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Dec 2

Detect Anything via Next Point Prediction

Object detection has long been dominated by traditional coordinate regression-based models, such as YOLO, DETR, and Grounding DINO. Although recent efforts have attempted to leverage MLLMs to tackle this task, they face challenges like low recall rate, duplicate predictions, coordinate misalignment, etc. In this work, we bridge this gap and propose Rex-Omni, a 3B-scale MLLM that achieves state-of-the-art object perception performance. On benchmarks like COCO and LVIS, Rex-Omni attains performance comparable to or exceeding regression-based models (e.g., DINO, Grounding DINO) in a zero-shot setting. This is enabled by three key designs: 1) Task Formulation: we use special tokens to represent quantized coordinates from 0 to 999, reducing the model's learning difficulty and improving token efficiency for coordinate prediction; 2) Data Engines: we construct multiple data engines to generate high-quality grounding, referring, and pointing data, providing semantically rich supervision for training; \3) Training Pipelines: we employ a two-stage training process, combining supervised fine-tuning on 22 million data with GRPO-based reinforcement post-training. This RL post-training leverages geometry-aware rewards to effectively bridge the discrete-to-continuous coordinate prediction gap, improve box accuracy, and mitigate undesirable behaviors like duplicate predictions that stem from the teacher-guided nature of the initial SFT stage. Beyond conventional detection, Rex-Omni's inherent language understanding enables versatile capabilities such as object referring, pointing, visual prompting, GUI grounding, spatial referring, OCR and key-pointing, all systematically evaluated on dedicated benchmarks. We believe that Rex-Omni paves the way for more versatile and language-aware visual perception systems.

Deep Implicit Surface Point Prediction Networks

Deep neural representations of 3D shapes as implicit functions have been shown to produce high fidelity models surpassing the resolution-memory trade-off faced by the explicit representations using meshes and point clouds. However, most such approaches focus on representing closed shapes. Unsigned distance function (UDF) based approaches have been proposed recently as a promising alternative to represent both open and closed shapes. However, since the gradients of UDFs vanish on the surface, it is challenging to estimate local (differential) geometric properties like the normals and tangent planes which are needed for many downstream applications in vision and graphics. There are additional challenges in computing these properties efficiently with a low-memory footprint. This paper presents a novel approach that models such surfaces using a new class of implicit representations called the closest surface-point (CSP) representation. We show that CSP allows us to represent complex surfaces of any topology (open or closed) with high fidelity. It also allows for accurate and efficient computation of local geometric properties. We further demonstrate that it leads to efficient implementation of downstream algorithms like sphere-tracing for rendering the 3D surface as well as to create explicit mesh-based representations. Extensive experimental evaluation on the ShapeNet dataset validate the above contributions with results surpassing the state-of-the-art.

  • 7 authors
·
Jun 10, 2021

Point, Detect, Count: Multi-Task Medical Image Understanding with Instruction-Tuned Vision-Language Models

We investigate fine-tuning Vision-Language Models (VLMs) for multi-task medical image understanding, focusing on detection, localization, and counting of findings in medical images. Our objective is to evaluate whether instruction-tuned VLMs can simultaneously improve these tasks, with the goal of enhancing diagnostic accuracy and efficiency. Using MedMultiPoints, a multimodal dataset with annotations from endoscopy (polyps and instruments) and microscopy (sperm cells), we reformulate each task into instruction-based prompts suitable for vision-language reasoning. We fine-tune Qwen2.5-VL-7B-Instruct using Low-Rank Adaptation (LoRA) across multiple task combinations. Results show that multi-task training improves robustness and accuracy. For example, it reduces the Count Mean Absolute Error (MAE) and increases Matching Accuracy in the Counting + Pointing task. However, trade-offs emerge, such as more zero-case point predictions, indicating reduced reliability in edge cases despite overall performance gains. Our study highlights the potential of adapting general-purpose VLMs to specialized medical tasks via prompt-driven fine-tuning. This approach mirrors clinical workflows, where radiologists simultaneously localize, count, and describe findings - demonstrating how VLMs can learn composite diagnostic reasoning patterns. The model produces interpretable, structured outputs, offering a promising step toward explainable and versatile medical AI. Code, model weights, and scripts will be released for reproducibility at https://github.com/simula/PointDetectCount.

  • 3 authors
·
May 22

ARTDECO: Towards Efficient and High-Fidelity On-the-Fly 3D Reconstruction with Structured Scene Representation

On-the-fly 3D reconstruction from monocular image sequences is a long-standing challenge in computer vision, critical for applications such as real-to-sim, AR/VR, and robotics. Existing methods face a major tradeoff: per-scene optimization yields high fidelity but is computationally expensive, whereas feed-forward foundation models enable real-time inference but struggle with accuracy and robustness. In this work, we propose ARTDECO, a unified framework that combines the efficiency of feed-forward models with the reliability of SLAM-based pipelines. ARTDECO uses 3D foundation models for pose estimation and point prediction, coupled with a Gaussian decoder that transforms multi-scale features into structured 3D Gaussians. To sustain both fidelity and efficiency at scale, we design a hierarchical Gaussian representation with a LoD-aware rendering strategy, which improves rendering fidelity while reducing redundancy. Experiments on eight diverse indoor and outdoor benchmarks show that ARTDECO delivers interactive performance comparable to SLAM, robustness similar to feed-forward systems, and reconstruction quality close to per-scene optimization, providing a practical path toward on-the-fly digitization of real-world environments with both accurate geometry and high visual fidelity. Explore more demos on our project page: https://city-super.github.io/artdeco/.

MEG-GPT: A transformer-based foundation model for magnetoencephalography data

Modelling the complex spatiotemporal patterns of large-scale brain dynamics is crucial for neuroscience, but traditional methods fail to capture the rich structure in modalities such as magnetoencephalography (MEG). Recent advances in deep learning have enabled significant progress in other domains, such as language and vision, by using foundation models at scale. Here, we introduce MEG-GPT, a transformer based foundation model that uses time-attention and next time-point prediction. To facilitate this, we also introduce a novel data-driven tokeniser for continuous MEG data, which preserves the high temporal resolution of continuous MEG signals without lossy transformations. We trained MEG-GPT on tokenised brain region time-courses extracted from a large-scale MEG dataset (N=612, eyes-closed rest, Cam-CAN data), and show that the learnt model can generate data with realistic spatio-spectral properties, including transient events and population variability. Critically, it performs well in downstream decoding tasks, improving downstream supervised prediction task, showing improved zero-shot generalisation across sessions (improving accuracy from 0.54 to 0.59) and subjects (improving accuracy from 0.41 to 0.49) compared to a baseline methods. Furthermore, we show the model can be efficiently fine-tuned on a smaller labelled dataset to boost performance in cross-subject decoding scenarios. This work establishes a powerful foundation model for electrophysiological data, paving the way for applications in computational neuroscience and neural decoding.

