Yunlong Zhang

Honglin Li, Chenglu Zhu, Yunlong Zhang et al.

While Multiple Instance Learning (MIL) has shown promising results in digital Pathology Whole Slide Image (WSI) classification, such a paradigm still faces performance and generalization problems due to challenges in high computational costs on Gigapixel WSIs and limited sample size for model training. To deal with the computation problem, most MIL methods utilize a frozen pretrained model from ImageNet to obtain representations first. This process may lose essential information owing to the large domain gap and hinder the generalization of model due to the lack of image-level training-time augmentations. Though Self-supervised Learning (SSL) proposes viable representation learning schemes, the improvement of the downstream task still needs to be further explored in the conversion from the task-agnostic features of SSL to the task-specifics under the partial label supervised learning. To alleviate the dilemma of computation cost and performance, we propose an efficient WSI fine-tuning framework motivated by the Information Bottleneck theory. The theory enables the framework to find the minimal sufficient statistics of WSI, thus supporting us to fine-tune the backbone into a task-specific representation only depending on WSI-level weak labels. The WSI-MIL problem is further analyzed to theoretically deduce our fine-tuning method. Our framework is evaluated on five pathology WSI datasets on various WSI heads. The experimental results of our fine-tuned representations show significant improvements in both accuracy and generalization compared with previous works. Source code will be available at https://github.com/invoker-LL/WSI-finetuning.

Yunlong Zhang, Yuxuan Sun, Honglin Li et al.

When designing a diagnostic model for a clinical application, it is crucial to guarantee the robustness of the model with respect to a wide range of image corruptions. Herein, an easy-to-use benchmark is established to evaluate how deep neural networks perform on corrupted pathology images. Specifically, corrupted images are generated by injecting nine types of common corruptions into validation images. Besides, two classification and one ranking metrics are designed to evaluate the prediction and confidence performance under corruption. Evaluated on two resulting benchmark datasets, we find that (1) a variety of deep neural network models suffer from a significant accuracy decrease (double the error on clean images) and the unreliable confidence estimation on corrupted images; (2) A low correlation between the validation and test errors while replacing the validation set with our benchmark can increase the correlation. Our codes are available on https://github.com/superjamessyx/robustness_benchmark.

Yunlong Zhang, Xin Lin, Yihong Zhuang et al.

Synthesizing a subject-specific pathology-free image from a pathological image is valuable for algorithm development and clinical practice. In recent years, several approaches based on the Generative Adversarial Network (GAN) have achieved promising results in pseudo-healthy synthesis. However, the discriminator (i.e., a classifier) in the GAN cannot accurately identify lesions and further hampers from generating admirable pseudo-healthy images. To address this problem, we present a new type of discriminator, the segmentor, to accurately locate the lesions and improve the visual quality of pseudo-healthy images. Then, we apply the generated images into medical image enhancement and utilize the enhanced results to cope with the low contrast problem existing in medical image segmentation. Furthermore, a reliable metric is proposed by utilizing two attributes of label noise to measure the health of synthetic images. Comprehensive experiments on the T2 modality of BraTS demonstrate that the proposed method substantially outperforms the state-of-the-art methods. The method achieves better performance than the existing methods with only 30\% of the training data. The effectiveness of the proposed method is also demonstrated on the LiTS and the T1 modality of BraTS. The code and the pre-trained model of this study are publicly available at https://github.com/Au3C2/Generator-Versus-Segmentor.

Yunlong Zhang, Honglin Li, Yuxuan Sun et al.

In the application of Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) classification, attention mechanisms often focus on a subset of discriminative instances, which are closely linked to overfitting. To mitigate overfitting, we present Attention-Challenging MIL (ACMIL). ACMIL combines two techniques based on separate analyses for attention value concentration. Firstly, UMAP of instance features reveals various patterns among discriminative instances, with existing attention mechanisms capturing only some of them. To remedy this, we introduce Multiple Branch Attention (MBA) to capture more discriminative instances using multiple attention branches. Secondly, the examination of the cumulative value of Top-K attention scores indicates that a tiny number of instances dominate the majority of attention. In response, we present Stochastic Top-K Instance Masking (STKIM), which masks out a portion of instances with Top-K attention values and allocates their attention values to the remaining instances. The extensive experimental results on three WSI datasets with two pre-trained backbones reveal that our ACMIL outperforms state-of-the-art methods. Additionally, through heatmap visualization and UMAP visualization, this paper extensively illustrates ACMIL's effectiveness in suppressing attention value concentration and overcoming the overfitting challenge. The source code is available at \url{https://github.com/dazhangyu123/ACMIL}.

