arXiv subjects

Donglai Wei

Publications and source records attributed to Donglai Wei.

At least 19 recordsLinked to original sources

arXiv2025

Frenet-Serret Frame-based Decomposition for Part Segmentation of 3D Curvilinear Structures

Accurately segmenting 3D curvilinear structures in medical imaging remains challenging due to their complex geometry and the scarcity of diverse, large-scale datasets for algorithm development and evaluation. In this paper, we use dendritic spine segmentation as a case study and address these challenges by introducing a novel Frenet--Serret Frame-based Decomposition, which decomposes 3D curvilinear structures into a globally $ C^2 $ continuous curve that captures the overall shape, and a cylindrical primitive that encodes local geometric properties. This approach leverages Frenet--Serret Frames and arc length parameterization to preserve essential geometric features while reducing representational complexity, facilitating data-efficient learning, improved segmentation accuracy, and generalization on 3D curvilinear structures. To rigorously evaluate our method, we introduce two datasets: CurviSeg, a synthetic dataset for 3D curvilinear structure segmentation that validates our method's key properties, and DenSpineEM, a benchmark for dendritic spine segmentation, which comprises 4,476 manually annotated spines from 70 dendrites across three public electron microscopy datasets, covering multiple brain regions and species. Our experiments on DenSpineEM demonstrate exceptional cross-region and cross-species generalization: models trained on the mouse somatosensory cortex subset achieve 91.9\% Dice, maintaining strong performance in zero-shot segmentation on both mouse visual cortex (94.1\% Dice) and human frontal lobe (81.8\% Dice) subsets. Moreover, we test the generalizability of our method on the IntrA dataset, where it achieves 77.08\% Dice (5.29\% higher than prior arts) on intracranial aneurysm segmentation. These findings demonstrate the potential of our approach for accurately analyzing complex curvilinear structures across diverse medical imaging fields.

cs.CV↗

arXiv2025

"See the World, Discover Knowledge": A Chinese Factuality Evaluation for Large Vision Language Models

The evaluation of factual accuracy in large vision language models (LVLMs) has lagged behind their rapid development, making it challenging to fully reflect these models' knowledge capacity and reliability. In this paper, we introduce the first factuality-based visual question-answering benchmark in Chinese, named ChineseSimpleVQA, aimed at assessing the visual factuality of LVLMs across 8 major topics and 56 subtopics. The key features of this benchmark include a focus on the Chinese language, diverse knowledge types, a multi-hop question construction, high-quality data, static consistency, and easy-to-evaluate through short answers. Moreover, we contribute a rigorous data construction pipeline and decouple the visual factuality into two parts: seeing the world (i.e., object recognition) and discovering knowledge. This decoupling allows us to analyze the capability boundaries and execution mechanisms of LVLMs. Subsequently, we evaluate 34 advanced open-source and closed-source models, revealing critical performance gaps within this field. Our evaluation-friendly code and data have already been open-sourced.

cs.CL↗

arXiv2025

Affordance-Aware Object Insertion via Mask-Aware Dual Diffusion

As a common image editing operation, image composition involves integrating foreground objects into background scenes. In this paper, we expand the application of the concept of Affordance from human-centered image composition tasks to a more general object-scene composition framework, addressing the complex interplay between foreground objects and background scenes. Following the principle of Affordance, we define the affordance-aware object insertion task, which aims to seamlessly insert any object into any scene with various position prompts. To address the limited data issue and incorporate this task, we constructed the SAM-FB dataset, which contains over 3 million examples across more than 3,000 object categories. Furthermore, we propose the Mask-Aware Dual Diffusion (MADD) model, which utilizes a dual-stream architecture to simultaneously denoise the RGB image and the insertion mask. By explicitly modeling the insertion mask in the diffusion process, MADD effectively facilitates the notion of affordance. Extensive experimental results show that our method outperforms the state-of-the-art methods and exhibits strong generalization performance on in-the-wild images. Please refer to our code on https://github.com/KaKituken/affordance-aware-any.