  • 5 authors
·
Oct 20

Retro-FPN: Retrospective Feature Pyramid Network for Point Cloud Semantic Segmentation

Learning per-point semantic features from the hierarchical feature pyramid is essential for point cloud semantic segmentation. However, most previous methods suffered from ambiguous region features or failed to refine per-point features effectively, which leads to information loss and ambiguous semantic identification. To resolve this, we propose Retro-FPN to model the per-point feature prediction as an explicit and retrospective refining process, which goes through all the pyramid layers to extract semantic features explicitly for each point. Its key novelty is a retro-transformer for summarizing semantic contexts from the previous layer and accordingly refining the features in the current stage. In this way, the categorization of each point is conditioned on its local semantic pattern. Specifically, the retro-transformer consists of a local cross-attention block and a semantic gate unit. The cross-attention serves to summarize the semantic pattern retrospectively from the previous layer. And the gate unit carefully incorporates the summarized contexts and refines the current semantic features. Retro-FPN is a pluggable neural network that applies to hierarchical decoders. By integrating Retro-FPN with three representative backbones, including both point-based and voxel-based methods, we show that Retro-FPN can significantly improve performance over state-of-the-art backbones. Comprehensive experiments on widely used benchmarks can justify the effectiveness of our design. The source is available at https://github.com/AllenXiangX/Retro-FPN

  • 6 authors
·
Aug 18, 2023

FRNet: Frustum-Range Networks for Scalable LiDAR Segmentation

LiDAR segmentation has become a crucial component in advanced autonomous driving systems. Recent range-view LiDAR segmentation approaches show promise for real-time processing. However, they inevitably suffer from corrupted contextual information and rely heavily on post-processing techniques for prediction refinement. In this work, we propose FRNet, a simple yet powerful method aimed at restoring the contextual information of range image pixels using corresponding frustum LiDAR points. Firstly, a frustum feature encoder module is used to extract per-point features within the frustum region, which preserves scene consistency and is crucial for point-level predictions. Next, a frustum-point fusion module is introduced to update per-point features hierarchically, enabling each point to extract more surrounding information via the frustum features. Finally, a head fusion module is used to fuse features at different levels for final semantic prediction. Extensive experiments conducted on four popular LiDAR segmentation benchmarks under various task setups demonstrate the superiority of FRNet. Notably, FRNet achieves 73.3% and 82.5% mIoU scores on the testing sets of SemanticKITTI and nuScenes. While achieving competitive performance, FRNet operates 5 times faster than state-of-the-art approaches. Such high efficiency opens up new possibilities for more scalable LiDAR segmentation. The code has been made publicly available at https://github.com/Xiangxu-0103/FRNet.

  • 4 authors
·
Dec 7, 2023

S3IM: Stochastic Structural SIMilarity and Its Unreasonable Effectiveness for Neural Fields

Recently, Neural Radiance Field (NeRF) has shown great success in rendering novel-view images of a given scene by learning an implicit representation with only posed RGB images. NeRF and relevant neural field methods (e.g., neural surface representation) typically optimize a point-wise loss and make point-wise predictions, where one data point corresponds to one pixel. Unfortunately, this line of research failed to use the collective supervision of distant pixels, although it is known that pixels in an image or scene can provide rich structural information. To the best of our knowledge, we are the first to design a nonlocal multiplex training paradigm for NeRF and relevant neural field methods via a novel Stochastic Structural SIMilarity (S3IM) loss that processes multiple data points as a whole set instead of process multiple inputs independently. Our extensive experiments demonstrate the unreasonable effectiveness of S3IM in improving NeRF and neural surface representation for nearly free. The improvements of quality metrics can be particularly significant for those relatively difficult tasks: e.g., the test MSE loss unexpectedly drops by more than 90% for TensoRF and DVGO over eight novel view synthesis tasks; a 198% F-score gain and a 64% Chamfer L_{1} distance reduction for NeuS over eight surface reconstruction tasks. Moreover, S3IM is consistently robust even with sparse inputs, corrupted images, and dynamic scenes.

  • 8 authors
·
Aug 14, 2023

Patherea: Cell Detection and Classification for the 2020s

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

  • 6 authors
·
Dec 20, 2024

GeoMAE: Masked Geometric Target Prediction for Self-supervised Point Cloud Pre-Training

This paper tries to address a fundamental question in point cloud self-supervised learning: what is a good signal we should leverage to learn features from point clouds without annotations? To answer that, we introduce a point cloud representation learning framework, based on geometric feature reconstruction. In contrast to recent papers that directly adopt masked autoencoder (MAE) and only predict original coordinates or occupancy from masked point clouds, our method revisits differences between images and point clouds and identifies three self-supervised learning objectives peculiar to point clouds, namely centroid prediction, normal estimation, and curvature prediction. Combined with occupancy prediction, these four objectives yield an nontrivial self-supervised learning task and mutually facilitate models to better reason fine-grained geometry of point clouds. Our pipeline is conceptually simple and it consists of two major steps: first, it randomly masks out groups of points, followed by a Transformer-based point cloud encoder; second, a lightweight Transformer decoder predicts centroid, normal, and curvature for points in each voxel. We transfer the pre-trained Transformer encoder to a downstream peception model. On the nuScene Datset, our model achieves 3.38 mAP improvment for object detection, 2.1 mIoU gain for segmentation, and 1.7 AMOTA gain for multi-object tracking. We also conduct experiments on the Waymo Open Dataset and achieve significant performance improvements over baselines as well.

  • 4 authors
·
May 15, 2023

VPOcc: Exploiting Vanishing Point for 3D Semantic Occupancy Prediction

Understanding 3D scenes semantically and spatially is crucial for the safe navigation of robots and autonomous vehicles, aiding obstacle avoidance and accurate trajectory planning. Camera-based 3D semantic occupancy prediction, which infers complete voxel grids from 2D images, is gaining importance in robot vision for its resource efficiency compared to 3D sensors. However, this task inherently suffers from a 2D-3D discrepancy, where objects of the same size in 3D space appear at different scales in a 2D image depending on their distance from the camera due to perspective projection. To tackle this issue, we propose a novel framework called VPOcc that leverages a vanishing point (VP) to mitigate the 2D-3D discrepancy at both the pixel and feature levels. As a pixel-level solution, we introduce a VPZoomer module, which warps images by counteracting the perspective effect using a VP-based homography transformation. In addition, as a feature-level solution, we propose a VP-guided cross-attention (VPCA) module that performs perspective-aware feature aggregation, utilizing 2D image features that are more suitable for 3D space. Lastly, we integrate two feature volumes extracted from the original and warped images to compensate for each other through a spatial volume fusion (SVF) module. By effectively incorporating VP into the network, our framework achieves improvements in both IoU and mIoU metrics on SemanticKITTI and SSCBench-KITTI360 datasets. Additional details are available at https://vision3d-lab.github.io/vpocc/.