Zhongyi Shui, Yunlong Zhang, Kai Yao et al.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at \url{github.com/windygoo/PromptNucSeg}

Haote Xu, Yunlong Zhang, Liyan Sun et al.

Anomaly Detection (AD) on medical images enables a model to recognize any type of anomaly pattern without lesion-specific supervised learning. Data augmentation based methods construct pseudo-healthy images by "pasting" fake lesions on real healthy ones, and a network is trained to predict healthy images in a supervised manner. The lesion can be found by difference between the unhealthy input and pseudo-healthy output. However, using only manually designed fake lesions fail to approximate to irregular real lesions, hence limiting the model generalization. We assume by exploring the intrinsic data property within images, we can distinguish previously unseen lesions from healthy regions in an unhealthy image. In this study, we propose an Adaptive Fourier Space Compression (AFSC) module to distill healthy feature for AD. The compression of both magnitude and phase in frequency domain addresses the hyper intensity and diverse position of lesions. Experimental results on the BraTS and MS-SEG datasets demonstrate an AFSC baseline is able to produce promising detection results, and an AFSC module can be effectively embedded into existing AD methods.

Yunlong Zhang, Yuxuan Sun, Sunyi Zheng et al.

Although deep learning-based segmentation models have achieved impressive performance on public benchmarks, generalizing well to unseen environments remains a major challenge. To improve the model's generalization ability to the new domain during evaluation, the test-time training (TTT) is a challenging paradigm that adapts the source-pretrained model in an online fashion. Early efforts on TTT mainly focus on the image classification task. Directly extending these methods to semantic segmentation easily experiences unstable adaption due to segmentation's inherent characteristics, such as extreme class imbalance and complex decision spaces. To stabilize the adaptation process, we introduce contrastive loss (CL), known for its capability to learn robust and generalized representations. Nevertheless, the traditional CL operates in the representation space and cannot directly enhance predictions. In this paper, we resolve this limitation by adapting the CL to the output space, employing a high temperature, and simplifying the formulation, resulting in a straightforward yet effective loss function called Output Contrastive Loss (OCL). Our comprehensive experiments validate the efficacy of our approach across diverse evaluation scenarios. Notably, our method excels even when applied to models initially pre-trained using domain adaptation methods on test domain data, showcasing its resilience and adaptability.\footnote{Code and more information could be found at~ \url{https://github.com/dazhangyu123/OCL}}

Zhongyi Shui, Yizhi Zhao, Sunyi Zheng et al.

Cell recognition is a fundamental task in digital histopathology image analysis. Point-based cell recognition (PCR) methods normally require a vast number of annotations, which is extremely costly, time-consuming and labor-intensive. Semi-supervised learning (SSL) can provide a shortcut to make full use of cell information in gigapixel whole slide images without exhaustive labeling. However, research into semi-supervised point-based cell recognition (SSPCR) remains largely overlooked. Previous SSPCR works are all built on density map-based PCR models, which suffer from unsatisfactory accuracy, slow inference speed and high sensitivity to hyper-parameters. To address these issues, end-to-end PCR models are proposed recently. In this paper, we develop a SSPCR framework suitable for the end-to-end PCR models for the first time. Overall, we use the current models to generate pseudo labels for unlabeled images, which are in turn utilized to supervise the models training. Besides, we introduce a co-teaching strategy to overcome the confirmation bias problem that generally exists in self-training. A distribution alignment technique is also incorporated to produce high-quality, unbiased pseudo labels for unlabeled data. Experimental results on four histopathology datasets concerning different types of staining styles show the effectiveness and versatility of the proposed framework. Code is available at \textcolor{magenta}{\url{https://github.com/windygooo/SSPCR}

Jingxiong Li, Sunyi Zheng, Zhongyi Shui et al.

