model learning are often changing. The dynamic and intricate nature of the open environment poses novel and formidable challenges to object detectors. Unfortunately, current research on object detectors in open environments lacks a comprehensive analysis of their distinctive characteristics, challenges, and corresponding solutions, which hinders their secure deployment in critical real-world scenarios. This paper aims to bridge this gap by conducting a comprehensive review and analysis of object detectors in open environments. We initially identified limitations of key structural components within the existing detection pipeline and propose the open environment object detector challenge framework that includes four quadrants (i.e., out-of-domain, out-of-category, robust learning, and incremental learning) based on the dimensions of the data / target changes. For each quadrant of challenges in the proposed framework, we present a detailed description and systematic analysis of the overarching goals and core difficulties, systematically review the corresponding solutions, and benchmark their performance over multiple widely adopted datasets. In addition, we engage in a discussion of open problems and potential avenues for future research. This paper aims to provide a fresh, comprehensive, and systematic understanding of the challenges and solutions associated with open-environment object detectors, thus catalyzing the development of more solid applications in real-world scenarios. A project related to this survey can be found at https://github.com/LiangSiyuan21/OEOD_Survey.

  • 8 authors
·
Mar 24, 2024

Prefix Grouper: Efficient GRPO Training through Shared-Prefix Forward

Group Relative Policy Optimization (GRPO) enhances policy learning by computing gradients from relative comparisons among candidate outputs that share a common input prefix. Despite its effectiveness, GRPO introduces substantial computational overhead when processing long shared prefixes, which must be redundantly encoded for each group member. This inefficiency becomes a major scalability bottleneck in long-context learning scenarios. We propose Prefix Grouper, an efficient GRPO training algorithm that eliminates redundant prefix computation via a Shared-Prefix Forward strategy. In particular, by restructuring self-attention into two parts, our method enables the shared prefix to be encoded only once, while preserving full differentiability and compatibility with end-to-end training. We provide both theoretical and empirical evidence that Prefix Grouper is training-equivalent to standard GRPO: it yields identical forward outputs and backward gradients, ensuring that the optimization dynamics and final policy performance remain unchanged. Empirically, our experiments confirm that Prefix Grouper achieves consistent results while significantly reducing the computational cost of training, particularly in long-prefix scenarios. The proposed method is fully plug-and-play: it is compatible with existing GRPO-based architectures and can be seamlessly integrated into current training pipelines as a drop-in replacement, requiring no structural modifications and only minimal changes to input construction and attention computation. Prefix Grouper enables the use of larger group sizes under the same computational budget, thereby improving the scalability of GRPO to more complex tasks and larger models. Code is now available at https://github.com/johncaged/PrefixGrouper

LISA++: An Improved Baseline for Reasoning Segmentation with Large Language Model

While LISA effectively bridges the gap between segmentation and large language models to enable reasoning segmentation, it poses certain limitations: unable to distinguish different instances of the target region, and constrained by the pre-defined textual response formats. In this work, we introduce LISA++, an update to the existing LISA model, focusing on improving core functionalities while keeping the base architecture intact. The main enhancements in LISA++ include: 1) Enhanced Segmentation: The instance segmentation ability has been added, providing a more detailed scene analysis along with the existing multi-region semantic segmentation. 2) More Natural Conversation: Improved capability for multi-turn dialogue, with the ability to incorporate segmentation results directly into text responses, i.e., Segmentation in Dialogue (SiD). These improvements are achieved by curating the existing samples of generic segmentation datasets, aimed specifically at enhancing the segmentation and conversational skills without structural change and additional data sources. Comparative analysis with the original LISA model shows significant advancements in these areas, positioning LISA++ as a notable upgrade in visual understanding and interaction. LISA++'s adaptability and improved features highlight the versatility of the mask-as-embedding paradigm proposed by LISA, and the potential as a foundational model for diverse applications.

  • 7 authors
·
Dec 28, 2023 1