  • 5 authors
·
Aug 7, 2024

Point Linguist Model: Segment Any Object via Bridged Large 3D-Language Model

3D object segmentation with Large Language Models (LLMs) has become a prevailing paradigm due to its broad semantics, task flexibility, and strong generalization. However, this paradigm is hindered by representation misalignment: LLMs process high-level semantic tokens, whereas 3D point clouds convey only dense geometric structures. In prior methods, misalignment limits both input and output. At the input stage, dense point patches require heavy pre-alignment, weakening object-level semantics and confusing similar distractors. At the output stage, predictions depend only on dense features without explicit geometric cues, leading to a loss of fine-grained accuracy. To address these limitations, we present the Point Linguist Model (PLM), a general framework that bridges the representation gap between LLMs and dense 3D point clouds without requiring large-scale pre-alignment between 3D-text or 3D-images. Specifically, we introduce Object-centric Discriminative Representation (OcDR), which learns object-centric tokens that capture target semantics and scene relations under a hard negative-aware training objective. This mitigates the misalignment between LLM tokens and 3D points, enhances resilience to distractors, and facilitates semantic-level reasoning within LLMs. For accurate segmentation, we introduce the Geometric Reactivation Decoder (GRD), which predicts masks by combining OcDR tokens carrying LLM-inferred geometry with corresponding dense features, preserving comprehensive dense features throughout the pipeline. Extensive experiments show that PLM achieves significant improvements of +7.3 mIoU on ScanNetv2 and +6.0 mIoU on Multi3DRefer for 3D referring segmentation, with consistent gains across 7 benchmarks spanning 4 different tasks, demonstrating the effectiveness of comprehensive object-centric reasoning for robust 3D understanding.

  • 3 authors
·
Sep 9

Improving Diffusion-Based Image Synthesis with Context Prediction

Diffusion models are a new class of generative models, and have dramatically promoted image generation with unprecedented quality and diversity. Existing diffusion models mainly try to reconstruct input image from a corrupted one with a pixel-wise or feature-wise constraint along spatial axes. However, such point-based reconstruction may fail to make each predicted pixel/feature fully preserve its neighborhood context, impairing diffusion-based image synthesis. As a powerful source of automatic supervisory signal, context has been well studied for learning representations. Inspired by this, we for the first time propose ConPreDiff to improve diffusion-based image synthesis with context prediction. We explicitly reinforce each point to predict its neighborhood context (i.e., multi-stride features/tokens/pixels) with a context decoder at the end of diffusion denoising blocks in training stage, and remove the decoder for inference. In this way, each point can better reconstruct itself by preserving its semantic connections with neighborhood context. This new paradigm of ConPreDiff can generalize to arbitrary discrete and continuous diffusion backbones without introducing extra parameters in sampling procedure. Extensive experiments are conducted on unconditional image generation, text-to-image generation and image inpainting tasks. Our ConPreDiff consistently outperforms previous methods and achieves a new SOTA text-to-image generation results on MS-COCO, with a zero-shot FID score of 6.21.

  • 8 authors
·
Jan 3, 2024 1

Approximately Piecewise E(3) Equivariant Point Networks

Integrating a notion of symmetry into point cloud neural networks is a provably effective way to improve their generalization capability. Of particular interest are E(3) equivariant point cloud networks where Euclidean transformations applied to the inputs are preserved in the outputs. Recent efforts aim to extend networks that are E(3) equivariant, to accommodate inputs made of multiple parts, each of which exhibits local E(3) symmetry. In practical settings, however, the partitioning into individually transforming regions is unknown a priori. Errors in the partition prediction would unavoidably map to errors in respecting the true input symmetry. Past works have proposed different ways to predict the partition, which may exhibit uncontrolled errors in their ability to maintain equivariance to the actual partition. To this end, we introduce APEN: a general framework for constructing approximate piecewise-E(3) equivariant point networks. Our primary insight is that functions that are equivariant with respect to a finer partition will also maintain equivariance in relation to the true partition. Leveraging this observation, we propose a design where the equivariance approximation error at each layers can be bounded solely in terms of (i) uncertainty quantification of the partition prediction, and (ii) bounds on the probability of failing to suggest a proper subpartition of the ground truth one. We demonstrate the effectiveness of APEN using two data types exemplifying part-based symmetry: (i) real-world scans of room scenes containing multiple furniture-type objects; and, (ii) human motions, characterized by articulated parts exhibiting rigid movement. Our empirical results demonstrate the advantage of integrating piecewise E(3) symmetry into network design, showing a distinct improvement in generalization compared to prior works for both classification and segmentation tasks.

  • 4 authors
·
Feb 13, 2024

GridFormer: Point-Grid Transformer for Surface Reconstruction

Implicit neural networks have emerged as a crucial technology in 3D surface reconstruction. To reconstruct continuous surfaces from discrete point clouds, encoding the input points into regular grid features (plane or volume) has been commonly employed in existing approaches. However, these methods typically use the grid as an index for uniformly scattering point features. Compared with the irregular point features, the regular grid features may sacrifice some reconstruction details but improve efficiency. To take full advantage of these two types of features, we introduce a novel and high-efficiency attention mechanism between the grid and point features named Point-Grid Transformer (GridFormer). This mechanism treats the grid as a transfer point connecting the space and point cloud. Our method maximizes the spatial expressiveness of grid features and maintains computational efficiency. Furthermore, optimizing predictions over the entire space could potentially result in blurred boundaries. To address this issue, we further propose a boundary optimization strategy incorporating margin binary cross-entropy loss and boundary sampling. This approach enables us to achieve a more precise representation of the object structure. Our experiments validate that our method is effective and outperforms the state-of-the-art approaches under widely used benchmarks by producing more precise geometry reconstructions. The code is available at https://github.com/list17/GridFormer.

  • 5 authors
·
Jan 4, 2024

PointOBB: Learning Oriented Object Detection via Single Point Supervision

Single point-supervised object detection is gaining attention due to its cost-effectiveness. However, existing approaches focus on generating horizontal bounding boxes (HBBs) while ignoring oriented bounding boxes (OBBs) commonly used for objects in aerial images. This paper proposes PointOBB, the first single Point-based OBB generation method, for oriented object detection. PointOBB operates through the collaborative utilization of three distinctive views: an original view, a resized view, and a rotated/flipped (rot/flp) view. Upon the original view, we leverage the resized and rot/flp views to build a scale augmentation module and an angle acquisition module, respectively. In the former module, a Scale-Sensitive Consistency (SSC) loss is designed to enhance the deep network's ability to perceive the object scale. For accurate object angle predictions, the latter module incorporates self-supervised learning to predict angles, which is associated with a scale-guided Dense-to-Sparse (DS) matching strategy for aggregating dense angles corresponding to sparse objects. The resized and rot/flp views are switched using a progressive multi-view switching strategy during training to achieve coupled optimization of scale and angle. Experimental results on the DIOR-R and DOTA-v1.0 datasets demonstrate that PointOBB achieves promising performance, and significantly outperforms potential point-supervised baselines.