Karyotyping is of importance for detecting chromosomal aberrations in human disease. However, chromosomes easily appear curved in microscopic images, which prevents cytogeneticists from analyzing chromosome types. To address this issue, we propose a framework for chromosome straightening, which comprises a preliminary processing algorithm and a generative model called masked conditional variational autoencoders (MC-VAE). The processing method utilizes patch rearrangement to address the difficulty in erasing low degrees of curvature, providing reasonable preliminary results for the MC-VAE. The MC-VAE further straightens the results by leveraging chromosome patches conditioned on their curvatures to learn the mapping between banding patterns and conditions. During model training, we apply a masking strategy with a high masking ratio to train the MC-VAE with eliminated redundancy. This yields a non-trivial reconstruction task, allowing the model to effectively preserve chromosome banding patterns and structure details in the reconstructed results. Extensive experiments on three public datasets with two stain styles show that our framework surpasses the performance of state-of-the-art methods in retaining banding patterns and structure details. Compared to using real-world bent chromosomes, the use of high-quality straightened chromosomes generated by our proposed method can improve the performance of various deep learning models for chromosome classification by a large margin. Such a straightening approach has the potential to be combined with other karyotyping systems to assist cytogeneticists in chromosome analysis.

Honglin Li, Yunlong Zhang, Chenglu Zhu et al.

Histopathology image analysis is the golden standard of clinical diagnosis for Cancers. In doctors daily routine and computer-aided diagnosis, the Whole Slide Image (WSI) of histopathology tissue is used for analysis. Because of the extremely large scale of resolution, previous methods generally divide the WSI into a large number of patches, then aggregate all patches within a WSI by Multi-Instance Learning (MIL) to make the slide-level prediction when developing computer-aided diagnosis tools. However, most previous WSI-MIL models using global-attention without pairwise interaction and any positional information, or self-attention with absolute position embedding can not well handle shape varying large WSIs, e.g. testing WSIs after model deployment may be larger than training WSIs, since the model development set is always limited due to the difficulty of histopathology WSIs collection. To deal with the problem, in this paper, we propose to amend position embedding for shape varying long-contextual WSI by introducing Linear Bias into Attention, and adapt it from 1-d long sequence into 2-d long-contextual WSI which helps model extrapolate position embedding to unseen or under-fitted positions. We further utilize Flash-Attention module to tackle the computational complexity of Transformer, which also keep full self-attention performance compared to previous attention approximation work. Our method, Long-contextual MIL (Long-MIL) are evaluated on extensive experiments including 4 dataset including WSI classification and survival prediction tasks to validate the superiority on shape varying WSIs. The source code will be open-accessed soon.

Honglin Li, Yusuan Sun, Chenglu Zhu et al.

Cervical Cancer continues to be the leading gynecological malignancy, posing a persistent threat to women's health on a global scale. Early screening via cytology Whole Slide Image (WSI) diagnosis is critical to prevent this Cancer progression and improve survival rate, but pathologist's single test suffers inevitable false negative due to the immense number of cells that need to be reviewed within a WSI. Though computer-aided automated diagnostic models can serve as strong complement for pathologists, their effectiveness is hampered by the paucity of extensive and detailed annotations, coupled with the limited interpretability and robustness. These factors significantly hinder their practical applicability and reliability in clinical settings. To tackle these challenges, we develop an AI approach, which is a Scalable Technology for Robust and Interpretable Diagnosis built on Extensive data (STRIDE) of cervical cytology. STRIDE addresses the bottleneck of limited annotations by integrating patient-level labels with a small portion of cell-level labels through an end-to-end training strategy, facilitating scalable learning across extensive datasets. To further improve the robustness to real-world domain shifts of cytology slide-making and imaging, STRIDE employs color adversarial samples training that mimic staining and imaging variations. Lastly, to achieve pathologist-level interpretability for the trustworthiness in clinical settings, STRIDE can generate explanatory textual descriptions that simulates pathologists' diagnostic processes by cell image feature and textual description alignment. Conducting extensive experiments and evaluations in 183 medical centers with a dataset of 341,889 WSIs and 0.1 billion cells from cervical cytology patients, STRIDE has demonstrated a remarkable superiority over previous state-of-the-art techniques.

Sunyi Zheng, Jingxiong Li, Zhongyi Shui et al.

Karyotyping is an important procedure to assess the possible existence of chromosomal abnormalities. However, because of the non-rigid nature, chromosomes are usually heavily curved in microscopic images and such deformed shapes hinder the chromosome analysis for cytogeneticists. In this paper, we present a self-attention guided framework to erase the curvature of chromosomes. The proposed framework extracts spatial information and local textures to preserve banding patterns in a regression module. With complementary information from the bent chromosome, a refinement module is designed to further improve fine details. In addition, we propose two dedicated geometric constraints to maintain the length and restore the distortion of chromosomes. To train our framework, we create a synthetic dataset where curved chromosomes are generated from the real-world straight chromosomes by grid-deformation. Quantitative and qualitative experiments are conducted on synthetic and real-world data. Experimental results show that our proposed method can effectively straighten bent chromosomes while keeping banding details and length.