cs.CV↗

arXiv2024

SocialGPT: Prompting LLMs for Social Relation Reasoning via Greedy Segment Optimization

Social relation reasoning aims to identify relation categories such as friends, spouses, and colleagues from images. While current methods adopt the paradigm of training a dedicated network end-to-end using labeled image data, they are limited in terms of generalizability and interpretability. To address these issues, we first present a simple yet well-crafted framework named {\name}, which combines the perception capability of Vision Foundation Models (VFMs) and the reasoning capability of Large Language Models (LLMs) within a modular framework, providing a strong baseline for social relation recognition. Specifically, we instruct VFMs to translate image content into a textual social story, and then utilize LLMs for text-based reasoning. {\name} introduces systematic design principles to adapt VFMs and LLMs separately and bridge their gaps. Without additional model training, it achieves competitive zero-shot results on two databases while offering interpretable answers, as LLMs can generate language-based explanations for the decisions. The manual prompt design process for LLMs at the reasoning phase is tedious and an automated prompt optimization method is desired. As we essentially convert a visual classification task into a generative task of LLMs, automatic prompt optimization encounters a unique long prompt optimization issue. To address this issue, we further propose the Greedy Segment Prompt Optimization (GSPO), which performs a greedy search by utilizing gradient information at the segment level. Experimental results show that GSPO significantly improves performance, and our method also generalizes to different image styles. The code is available at https://github.com/Mengzibin/SocialGPT.

cs.CV↗

arXiv2024

Efficient Anatomical Labeling of Pulmonary Tree Structures via Deep Point-Graph Representation-based Implicit Fields

Pulmonary diseases rank prominently among the principal causes of death worldwide. Curing them will require, among other things, a better understanding of the complex 3D tree-shaped structures within the pulmonary system, such as airways, arteries, and veins. Traditional approaches using high-resolution image stacks and standard CNNs on dense voxel grids face challenges in computational efficiency, limited resolution, local context, and inadequate preservation of shape topology. Our method addresses these issues by shifting from dense voxel to sparse point representation, offering better memory efficiency and global context utilization. However, the inherent sparsity in point representation can lead to a loss of crucial connectivity in tree-shaped structures. To mitigate this, we introduce graph learning on skeletonized structures, incorporating differentiable feature fusion for improved topology and long-distance context capture. Furthermore, we employ an implicit function for efficient conversion of sparse representations into dense reconstructions end-to-end. The proposed method not only delivers state-of-the-art performance in labeling accuracy, both overall and at key locations, but also enables efficient inference and the generation of closed surface shapes. Addressing data scarcity in this field, we have also curated a comprehensive dataset to validate our approach. Data and code are available at \url{https://github.com/M3DV/pulmonary-tree-labeling}.

cs.CV↗

arXiv2024

The time is ripe to reverse engineer an entire nervous system: simulating behavior from neural interactions

Just like electrical engineers understand how microprocessors execute programs in terms of how transistor currents are affected by their inputs, neuroscientists want to understand behavior production in terms of how neuronal outputs are affected by their inputs and internal states. This dependency of neuronal outputs on inputs can be described by a state-dependent input-output (IO)-function. However, to reliably identify these IO-functions, we need to perturb each input and combinations of inputs while observing all the outputs. Here, we argue that such completeness is possible in C. elegans; a complete description that goes all the way from the activity of every neuron to predict behavior. The established and growing toolkit of optophysiology can non-invasively capture and control every neuron's activity and scale to countless experiments. The information from many such experiments can be pooled while capturing the inter-individual variability because neuronal identity and function are largely conserved across individuals. Just like electrical engineers use transistor IO-functions to simulate program execution, we argue that neuronal IO-functions could be used to simulate the impressive breadth of brain states and behaviors of C. elegans.

q-bio.NC↗

arXiv2024

VizAbility: Enhancing Chart Accessibility with LLM-based Conversational Interaction