  • 6 authors
·
Nov 23, 2023

Radar Meets Vision: Robustifying Monocular Metric Depth Prediction for Mobile Robotics

Mobile robots require accurate and robust depth measurements to understand and interact with the environment. While existing sensing modalities address this problem to some extent, recent research on monocular depth estimation has leveraged the information richness, yet low cost and simplicity of monocular cameras. These works have shown significant generalization capabilities, mainly in automotive and indoor settings. However, robots often operate in environments with limited scale cues, self-similar appearances, and low texture. In this work, we encode measurements from a low-cost mmWave radar into the input space of a state-of-the-art monocular depth estimation model. Despite the radar's extreme point cloud sparsity, our method demonstrates generalization and robustness across industrial and outdoor experiments. Our approach reduces the absolute relative error of depth predictions by 9-64% across a range of unseen, real-world validation datasets. Importantly, we maintain consistency of all performance metrics across all experiments and scene depths where current vision-only approaches fail. We further address the present deficit of training data in mobile robotics environments by introducing a novel methodology for synthesizing rendered, realistic learning datasets based on photogrammetric data that simulate the radar sensor observations for training. Our code, datasets, and pre-trained networks are made available at https://github.com/ethz-asl/radarmeetsvision.

  • 5 authors
·
Oct 1, 2024

CPCM: Contextual Point Cloud Modeling for Weakly-supervised Point Cloud Semantic Segmentation

We study the task of weakly-supervised point cloud semantic segmentation with sparse annotations (e.g., less than 0.1% points are labeled), aiming to reduce the expensive cost of dense annotations. Unfortunately, with extremely sparse annotated points, it is very difficult to extract both contextual and object information for scene understanding such as semantic segmentation. Motivated by masked modeling (e.g., MAE) in image and video representation learning, we seek to endow the power of masked modeling to learn contextual information from sparsely-annotated points. However, directly applying MAE to 3D point clouds with sparse annotations may fail to work. First, it is nontrivial to effectively mask out the informative visual context from 3D point clouds. Second, how to fully exploit the sparse annotations for context modeling remains an open question. In this paper, we propose a simple yet effective Contextual Point Cloud Modeling (CPCM) method that consists of two parts: a region-wise masking (RegionMask) strategy and a contextual masked training (CMT) method. Specifically, RegionMask masks the point cloud continuously in geometric space to construct a meaningful masked prediction task for subsequent context learning. CMT disentangles the learning of supervised segmentation and unsupervised masked context prediction for effectively learning the very limited labeled points and mass unlabeled points, respectively. Extensive experiments on the widely-tested ScanNet V2 and S3DIS benchmarks demonstrate the superiority of CPCM over the state-of-the-art.

  • 8 authors
·
Jul 19, 2023

Assembler: Scalable 3D Part Assembly via Anchor Point Diffusion

We present Assembler, a scalable and generalizable framework for 3D part assembly that reconstructs complete objects from input part meshes and a reference image. Unlike prior approaches that mostly rely on deterministic part pose prediction and category-specific training, Assembler is designed to handle diverse, in-the-wild objects with varying part counts, geometries, and structures. It addresses the core challenges of scaling to general 3D part assembly through innovations in task formulation, representation, and data. First, Assembler casts part assembly as a generative problem and employs diffusion models to sample plausible configurations, effectively capturing ambiguities arising from symmetry, repeated parts, and multiple valid assemblies. Second, we introduce a novel shape-centric representation based on sparse anchor point clouds, enabling scalable generation in Euclidean space rather than SE(3) pose prediction. Third, we construct a large-scale dataset of over 320K diverse part-object assemblies using a synthesis and filtering pipeline built on existing 3D shape repositories. Assembler achieves state-of-the-art performance on PartNet and is the first to demonstrate high-quality assembly for complex, real-world objects. Based on Assembler, we further introduce an interesting part-aware 3D modeling system that generates high-resolution, editable objects from images, demonstrating potential for interactive and compositional design. Project page: https://assembler3d.github.io

  • 5 authors
·
Jun 20

Post-Hoc Split-Point Self-Consistency Verification for Efficient, Unified Quantification of Aleatoric and Epistemic Uncertainty in Deep Learning

Uncertainty quantification (UQ) is vital for trustworthy deep learning, yet existing methods are either computationally intensive, such as Bayesian or ensemble methods, or provide only partial, task-specific estimates, such as single-forward-pass techniques. In this paper, we propose a post-hoc single-forward-pass framework that jointly captures aleatoric and epistemic uncertainty without modifying or retraining pretrained models. Our method applies Split-Point Analysis (SPA) to decompose predictive residuals into upper and lower subsets, computing Mean Absolute Residuals (MARs) on each side. We prove that, under ideal conditions, the total MAR equals the harmonic mean of subset MARs; deviations define a novel Self-consistency Discrepancy Score (SDS) for fine-grained epistemic estimation across regression and classification. For regression, side-specific quantile regression yields prediction intervals with improved empirical coverage, which are further calibrated via SDS. For classification, when calibration data are available, we apply SPA-based calibration identities to adjust the softmax outputs and then compute predictive entropy on these calibrated probabilities. Extensive experiments on diverse regression and classification benchmarks demonstrate that our framework matches or exceeds several state-of-the-art UQ methods while incurring minimal overhead. Our source code is available at https://github.com/zzz0527/SPC-UQ.

  • 2 authors
·
Sep 16

Exploring Temporally-Aware Features for Point Tracking

Point tracking in videos is a fundamental task with applications in robotics, video editing, and more. While many vision tasks benefit from pre-trained feature backbones to improve generalizability, point tracking has primarily relied on simpler backbones trained from scratch on synthetic data, which may limit robustness in real-world scenarios. Additionally, point tracking requires temporal awareness to ensure coherence across frames, but using temporally-aware features is still underexplored. Most current methods often employ a two-stage process: an initial coarse prediction followed by a refinement stage to inject temporal information and correct errors from the coarse stage. These approach, however, is computationally expensive and potentially redundant if the feature backbone itself captures sufficient temporal information. In this work, we introduce Chrono, a feature backbone specifically designed for point tracking with built-in temporal awareness. Leveraging pre-trained representations from self-supervised learner DINOv2 and enhanced with a temporal adapter, Chrono effectively captures long-term temporal context, enabling precise prediction even without the refinement stage. Experimental results demonstrate that Chrono achieves state-of-the-art performance in a refiner-free setting on the TAP-Vid-DAVIS and TAP-Vid-Kinetics datasets, among common feature backbones used in point tracking as well as DINOv2, with exceptional efficiency. Project page: https://cvlab-kaist.github.io/Chrono/

  • 6 authors
·
Jan 21

Point-PRC: A Prompt Learning Based Regulation Framework for Generalizable Point Cloud Analysis

This paper investigates the 3D domain generalization (3DDG) ability of large 3D models based on prevalent prompt learning. Recent works demonstrate the performances of 3D point cloud recognition can be boosted remarkably by parameter-efficient prompt tuning. However, we observe that the improvement on downstream tasks comes at the expense of a severe drop in 3D domain generalization. To resolve this challenge, we present a comprehensive regulation framework that allows the learnable prompts to actively interact with the well-learned general knowledge in large 3D models to maintain good generalization. Specifically, the proposed framework imposes multiple explicit constraints on the prompt learning trajectory by maximizing the mutual agreement between task-specific predictions and task-agnostic knowledge. We design the regulation framework as a plug-and-play module to embed into existing representative large 3D models. Surprisingly, our method not only realizes consistently increasing generalization ability but also enhances task-specific 3D recognition performances across various 3DDG benchmarks by a clear margin. Considering the lack of study and evaluation on 3DDG, we also create three new benchmarks, namely base-to-new, cross-dataset and few-shot generalization benchmarks, to enrich the field and inspire future research. Code and benchmarks are available at https://github.com/auniquesun/Point-PRC.