Yuxuan Sun, Hao Wu, Chenglu Zhu et al.

The emergence of large multimodal models has unlocked remarkable potential in AI, particularly in pathology. However, the lack of specialized, high-quality benchmark impeded their development and precise evaluation. To address this, we introduce PathMMU, the largest and highest-quality expert-validated pathology benchmark for Large Multimodal Models (LMMs). It comprises 33,428 multimodal multi-choice questions and 24,067 images from various sources, each accompanied by an explanation for the correct answer. The construction of PathMMU harnesses GPT-4V's advanced capabilities, utilizing over 30,000 image-caption pairs to enrich captions and generate corresponding Q&As in a cascading process. Significantly, to maximize PathMMU's authority, we invite seven pathologists to scrutinize each question under strict standards in PathMMU's validation and test sets, while simultaneously setting an expert-level performance benchmark for PathMMU. We conduct extensive evaluations, including zero-shot assessments of 14 open-sourced and 4 closed-sourced LMMs and their robustness to image corruption. We also fine-tune representative LMMs to assess their adaptability to PathMMU. The empirical findings indicate that advanced LMMs struggle with the challenging PathMMU benchmark, with the top-performing LMM, GPT-4V, achieving only a 49.8% zero-shot performance, significantly lower than the 71.8% demonstrated by human pathologists. After fine-tuning, significantly smaller open-sourced LMMs can outperform GPT-4V but still fall short of the expertise shown by pathologists. We hope that the PathMMU will offer valuable insights and foster the development of more specialized, next-generation LMMs for pathology.

Honglin Li, Yunlong Zhang, Pingyi Chen et al.

Histopathology Whole Slide Image (WSI) analysis serves as the gold standard for clinical cancer diagnosis in the daily routines of doctors. To develop computer-aided diagnosis model for WSIs, previous methods typically employ Multi-Instance Learning to enable slide-level prediction given only slide-level labels. Among these models, vanilla attention mechanisms without pairwise interactions have traditionally been employed but are unable to model contextual information. More recently, self-attention models have been utilized to address this issue. To alleviate the computational complexity of long sequences in large WSIs, methods like HIPT use region-slicing, and TransMIL employs approximation of full self-attention. Both approaches suffer from suboptimal performance due to the loss of key information. Moreover, their use of absolute positional embedding struggles to effectively handle long contextual dependencies in shape-varying WSIs. In this paper, we first analyze how the low-rank nature of the long-sequence attention matrix constrains the representation ability of WSI modelling. Then, we demonstrate that the rank of attention matrix can be improved by focusing on local interactions via a local attention mask. Our analysis shows that the local mask aligns with the attention patterns in the lower layers of the Transformer. Furthermore, the local attention mask can be implemented during chunked attention calculation, reducing the quadratic computational complexity to linear with a small local bandwidth. Building on this, we propose a local-global hybrid Transformer for both computational acceleration and local-global information interactions modelling. Our method, Long-contextual MIL (LongMIL), is evaluated through extensive experiments on various WSI tasks to validate its superiority. Our code will be available at github.com/invoker-LL/Long-MIL.

Chaolun Ma, Bruce Wang, Zihao Li et al.

In traffic signal control, flow-based (optimizing the overall flow) and pressure-based methods (equalizing and alleviating congestion) are commonly used but often considered separately. This study introduces a unified framework using Lyapunov control theory, defining specific Lyapunov functions respectively for these methods. We have found interesting results. For example, the well-recognized back-pressure method is equal to differential queue lengths weighted by intersection lane saturation flows. We further improve it by adding basic traffic flow theory. Rather than ensuring that the control system be stable, the system should be also capable of adaptive to various performance metrics. Building on insights from Lyapunov theory, this study designs a reward function for the Reinforcement Learning (RL)-based network signal control, whose agent is trained with Double Deep Q-Network (DDQN) for effective control over complex traffic networks. The proposed algorithm is compared with several traditional and RL-based methods under pure passenger car flow and heterogenous traffic flow including freight, respectively. The numerical tests demonstrate that the proposed method outperforms the alternative control methods across different traffic scenarios, covering corridor and general network situations each with varying traffic demands, in terms of the average network vehicle waiting time per vehicle.