Traditional accessibility methods like alternative text and data tables typically underrepresent data visualization's full potential. Keyboard-based chart navigation has emerged as a potential solution, yet efficient data exploration remains challenging. We present VizAbility, a novel system that enriches chart content navigation with conversational interaction, enabling users to use natural language for querying visual data trends. VizAbility adapts to the user's navigation context for improved response accuracy and facilitates verbal command-based chart navigation. Furthermore, it can address queries for contextual information, designed to address the needs of visually impaired users. We designed a large language model (LLM)-based pipeline to address these user queries, leveraging chart data & encoding, user context, and external web knowledge. We conducted both qualitative and quantitative studies to evaluate VizAbility's multimodal approach. We discuss further opportunities based on the results, including improved benchmark testing, incorporation of vision models, and integration with visualization workflows.

cs.HC↗

arXiv2024

TriSAM: Tri-Plane SAM for zero-shot cortical blood vessel segmentation in VEM images

While imaging techniques at macro and mesoscales have garnered substantial attention and resources, microscale Volume Electron Microscopy (vEM) imaging, capable of revealing intricate vascular details, has lacked the necessary benchmarking infrastructure. In this paper, we address a significant gap in this field of neuroimaging by introducing the first-in-class public benchmark, BvEM, designed specifically for cortical blood vessel segmentation in vEM images. Our BvEM benchmark is based on vEM image volumes from three mammals: adult mouse, macaque, and human. We standardized the resolution, addressed imaging variations, and meticulously annotated blood vessels through semi-automatic, manual, and quality control processes, ensuring high-quality 3D segmentation. Furthermore, we developed a zero-shot cortical blood vessel segmentation method named TriSAM, which leverages the powerful segmentation model SAM for 3D segmentation. To extend SAM from 2D to 3D volume segmentation, TriSAM employs a multi-seed tracking framework, leveraging the reliability of certain image planes for tracking while using others to identify potential turning points. This approach effectively achieves long-term 3D blood vessel segmentation without model training or fine-tuning. Experimental results show that TriSAM achieved superior performances on the BvEM benchmark across three species. Our dataset, code, and model are available online at \url{https://jia-wan.github.io/bvem}.

cs.CV↗

arXiv2024

$R^2$-Tuning: Efficient Image-to-Video Transfer Learning for Video Temporal Grounding

Video temporal grounding (VTG) is a fine-grained video understanding problem that aims to ground relevant clips in untrimmed videos given natural language queries. Most existing VTG models are built upon frame-wise final-layer CLIP features, aided by additional temporal backbones (e.g., SlowFast) with sophisticated temporal reasoning mechanisms. In this work, we claim that CLIP itself already shows great potential for fine-grained spatial-temporal modeling, as each layer offers distinct yet useful information under different granularity levels. Motivated by this, we propose Reversed Recurrent Tuning ($R^2$-Tuning), a parameter- and memory-efficient transfer learning framework for video temporal grounding. Our method learns a lightweight $R^2$ Block containing only 1.5% of the total parameters to perform progressive spatial-temporal modeling. Starting from the last layer of CLIP, $R^2$ Block recurrently aggregates spatial features from earlier layers, then refines temporal correlation conditioning on the given query, resulting in a coarse-to-fine scheme. $R^2$-Tuning achieves state-of-the-art performance across three VTG tasks (i.e., moment retrieval, highlight detection, and video summarization) on six public benchmarks (i.e., QVHighlights, Charades-STA, Ego4D-NLQ, TACoS, YouTube Highlights, and TVSum) even without the additional backbone, demonstrating the significance and effectiveness of the proposed scheme. Our code is available at https://github.com/yeliudev/R2-Tuning.

cs.CV↗

arXiv2024

Learning Causal Domain-Invariant Temporal Dynamics for Few-Shot Action Recognition