  • 7 authors
·
Oct 27, 2024

SHS-Net: Learning Signed Hyper Surfaces for Oriented Normal Estimation of Point Clouds

We propose a novel method called SHS-Net for oriented normal estimation of point clouds by learning signed hyper surfaces, which can accurately predict normals with global consistent orientation from various point clouds. Almost all existing methods estimate oriented normals through a two-stage pipeline, i.e., unoriented normal estimation and normal orientation, and each step is implemented by a separate algorithm. However, previous methods are sensitive to parameter settings, resulting in poor results from point clouds with noise, density variations and complex geometries. In this work, we introduce signed hyper surfaces (SHS), which are parameterized by multi-layer perceptron (MLP) layers, to learn to estimate oriented normals from point clouds in an end-to-end manner. The signed hyper surfaces are implicitly learned in a high-dimensional feature space where the local and global information is aggregated. Specifically, we introduce a patch encoding module and a shape encoding module to encode a 3D point cloud into a local latent code and a global latent code, respectively. Then, an attention-weighted normal prediction module is proposed as a decoder, which takes the local and global latent codes as input to predict oriented normals. Experimental results show that our SHS-Net outperforms the state-of-the-art methods in both unoriented and oriented normal estimation on the widely used benchmarks. The code, data and pretrained models are publicly available.

  • 7 authors
·
May 9, 2023

Modeling Inter-Dependence Between Time and Mark in Multivariate Temporal Point Processes

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

  • 4 authors
·
Oct 27, 2022

Binary and Multitask Classification Model for Dutch Anaphora Resolution: Die/Dat Prediction

The correct use of Dutch pronouns 'die' and 'dat' is a stumbling block for both native and non-native speakers of Dutch due to the multiplicity of syntactic functions and the dependency on the antecedent's gender and number. Drawing on previous research conducted on neural context-dependent dt-mistake correction models (Heyman et al. 2018), this study constructs the first neural network model for Dutch demonstrative and relative pronoun resolution that specifically focuses on the correction and part-of-speech prediction of these two pronouns. Two separate datasets are built with sentences obtained from, respectively, the Dutch Europarl corpus (Koehn 2015) - which contains the proceedings of the European Parliament from 1996 to the present - and the SoNaR corpus (Oostdijk et al. 2013) - which contains Dutch texts from a variety of domains such as newspapers, blogs and legal texts. Firstly, a binary classification model solely predicts the correct 'die' or 'dat'. The classifier with a bidirectional long short-term memory architecture achieves 84.56% accuracy. Secondly, a multitask classification model simultaneously predicts the correct 'die' or 'dat' and its part-of-speech tag. The model containing a combination of a sentence and context encoder with both a bidirectional long short-term memory architecture results in 88.63% accuracy for die/dat prediction and 87.73% accuracy for part-of-speech prediction. More evenly-balanced data, larger word embeddings, an extra bidirectional long short-term memory layer and integrated part-of-speech knowledge positively affects die/dat prediction performance, while a context encoder architecture raises part-of-speech prediction performance. This study shows promising results and can serve as a starting point for future research on machine learning models for Dutch anaphora resolution.

  • 3 authors
·
Jan 9, 2020

Generative Point Tracking with Flow Matching

Tracking a point through a video can be a challenging task due to uncertainty arising from visual obfuscations, such as appearance changes and occlusions. Although current state-of-the-art discriminative models excel in regressing long-term point trajectory estimates -- even through occlusions -- they are limited to regressing to a mean (or mode) in the presence of uncertainty, and fail to capture multi-modality. To overcome this limitation, we introduce Generative Point Tracker (GenPT), a generative framework for modelling multi-modal trajectories. GenPT is trained with a novel flow matching formulation that combines the iterative refinement of discriminative trackers, a window-dependent prior for cross-window consistency, and a variance schedule tuned specifically for point coordinates. We show how our model's generative capabilities can be leveraged to improve point trajectory estimates by utilizing a best-first search strategy on generated samples during inference, guided by the model's own confidence of its predictions. Empirically, we evaluate GenPT against the current state of the art on the standard PointOdyssey, Dynamic Replica, and TAP-Vid benchmarks. Further, we introduce a TAP-Vid variant with additional occlusions to assess occluded point tracking performance and highlight our model's ability to capture multi-modality. GenPT is capable of capturing the multi-modality in point trajectories, which translates to state-of-the-art tracking accuracy on occluded points, while maintaining competitive tracking accuracy on visible points compared to extant discriminative point trackers.

  • 5 authors
·
Oct 23

The Missing Point in Vision Transformers for Universal Image Segmentation

Image segmentation remains a challenging task in computer vision, demanding robust mask generation and precise classification. Recent mask-based approaches yield high-quality masks by capturing global context. However, accurately classifying these masks, especially in the presence of ambiguous boundaries and imbalanced class distributions, remains an open challenge. In this work, we introduce ViT-P, a novel two-stage segmentation framework that decouples mask generation from classification. The first stage employs a proposal generator to produce class-agnostic mask proposals, while the second stage utilizes a point-based classification model built on the Vision Transformer (ViT) to refine predictions by focusing on mask central points. ViT-P serves as a pre-training-free adapter, allowing the integration of various pre-trained vision transformers without modifying their architecture, ensuring adaptability to dense prediction tasks. Furthermore, we demonstrate that coarse and bounding box annotations can effectively enhance classification without requiring additional training on fine annotation datasets, reducing annotation costs while maintaining strong performance. Extensive experiments across COCO, ADE20K, and Cityscapes datasets validate the effectiveness of ViT-P, achieving state-of-the-art results with 54.0 PQ on ADE20K panoptic segmentation, 87.4 mIoU on Cityscapes semantic segmentation, and 63.6 mIoU on ADE20K semantic segmentation. The code and pretrained models are available at: https://github.com/sajjad-sh33/ViT-P}{https://github.com/sajjad-sh33/ViT-P.