Zhongyi Shui, Ruizhe Guo, Honglin Li et al.

Nucleus detection in histopathology whole slide images (WSIs) is crucial for a broad spectrum of clinical applications. Current approaches for nucleus detection in gigapixel WSIs utilize a sliding window methodology, which overlooks boarder contextual information (eg, tissue structure) and easily leads to inaccurate predictions. To address this problem, recent studies additionally crops a large Filed-of-View (FoV) region around each sliding window to extract contextual features. However, such methods substantially increases the inference latency. In this paper, we propose an effective and efficient context-aware nucleus detection algorithm. Specifically, instead of leveraging large FoV regions, we aggregate contextual clues from off-the-shelf features of historically visited sliding windows. This design greatly reduces computational overhead. Moreover, compared to large FoV regions at a low magnification, the sliding window patches have higher magnification and provide finer-grained tissue details, thereby enhancing the detection accuracy. To further improve the efficiency, we propose a grid pooling technique to compress dense feature maps of each patch into a few contextual tokens. Finally, we craft OCELOT-seg, the first benchmark dedicated to context-aware nucleus instance segmentation. Code, dataset, and model checkpoints will be available at https://github.com/windygoo/PathContext.

Chenchen Kuai, Chenhao Wu, Yang Zhou et al.

As tropical cyclones intensify and track forecasts become increasingly uncertain, U.S. ports face heightened supply-chain risk under extreme weather conditions. Port operators need to rapidly synthesize diverse multimodal forecast products, such as probabilistic wind maps, track cones, and official advisories, into clear, actionable guidance as cyclones approach. Multimodal large language models (MLLMs) offer a powerful means to integrate these heterogeneous data sources alongside broader contextual knowledge, yet their accuracy and reliability in the specific context of port cyclone preparedness have not been rigorously evaluated. To fill this gap, we introduce CyPortQA, the first multimodal benchmark tailored to port operations under cyclone threat. CyPortQA assembles 2,917 realworld disruption scenarios from 2015 through 2023, spanning 145 U.S. principal ports and 90 named storms. Each scenario fuses multisource data (i.e., tropical cyclone products, port operational impact records, and port condition bulletins) and is expanded through an automated pipeline into 117,178 structured question answer pairs. Using this benchmark, we conduct extensive experiments on diverse MLLMs, including both open-source and proprietary model. MLLMs demonstrate great potential in situation understanding but still face considerable challenges in reasoning tasks, including potential impact estimation and decision reasoning.

Natchaphon Leungbootnak, Zihao Li, Zihang Wei et al.

The ability of existing headway distributions to accurately reflect the diverse behaviors and characteristics in heterogeneous traffic (different types of vehicles) and mixed traffic (human-driven vehicles with autonomous vehicles) is limited, leading to unsatisfactory goodness of fit. To address these issues, we modified the exponential function to obtain a novel headway distribution. Rather than employing Euler's number (e) as the base of the exponential function, we utilized a real number base to provide greater flexibility in modeling the observed headway. However, the proposed is not a probability function. We normalize it to calculate the probability and derive the closed-form equation. In this study, we utilized a comprehensive experiment with five open datasets: highD, exiD, NGSIM, Waymo, and Lyft to evaluate the performance of the proposed distribution and compared its performance with six existing distributions under mixed and heterogeneous traffic flow. The results revealed that the proposed distribution not only captures the fundamental characteristics of headway distribution but also provides physically meaningful parameters that describe the distribution shape of observed headways. Under heterogeneous flow on highways (i.e., uninterrupted traffic flow), the proposed distribution outperforms other candidate distributions. Under urban road conditions (i.e., interrupted traffic flow), including heterogeneous and mixed traffic, the proposed distribution still achieves decent results.

Linggang Kong, Lei Wu, Yunlong Zhang et al.

Despite the groundbreaking advancements made by large language models (LLMs), hallucination remains a critical bottleneck for their deployment in high-stakes domains. Existing classification-based methods mainly rely on static and passive signals from internal states, which often captures the noise and spurious correlations, while overlooking the underlying causal mechanisms. To address this limitation, we shift the paradigm from passive observation to active intervention by introducing CausalGaze, a novel hallucination detection framework based on structural causal models (SCMs). CausalGaze models LLMs' internal states as dynamic causal graphs and employs counterfactual interventions to disentangle causal reasoning paths from incidental noise, thereby enhancing model interpretability. Extensive experiments across four datasets and three widely used LLMs demonstrate the effectiveness of CausalGaze, especially achieving over 5.2\% improvement in AUROC on the TruthfulQA dataset compared to state-of-the-art baselines.