Few-shot action recognition aims at quickly adapting a pre-trained model to the novel data with a distribution shift using only a limited number of samples. Key challenges include how to identify and leverage the transferable knowledge learned by the pre-trained model. We therefore propose CDTD, or Causal Domain-Invariant Temporal Dynamics for knowledge transfer. To identify the temporally invariant and variant representations, we employ the causal representation learning methods for unsupervised pertaining, and then tune the classifier with supervisions in next stage. Specifically, we assume the domain information can be well estimated and the pre-trained image decoder and transition models can be well transferred. During adaptation, we fix the transferable temporal dynamics and update the image encoder and domain estimator. The efficacy of our approach is revealed by the superior accuracy of CDTD over leading alternatives across standard few-shot action recognition datasets.

cs.CV↗

arXiv2024

Learning Gaze-aware Compositional GAN

Gaze-annotated facial data is crucial for training deep neural networks (DNNs) for gaze estimation. However, obtaining these data is labor-intensive and requires specialized equipment due to the challenge of accurately annotating the gaze direction of a subject. In this work, we present a generative framework to create annotated gaze data by leveraging the benefits of labeled and unlabeled data sources. We propose a Gaze-aware Compositional GAN that learns to generate annotated facial images from a limited labeled dataset. Then we transfer this model to an unlabeled data domain to take advantage of the diversity it provides. Experiments demonstrate our approach's effectiveness in generating within-domain image augmentations in the ETH-XGaze dataset and cross-domain augmentations in the CelebAMask-HQ dataset domain for gaze estimation DNN training. We also show additional applications of our work, which include facial image editing and gaze redirection.

cs.CV↗

arXiv2024

OccTransformer: Improving BEVFormer for 3D camera-only occupancy prediction

This technical report presents our solution, "occTransformer" for the 3D occupancy prediction track in the autonomous driving challenge at CVPR 2023. Our method builds upon the strong baseline BEVFormer and improves its performance through several simple yet effective techniques. Firstly, we employed data augmentation to increase the diversity of the training data and improve the model's generalization ability. Secondly, we used a strong image backbone to extract more informative features from the input data. Thirdly, we incorporated a 3D unet head to better capture the spatial information of the scene. Fourthly, we added more loss functions to better optimize the model. Additionally, we used an ensemble approach with the occ model BevDet and SurroundOcc to further improve the performance. Most importantly, we integrated 3D detection model StreamPETR to enhance the model's ability to detect objects in the scene. Using these methods, our solution achieved 49.23 miou on the 3D occupancy prediction track in the autonomous driving challenge.

cs.CV↗

arXiv2024

Deep Rib Fracture Instance Segmentation and Classification from CT on the RibFrac Challenge

Rib fractures are a common and potentially severe injury that can be challenging and labor-intensive to detect in CT scans. While there have been efforts to address this field, the lack of large-scale annotated datasets and evaluation benchmarks has hindered the development and validation of deep learning algorithms. To address this issue, the RibFrac Challenge was introduced, providing a benchmark dataset of over 5,000 rib fractures from 660 CT scans, with voxel-level instance mask annotations and diagnosis labels for four clinical categories (buckle, nondisplaced, displaced, or segmental). The challenge includes two tracks: a detection (instance segmentation) track evaluated by an FROC-style metric and a classification track evaluated by an F1-style metric. During the MICCAI 2020 challenge period, 243 results were evaluated, and seven teams were invited to participate in the challenge summary. The analysis revealed that several top rib fracture detection solutions achieved performance comparable or even better than human experts. Nevertheless, the current rib fracture classification solutions are hardly clinically applicable, which can be an interesting area in the future. As an active benchmark and research resource, the data and online evaluation of the RibFrac Challenge are available at the challenge website. As an independent contribution, we have also extended our previous internal baseline by incorporating recent advancements in large-scale pretrained networks and point-based rib segmentation techniques. The resulting FracNet+ demonstrates competitive performance in rib fracture detection, which lays a foundation for further research and development in AI-assisted rib fracture detection and diagnosis.

eess.IV↗

arXiv2024

S$^3$-TTA: Scale-Style Selection for Test-Time Augmentation in Biomedical Image Segmentation