  • 6 authors
·
May 26

VICON: Vision In-Context Operator Networks for Multi-Physics Fluid Dynamics Prediction

In-Context Operator Networks (ICONs) have demonstrated the ability to learn operators across diverse partial differential equations using few-shot, in-context learning. However, existing ICONs process each spatial point as an individual token, severely limiting computational efficiency when handling dense data in higher spatial dimensions. We propose Vision In-Context Operator Networks (VICON), which integrates vision transformer architectures to efficiently process 2D data through patch-wise operations while preserving ICON's adaptability to multiphysics systems and varying timesteps. Evaluated across three fluid dynamics benchmarks, VICON significantly outperforms state-of-the-art baselines: DPOT and MPP, reducing the averaged last-step rollout error by 37.9% compared to DPOT and 44.7% compared to MPP, while requiring only 72.5% and 34.8% of their respective inference times. VICON naturally supports flexible rollout strategies with varying timestep strides, enabling immediate deployment in imperfect measurement systems where sampling frequencies may differ or frames might be dropped - common challenges in real-world settings - without requiring retraining or interpolation. In these realistic scenarios, VICON exhibits remarkable robustness, experiencing only 24.41% relative performance degradation compared to 71.37%-74.49% degradation in baseline methods, demonstrating its versatility for deploying in realistic applications. Our scripts for processing datasets and code are publicly available at https://github.com/Eydcao/VICON.

  • 6 authors
·
Nov 24, 2024

SpecDETR: A Transformer-based Hyperspectral Point Object Detection Network

Hyperspectral target detection (HTD) aims to identify specific materials based on spectral information in hyperspectral imagery and can detect extremely small objects, some of which occupy a smaller than one-pixel area. However, existing HTD methods are developed based on per-pixel binary classification, which limits the feature representation capability for instance-level objects. In this paper, we rethink the hyperspectral target detection from the point object detection perspective, and propose the first specialized network for hyperspectral multi-class point object detection, SpecDETR. Without the visual foundation model of the current object detection framework, SpecDETR treats each pixel in input images as a token and uses a multi-layer Transformer encoder with self-excited subpixel-scale attention modules to directly extract joint spatial-spectral features from images. During feature extraction, we introduce a self-excited mechanism to enhance object features through self-excited amplification, thereby accelerating network convergence. Additionally, SpecDETR regards point object detection as a one-to-many set prediction problem, thereby achieving a concise and efficient DETR decoder that surpasses the state-of-the-art (SOTA) DETR decoder. We develop a simulated hyperSpectral Point Object Detection benchmark termed SPOD, and for the first time, evaluate and compare the performance of current object detection networks and HTD methods on hyperspectral point object detection. Extensive experiments demonstrate that our proposed SpecDETR outperforms SOTA object detection networks and HTD methods. Our code and dataset are available at https://github.com/ZhaoxuLi123/SpecDETR.

  • 6 authors
·
May 16, 2024

xTrimoABFold: De novo Antibody Structure Prediction without MSA

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

  • 10 authors
·
Nov 30, 2022

Dens3R: A Foundation Model for 3D Geometry Prediction

Recent advances in dense 3D reconstruction have led to significant progress, yet achieving accurate unified geometric prediction remains a major challenge. Most existing methods are limited to predicting a single geometry quantity from input images. However, geometric quantities such as depth, surface normals, and point maps are inherently correlated, and estimating them in isolation often fails to ensure consistency, thereby limiting both accuracy and practical applicability. This motivates us to explore a unified framework that explicitly models the structural coupling among different geometric properties to enable joint regression. In this paper, we present Dens3R, a 3D foundation model designed for joint geometric dense prediction and adaptable to a wide range of downstream tasks. Dens3R adopts a two-stage training framework to progressively build a pointmap representation that is both generalizable and intrinsically invariant. Specifically, we design a lightweight shared encoder-decoder backbone and introduce position-interpolated rotary positional encoding to maintain expressive power while enhancing robustness to high-resolution inputs. By integrating image-pair matching features with intrinsic invariance modeling, Dens3R accurately regresses multiple geometric quantities such as surface normals and depth, achieving consistent geometry perception from single-view to multi-view inputs. Additionally, we propose a post-processing pipeline that supports geometrically consistent multi-view inference. Extensive experiments demonstrate the superior performance of Dens3R across various dense 3D prediction tasks and highlight its potential for broader applications.

Towards Fewer Annotations: Active Learning via Region Impurity and Prediction Uncertainty for Domain Adaptive Semantic Segmentation

Self-training has greatly facilitated domain adaptive semantic segmentation, which iteratively generates pseudo labels on unlabeled target data and retrains the network. However, realistic segmentation datasets are highly imbalanced, pseudo labels are typically biased to the majority classes and basically noisy, leading to an error-prone and suboptimal model. In this paper, we propose a simple region-based active learning approach for semantic segmentation under a domain shift, aiming to automatically query a small partition of image regions to be labeled while maximizing segmentation performance. Our algorithm, Region Impurity and Prediction Uncertainty (RIPU), introduces a new acquisition strategy characterizing the spatial adjacency of image regions along with the prediction confidence. We show that the proposed region-based selection strategy makes more efficient use of a limited budget than image-based or point-based counterparts. Further, we enforce local prediction consistency between a pixel and its nearest neighbors on a source image. Alongside, we develop a negative learning loss to make the features more discriminative. Extensive experiments demonstrate that our method only requires very few annotations to almost reach the supervised performance and substantially outperforms state-of-the-art methods. The code is available at https://github.com/BIT-DA/RIPU.

  • 5 authors
·
Nov 25, 2021

Deep SNP: An End-to-end Deep Neural Network with Attention-based Localization for Break-point Detection in SNP Array Genomic data

Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming manual curation. As deep-learning methods outperformed classical state-of-the-art algorithms in various domains and have also been successfully applied to life science problems including medicine and biology, we here propose Deep SNP, a novel Deep Neural Network to learn from genomic data. Specifically, we used a manually curated dataset from 12 genomic single nucleotide polymorphism array (SNPa) profiles as truth-set and aimed at predicting the presence or absence of genomic breakpoints, an indicator of structural chromosomal variations, in windows of 40,000 probes. We compare our results with well-known neural network models as well as Rawcopy though this tool is designed to predict breakpoints and in addition genomic segments with high sensitivity. We show, that Deep SNP is capable of successfully predicting the presence or absence of a breakpoint in large genomic windows and outperforms state-of-the-art neural network models. Qualitative examples suggest that integration of a localization unit may enable breakpoint detection and prediction of genomic segments, even if the breakpoint coordinates were not provided for network training. These results warrant further evaluation of DeepSNP for breakpoint localization and subsequent calling of genomic segments.