Yunlong Zhang, Honglin Li, Yunxuan Sun et al.

Multiple Instance Learning (MIL) effectively analyzes whole slide images but faces overfitting due to attention over-concentration. While existing solutions rely on complex architectural modifications or additional processing steps, we introduce Attention Entropy Maximization (AEM), a simple yet effective regularization technique. Our investigation reveals the positive correlation between attention entropy and model performance. Building on this insight, we integrate AEM regularization into the MIL framework to penalize excessive attention concentration. To address sensitivity to the AEM weight parameter, we implement Cosine Weight Annealing, reducing parameter dependency. Extensive evaluations demonstrate AEM's superior performance across diverse feature extractors, MIL frameworks, attention mechanisms, and augmentation techniques. Here is our anonymous code: https://github.com/dazhangyu123/AEM.

Sunyi Zheng, Xiaonan Cui, Yuxuan Sun et al.

Accurate image classification and retrieval are of importance for clinical diagnosis and treatment decision-making. The recent contrastive language-image pretraining (CLIP) model has shown remarkable proficiency in understanding natural images. Drawing inspiration from CLIP, PathCLIP is specifically designed for pathology image analysis, utilizing over 200,000 image and text pairs in training. While the performance the PathCLIP is impressive, its robustness under a wide range of image corruptions remains unknown. Therefore, we conduct an extensive evaluation to analyze the performance of PathCLIP on various corrupted images from the datasets of Osteosarcoma and WSSS4LUAD. In our experiments, we introduce seven corruption types including brightness, contrast, Gaussian blur, resolution, saturation, hue, and markup at four severity levels. Through experiments, we find that PathCLIP is relatively robustness to image corruptions and surpasses OpenAI-CLIP and PLIP in zero-shot classification. Among the seven corruptions, blur and resolution can cause server performance degradation of the PathCLIP. This indicates that ensuring the quality of images is crucial before conducting a clinical test. Additionally, we assess the robustness of PathCLIP in the task of image-image retrieval, revealing that PathCLIP performs less effectively than PLIP on Osteosarcoma but performs better on WSSS4LUAD under diverse corruptions. Overall, PathCLIP presents impressive zero-shot classification and retrieval performance for pathology images, but appropriate care needs to be taken when using it. We hope this study provides a qualitative impression of PathCLIP and helps understand its differences from other CLIP models.

Kexin Tian, Jingrui Mao, Yunlong Zhang et al.

Recent advancements in Vision-Language Models (VLMs) have demonstrated strong potential for autonomous driving tasks. However, their spatial understanding and reasoning-key capabilities for autonomous driving-still exhibit significant limitations. Notably, none of the existing benchmarks systematically evaluate VLMs' spatial reasoning capabilities in driving scenarios. To fill this gap, we propose NuScenes-SpatialQA, the first large-scale ground-truth-based Question-Answer (QA) benchmark specifically designed to evaluate the spatial understanding and reasoning capabilities of VLMs in autonomous driving. Built upon the NuScenes dataset, the benchmark is constructed through an automated 3D scene graph generation pipeline and a QA generation pipeline. The benchmark systematically evaluates VLMs' performance in both spatial understanding and reasoning across multiple dimensions. Using this benchmark, we conduct extensive experiments on diverse VLMs, including both general and spatial-enhanced models, providing the first comprehensive evaluation of their spatial capabilities in autonomous driving. Surprisingly, the experimental results show that the spatial-enhanced VLM outperforms in qualitative QA but does not demonstrate competitiveness in quantitative QA. In general, VLMs still face considerable challenges in spatial understanding and reasoning.

Zihao Li, Xinyuan Cao, Xiangbo Gao et al.