Deep-learning models have been successful in biomedical image segmentation. To generalize for real-world deployment, test-time augmentation (TTA) methods are often used to transform the test image into different versions that are hopefully closer to the training domain. Unfortunately, due to the vast diversity of instance scale and image styles, many augmented test images produce undesirable results, thus lowering the overall performance. This work proposes a new TTA framework, S$^3$-TTA, which selects the suitable image scale and style for each test image based on a transformation consistency metric. In addition, S$^3$-TTA constructs an end-to-end augmentation-segmentation joint-training pipeline to ensure a task-oriented augmentation. On public benchmarks for cell and lung segmentation, S$^3$-TTA demonstrates improvements over the prior art by 3.4% and 1.3%, respectively, by simply augmenting the input data in testing phase.

cs.CV↗

arXiv2023

Learning Socio-Temporal Graphs for Multi-Agent Trajectory Prediction

In order to predict a pedestrian's trajectory in a crowd accurately, one has to take into account her/his underlying socio-temporal interactions with other pedestrians consistently. Unlike existing work that represents the relevant information separately, partially, or implicitly, we propose a complete representation for it to be fully and explicitly captured and analyzed. In particular, we introduce a Directed Acyclic Graph-based structure, which we term Socio-Temporal Graph (STG), to explicitly capture pair-wise socio-temporal interactions among a group of people across both space and time. Our model is built on a time-varying generative process, whose latent variables determine the structure of the STGs. We design an attention-based model named STGformer that affords an end-to-end pipeline to learn the structure of the STGs for trajectory prediction. Our solution achieves overall state-of-the-art prediction accuracy in two large-scale benchmark datasets. Our analysis shows that a person's past trajectory is critical for predicting another person's future path. Our model learns this relationship with a strong notion of socio-temporal localities. Statistics show that utilizing this information explicitly for prediction yields a noticeable performance gain with respect to the trajectory-only approaches.

cs.CV↗

arXiv2023

Structure-Preserving Instance Segmentation via Skeleton-Aware Distance Transform

Objects with complex structures pose significant challenges to existing instance segmentation methods that rely on boundary or affinity maps, which are vulnerable to small errors around contacting pixels that cause noticeable connectivity change. While the distance transform (DT) makes instance interiors and boundaries more distinguishable, it tends to overlook the intra-object connectivity for instances with varying width and result in over-segmentation. To address these challenges, we propose a skeleton-aware distance transform (SDT) that combines the merits of object skeleton in preserving connectivity and DT in modeling geometric arrangement to represent instances with arbitrary structures. Comprehensive experiments on histopathology image segmentation demonstrate that SDT achieves state-of-the-art performance.

cs.CV↗

arXiv2023

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

cs.CV↗

arXiv2023

CLIPTrans: Transferring Visual Knowledge with Pre-trained Models for Multimodal Machine Translation

There has been a growing interest in developing multimodal machine translation (MMT) systems that enhance neural machine translation (NMT) with visual knowledge. This problem setup involves using images as auxiliary information during training, and more recently, eliminating their use during inference. Towards this end, previous works face a challenge in training powerful MMT models from scratch due to the scarcity of annotated multilingual vision-language data, especially for low-resource languages. Simultaneously, there has been an influx of multilingual pre-trained models for NMT and multimodal pre-trained models for vision-language tasks, primarily in English, which have shown exceptional generalisation ability. However, these are not directly applicable to MMT since they do not provide aligned multimodal multilingual features for generative tasks. To alleviate this issue, instead of designing complex modules for MMT, we propose CLIPTrans, which simply adapts the independently pre-trained multimodal M-CLIP and the multilingual mBART. In order to align their embedding spaces, mBART is conditioned on the M-CLIP features by a prefix sequence generated through a lightweight mapping network. We train this in a two-stage pipeline which warms up the model with image captioning before the actual translation task. Through experiments, we demonstrate the merits of this framework and consequently push forward the state-of-the-art across standard benchmarks by an average of +2.67 BLEU. The code can be found at www.github.com/devaansh100/CLIPTrans.

cs.CV↗