  • 12 authors
·
Jun 22, 2018

LiDAR-PTQ: Post-Training Quantization for Point Cloud 3D Object Detection

Due to highly constrained computing power and memory, deploying 3D lidar-based detectors on edge devices equipped in autonomous vehicles and robots poses a crucial challenge. Being a convenient and straightforward model compression approach, Post-Training Quantization (PTQ) has been widely adopted in 2D vision tasks. However, applying it directly to 3D lidar-based tasks inevitably leads to performance degradation. As a remedy, we propose an effective PTQ method called LiDAR-PTQ, which is particularly curated for 3D lidar detection (both SPConv-based and SPConv-free). Our LiDAR-PTQ features three main components, (1) a sparsity-based calibration method to determine the initialization of quantization parameters, (2) a Task-guided Global Positive Loss (TGPL) to reduce the disparity between the final predictions before and after quantization, (3) an adaptive rounding-to-nearest operation to minimize the layerwise reconstruction error. Extensive experiments demonstrate that our LiDAR-PTQ can achieve state-of-the-art quantization performance when applied to CenterPoint (both Pillar-based and Voxel-based). To our knowledge, for the very first time in lidar-based 3D detection tasks, the PTQ INT8 model's accuracy is almost the same as the FP32 model while enjoying 3times inference speedup. Moreover, our LiDAR-PTQ is cost-effective being 30times faster than the quantization-aware training method. Code will be released at https://github.com/StiphyJay/LiDAR-PTQ.

  • 9 authors
·
Jan 28, 2024

VolSplat: Rethinking Feed-Forward 3D Gaussian Splatting with Voxel-Aligned Prediction

Feed-forward 3D Gaussian Splatting (3DGS) has emerged as a highly effective solution for novel view synthesis. Existing methods predominantly rely on a pixel-aligned Gaussian prediction paradigm, where each 2D pixel is mapped to a 3D Gaussian. We rethink this widely adopted formulation and identify several inherent limitations: it renders the reconstructed 3D models heavily dependent on the number of input views, leads to view-biased density distributions, and introduces alignment errors, particularly when source views contain occlusions or low texture. To address these challenges, we introduce VolSplat, a new multi-view feed-forward paradigm that replaces pixel alignment with voxel-aligned Gaussians. By directly predicting Gaussians from a predicted 3D voxel grid, it overcomes pixel alignment's reliance on error-prone 2D feature matching, ensuring robust multi-view consistency. Furthermore, it enables adaptive control over Gaussian density based on 3D scene complexity, yielding more faithful Gaussian point clouds, improved geometric consistency, and enhanced novel-view rendering quality. Experiments on widely used benchmarks including RealEstate10K and ScanNet demonstrate that VolSplat achieves state-of-the-art performance while producing more plausible and view-consistent Gaussian reconstructions. In addition to superior results, our approach establishes a more scalable framework for feed-forward 3D reconstruction with denser and more robust representations, paving the way for further research in wider communities. The video results, code and trained models are available on our project page: https://lhmd.top/volsplat.

  • 10 authors
·
Sep 23 4

3DHacker: Spectrum-based Decision Boundary Generation for Hard-label 3D Point Cloud Attack

With the maturity of depth sensors, the vulnerability of 3D point cloud models has received increasing attention in various applications such as autonomous driving and robot navigation. Previous 3D adversarial attackers either follow the white-box setting to iteratively update the coordinate perturbations based on gradients, or utilize the output model logits to estimate noisy gradients in the black-box setting. However, these attack methods are hard to be deployed in real-world scenarios since realistic 3D applications will not share any model details to users. Therefore, we explore a more challenging yet practical 3D attack setting, i.e., attacking point clouds with black-box hard labels, in which the attacker can only have access to the prediction label of the input. To tackle this setting, we propose a novel 3D attack method, termed 3D Hard-label attacker (3DHacker), based on the developed decision boundary algorithm to generate adversarial samples solely with the knowledge of class labels. Specifically, to construct the class-aware model decision boundary, 3DHacker first randomly fuses two point clouds of different classes in the spectral domain to craft their intermediate sample with high imperceptibility, then projects it onto the decision boundary via binary search. To restrict the final perturbation size, 3DHacker further introduces an iterative optimization strategy to move the intermediate sample along the decision boundary for generating adversarial point clouds with smallest trivial perturbations. Extensive evaluations show that, even in the challenging hard-label setting, 3DHacker still competitively outperforms existing 3D attacks regarding the attack performance as well as adversary quality.

  • 6 authors
·
Aug 14, 2023

3D-SPS: Single-Stage 3D Visual Grounding via Referred Point Progressive Selection

3D visual grounding aims to locate the referred target object in 3D point cloud scenes according to a free-form language description. Previous methods mostly follow a two-stage paradigm, i.e., language-irrelevant detection and cross-modal matching, which is limited by the isolated architecture. In such a paradigm, the detector needs to sample keypoints from raw point clouds due to the inherent properties of 3D point clouds (irregular and large-scale), to generate the corresponding object proposal for each keypoint. However, sparse proposals may leave out the target in detection, while dense proposals may confuse the matching model. Moreover, the language-irrelevant detection stage can only sample a small proportion of keypoints on the target, deteriorating the target prediction. In this paper, we propose a 3D Single-Stage Referred Point Progressive Selection (3D-SPS) method, which progressively selects keypoints with the guidance of language and directly locates the target. Specifically, we propose a Description-aware Keypoint Sampling (DKS) module to coarsely focus on the points of language-relevant objects, which are significant clues for grounding. Besides, we devise a Target-oriented Progressive Mining (TPM) module to finely concentrate on the points of the target, which is enabled by progressive intra-modal relation modeling and inter-modal target mining. 3D-SPS bridges the gap between detection and matching in the 3D visual grounding task, localizing the target at a single stage. Experiments demonstrate that 3D-SPS achieves state-of-the-art performance on both ScanRefer and Nr3D/Sr3D datasets.

  • 8 authors
·
Apr 13, 2022

Pep2Prob Benchmark: Predicting Fragment Ion Probability for MS$^2$-based Proteomics

Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS^2) is the major analytical technique in proteomics that identifies peptides by ionizing them, fragmenting them, and using the resulting mass spectra to identify and quantify proteins in biological samples. In MS^2 analysis, peptide fragment ion probability prediction plays a critical role, enhancing the accuracy of peptide identification from mass spectra as a complement to the intensity information. Current approaches rely on global statistics of fragmentation, which assumes that a fragment's probability is uniform across all peptides. Nevertheless, this assumption is oversimplified from a biochemical principle point of view and limits accurate prediction. To address this gap, we present Pep2Prob, the first comprehensive dataset and benchmark designed for peptide-specific fragment ion probability prediction. The proposed dataset contains fragment ion probability statistics for 608,780 unique precursors (each precursor is a pair of peptide sequence and charge state), summarized from more than 183 million high-quality, high-resolution, HCD MS^2 spectra with validated peptide assignments and fragmentation annotations. We establish baseline performance using simple statistical rules and learning-based methods, and find that models leveraging peptide-specific information significantly outperform previous methods using only global fragmentation statistics. Furthermore, performance across benchmark models with increasing capacities suggests that the peptide-fragmentation relationship exhibits complex nonlinearities requiring sophisticated machine learning approaches.