Traffic safety science has long been hindered by a fundamental data paradox: the crashes we most wish to prevent are precisely those events we rarely observe. Existing crash-frequency models and surrogate safety metrics rely heavily on sparse, noisy, and under-reported records, while even sophisticated, high-fidelity simulations undersample the long-tailed situations that trigger catastrophic outcomes such as fatalities. We argue that the path to achieving Vision Zero, i.e., the complete elimination of traffic fatalities and severe injuries, requires a paradigm shift from traditional crash-only learning to a new form of counterfactual safety learning: reasoning not only about what happened, but also about the vast set of plausible yet perilous scenarios that could have happened under slightly different circumstances. To operationalize this shift, our proposed agenda bridges macro to micro. Guided by crash-rate priors, generative scene engines, diverse driver models, and causal learning, near-miss events are synthesized and explained. A crash-focused digital twin testbed links micro scenes to macro patterns, while a multi-objective validator ensures that simulations maintain statistical realism. This pipeline transforms sparse crash data into rich signals for crash prediction, enabling the stress-testing of vehicles, roads, and policies before deployment. By learning from crashes that almost happened, we can shift traffic safety from reactive forensics to proactive prevention, advancing Vision Zero.

Chenchen Kuai, Jiwan Jiang, Zihao Zhu et al.

The rapid growth of the large language model (LLM) ecosystem raises a critical question: are seemingly diverse models truly independent? Shared pretraining data, distillation, and alignment pipelines can induce hidden behavioral dependencies, latent entanglement, that undermine multi-model systems such as LLM-as-a-judge pipelines and ensemble verification, which implicitly assume independent signals. In practice, this manifests as correlated reasoning patterns and synchronized failures, where apparent agreement reflects shared error modes rather than independent validation. To address this, we develop a statistical framework for auditing behavioral entanglement among black-box LLMs. Our approach introduces a multi-resolution hierarchy that characterizes the joint failure manifold through two information-theoretic metrics: (i) a Difficulty-Weighted Behavioral Entanglement Index, which amplifies synchronized failures on easy tasks, and (ii) a Cumulative Information Gain (CIG) metric, which captures directional alignment in erroneous responses. Through extensive experiments on 18 LLMs from six model families, we identify widespread behavioral entanglement and analyze its impact on LLM-as-a-judge evaluation. We find that CIG exhibits a statistically significant association with degradation in judge precision, with Spearman coefficient of 0.64 (p < 0.001) for GPT-4o-mini and 0.71 (p < 0.01) for Llama3-based judges, indicating that stronger dependency corresponds to increased over-endorsement bias. Finally, we demonstrate a practical use case of entanglement through de-entangled verifier ensemble reweighting. By adjusting model contributions based on inferred independence, the proposed method mitigates correlated bias and improves verification performance, achieving up to a 4.5% accuracy gain over majority voting.

Chenchen Kuai, Zihao Li, Braden Rosen et al.

Post-disaster reconnaissance reports contain critical evidence for understanding multi-hazard interactions, yet their unstructured narratives make systematic knowledge transfer difficult. Large language models (LLMs) offer new potential for analyzing these reports, but often generate unreliable or hallucinated outputs when domain grounding is absent. This study introduces the Mixture-of-Retrieval Agentic RAG (MoRA-RAG), a knowledge-grounded LLM framework that transforms reconnaissance reports into a structured foundation for multi-hazard reasoning. The framework integrates a Mixture-of-Retrieval mechanism that dynamically routes queries across hazard-specific databases while using agentic chunking to preserve contextual coherence during retrieval. It also includes a verification loop that assesses evidence sufficiency, refines queries, and initiates targeted searches when information remains incomplete. We construct HazardRecQA by deriving question-answer pairs from GEER reconnaissance reports, which document 90 global events across seven major hazard types. MoRA-RAG achieves up to 94.5 percent accuracy, outperforming zero-shot LLMs by 30 percent and state-of-the-art RAG systems by 10 percent, while reducing hallucinations across diverse LLM architectures. MoRA-RAG also enables open-weight LLMs to achieve performance comparable to proprietary models. It establishes a new paradigm for transforming post-disaster documentation into actionable, trustworthy intelligence for hazard resilience.

Honglin Li, Zhongyi Shui, Yunlong Zhang et al.