  • 5 authors
·
Aug 12

OneRec: Unifying Retrieve and Rank with Generative Recommender and Iterative Preference Alignment

Recently, generative retrieval-based recommendation systems have emerged as a promising paradigm. However, most modern recommender systems adopt a retrieve-and-rank strategy, where the generative model functions only as a selector during the retrieval stage. In this paper, we propose OneRec, which replaces the cascaded learning framework with a unified generative model. To the best of our knowledge, this is the first end-to-end generative model that significantly surpasses current complex and well-designed recommender systems in real-world scenarios. Specifically, OneRec includes: 1) an encoder-decoder structure, which encodes the user's historical behavior sequences and gradually decodes the videos that the user may be interested in. We adopt sparse Mixture-of-Experts (MoE) to scale model capacity without proportionally increasing computational FLOPs. 2) a session-wise generation approach. In contrast to traditional next-item prediction, we propose a session-wise generation, which is more elegant and contextually coherent than point-by-point generation that relies on hand-crafted rules to properly combine the generated results. 3) an Iterative Preference Alignment module combined with Direct Preference Optimization (DPO) to enhance the quality of the generated results. Unlike DPO in NLP, a recommendation system typically has only one opportunity to display results for each user's browsing request, making it impossible to obtain positive and negative samples simultaneously. To address this limitation, We design a reward model to simulate user generation and customize the sampling strategy. Extensive experiments have demonstrated that a limited number of DPO samples can align user interest preferences and significantly improve the quality of generated results. We deployed OneRec in the main scene of Kuaishou, achieving a 1.6\% increase in watch-time, which is a substantial improvement.

  • 8 authors
·
Feb 26 2

CPP-Net: Context-aware Polygon Proposal Network for Nucleus Segmentation

Nucleus segmentation is a challenging task due to the crowded distribution and blurry boundaries of nuclei. Recent approaches represent nuclei by means of polygons to differentiate between touching and overlapping nuclei and have accordingly achieved promising performance. Each polygon is represented by a set of centroid-to-boundary distances, which are in turn predicted by features of the centroid pixel for a single nucleus. However, using the centroid pixel alone does not provide sufficient contextual information for robust prediction and thus degrades the segmentation accuracy. To handle this problem, we propose a Context-aware Polygon Proposal Network (CPP-Net) for nucleus segmentation. First, we sample a point set rather than one single pixel within each cell for distance prediction. This strategy substantially enhances contextual information and thereby improves the robustness of the prediction. Second, we propose a Confidence-based Weighting Module, which adaptively fuses the predictions from the sampled point set. Third, we introduce a novel Shape-Aware Perceptual (SAP) loss that constrains the shape of the predicted polygons. Here, the SAP loss is based on an additional network that is pre-trained by means of mapping the centroid probability map and the pixel-to-boundary distance maps to a different nucleus representation. Extensive experiments justify the effectiveness of each component in the proposed CPP-Net. Finally, CPP-Net is found to achieve state-of-the-art performance on three publicly available databases, namely DSB2018, BBBC06, and PanNuke. Code of this paper is available at \url{https://github.com/csccsccsccsc/cpp-net

  • 5 authors
·
Feb 13, 2021

Calibrating Panoramic Depth Estimation for Practical Localization and Mapping

The absolute depth values of surrounding environments provide crucial cues for various assistive technologies, such as localization, navigation, and 3D structure estimation. We propose that accurate depth estimated from panoramic images can serve as a powerful and light-weight input for a wide range of downstream tasks requiring 3D information. While panoramic images can easily capture the surrounding context from commodity devices, the estimated depth shares the limitations of conventional image-based depth estimation; the performance deteriorates under large domain shifts and the absolute values are still ambiguous to infer from 2D observations. By taking advantage of the holistic view, we mitigate such effects in a self-supervised way and fine-tune the network with geometric consistency during the test phase. Specifically, we construct a 3D point cloud from the current depth prediction and project the point cloud at various viewpoints or apply stretches on the current input image to generate synthetic panoramas. Then we minimize the discrepancy of the 3D structure estimated from synthetic images without collecting additional data. We empirically evaluate our method in robot navigation and map-free localization where our method shows large performance enhancements. Our calibration method can therefore widen the applicability under various external conditions, serving as a key component for practical panorama-based machine vision systems.

  • 3 authors
·
Aug 27, 2023

LoRA3D: Low-Rank Self-Calibration of 3D Geometric Foundation Models

Emerging 3D geometric foundation models, such as DUSt3R, offer a promising approach for in-the-wild 3D vision tasks. However, due to the high-dimensional nature of the problem space and scarcity of high-quality 3D data, these pre-trained models still struggle to generalize to many challenging circumstances, such as limited view overlap or low lighting. To address this, we propose LoRA3D, an efficient self-calibration pipeline to specialize the pre-trained models to target scenes using their own multi-view predictions. Taking sparse RGB images as input, we leverage robust optimization techniques to refine multi-view predictions and align them into a global coordinate frame. In particular, we incorporate prediction confidence into the geometric optimization process, automatically re-weighting the confidence to better reflect point estimation accuracy. We use the calibrated confidence to generate high-quality pseudo labels for the calibrating views and use low-rank adaptation (LoRA) to fine-tune the models on the pseudo-labeled data. Our method does not require any external priors or manual labels. It completes the self-calibration process on a single standard GPU within just 5 minutes. Each low-rank adapter requires only 18MB of storage. We evaluated our method on more than 160 scenes from the Replica, TUM and Waymo Open datasets, achieving up to 88% performance improvement on 3D reconstruction, multi-view pose estimation and novel-view rendering.

  • 7 authors
·
Dec 10, 2024

Frame Averaging for Invariant and Equivariant Network Design

Many machine learning tasks involve learning functions that are known to be invariant or equivariant to certain symmetries of the input data. However, it is often challenging to design neural network architectures that respect these symmetries while being expressive and computationally efficient. For example, Euclidean motion invariant/equivariant graph or point cloud neural networks. We introduce Frame Averaging (FA), a general purpose and systematic framework for adapting known (backbone) architectures to become invariant or equivariant to new symmetry types. Our framework builds on the well known group averaging operator that guarantees invariance or equivariance but is intractable. In contrast, we observe that for many important classes of symmetries, this operator can be replaced with an averaging operator over a small subset of the group elements, called a frame. We show that averaging over a frame guarantees exact invariance or equivariance while often being much simpler to compute than averaging over the entire group. Furthermore, we prove that FA-based models have maximal expressive power in a broad setting and in general preserve the expressive power of their backbone architectures. Using frame averaging, we propose a new class of universal Graph Neural Networks (GNNs), universal Euclidean motion invariant point cloud networks, and Euclidean motion invariant Message Passing (MP) GNNs. We demonstrate the practical effectiveness of FA on several applications including point cloud normal estimation, beyond 2-WL graph separation, and n-body dynamics prediction, achieving state-of-the-art results in all of these benchmarks.

  • 7 authors
·
Oct 7, 2021