Computational pathology and whole-slide image (WSI) analysis are pivotal in cancer diagnosis and prognosis. However, the ultra-high resolution of WSIs presents significant modeling challenges. Recent advancements in pathology foundation models have improved performance, yet most approaches rely on [CLS] token representation of tile ViT as slide-level inputs (16x16 pixels is refereed as patch and 224x224 pixels as tile). This discards critical spatial details from patch tokens, limiting downstream WSI analysis tasks. We find that leveraging all spatial patch tokens benefits WSI analysis but incurs nearly 200x higher storage and training costs (e.g., 196 tokens in ViT$_{224}$). To address this, we introduce vector quantized (VQ) distillation on patch feature, which efficiently compresses spatial patch tokens using discrete indices and a decoder. Our method reduces token dimensionality from 1024 to 16, achieving a 64x compression rate while preserving reconstruction fidelity. Furthermore, we employ a multi-scale VQ (MSVQ) strategy, which not only enhances VQ reconstruction performance but also serves as a Self-supervised Learning (SSL) supervision for a seamless slide-level pretraining objective. Built upon the quantized patch features and supervision targets of tile via MSVQ, we develop a progressive convolutional module and slide-level SSL to extract representations with rich spatial-information for downstream WSI tasks. Extensive evaluations on multiple datasets demonstrate the effectiveness of our approach, achieving state-of-the-art performance in WSI analysis. Code will be available soon.

Yuxuan Sun, Yunlong Zhang, Yixuan Si et al.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

Yuxuan Sun, Chenglu Zhu, Sunyi Zheng et al.

As advances in large language models (LLMs) and multimodal techniques continue to mature, the development of general-purpose multimodal large language models (MLLMs) has surged, offering significant applications in interpreting natural images. However, the field of pathology has largely remained untapped, particularly in gathering high-quality data and designing comprehensive model frameworks. To bridge the gap in pathology MLLMs, we present PathAsst, a multimodal generative foundation AI assistant to revolutionize diagnostic and predictive analytics in pathology. The development of PathAsst involves three pivotal steps: data acquisition, CLIP model adaptation, and the training of PathAsst's multimodal generative capabilities. Firstly, we collect over 207K high-quality pathology image-text pairs from authoritative sources. Leveraging the advanced power of ChatGPT, we generate over 180K instruction-following samples. Furthermore, we devise additional instruction-following data specifically tailored for invoking eight pathology-specific sub-models we prepared, allowing the PathAsst to effectively collaborate with these models, enhancing its diagnostic ability. Secondly, by leveraging the collected data, we construct PathCLIP, a pathology-dedicated CLIP, to enhance PathAsst's capabilities in interpreting pathology images. Finally, we integrate PathCLIP with the Vicuna-13b and utilize pathology-specific instruction-tuning data to enhance the multimodal generation capacity of PathAsst and bolster its synergistic interactions with sub-models. The experimental results of PathAsst show the potential of harnessing AI-powered generative foundation model to improve pathology diagnosis and treatment processes.

Xiaoqiang Kong, Subasish Das, Hongmin Zhou et al.

This study aims to explore the associations between near-crash events and road geometry and trip features by investigating a naturalistic driving dataset and a corresponding roadway inventory dataset using an association rule mining method.

Chenxin Li, Yunlong Zhang, Zhehan Liang et al.

Retinal artery/vein (A/V) classification is a critical technique for diagnosing diabetes and cardiovascular diseases. Although deep learning based methods achieve impressive results in A/V classification, their performances usually degrade severely when being directly applied to another database, due to the domain shift, e.g., caused by the variations in imaging protocols. In this paper, we propose a novel vessel-mixing based consistency regularization framework, for cross-domain learning in retinal A/V classification. Specially, to alleviate the severe bias to source domain, based on the label smooth prior, the model is regularized to give consistent predictions for unlabeled target-domain inputs that are under perturbation. This consistency regularization implicitly introduces a mechanism where the model and the perturbation is opponent to each other, where the model is pushed to be robust enough to cope with the perturbation. Thus, we investigate a more difficult opponent to further inspire the robustness of model, in the scenario of retinal A/V, called vessel-mixing perturbation. Specially, it effectively disturbs the fundus images especially the vessel structures by mixing two images regionally. We conduct extensive experiments on cross-domain A/V classification using four public datasets, which are collected by diverse institutions and imaging devices. The results demonstrate that our method achieves the state-of-the-art cross-domain performance, which is also close to the upper bound obtained by fully supervised learning on target domain.

Chenxin Li, Yunlong Zhang, Jiongcheng Li et al.

The goal of unsupervised anomaly segmentation (UAS) is to detect the pixel-level anomalies unseen during training. It is a promising field in the medical imaging community, e.g, we can use the model trained with only healthy data to segment the lesions of rare diseases. Existing methods are mainly based on Information Bottleneck, whose underlying principle is modeling the distribution of normal anatomy via learning to compress and recover the healthy data with a low-dimensional manifold, and then detecting lesions as the outlier from this learned distribution. However, this dimensionality reduction inevitably damages the localization information, which is especially essential for pixel-level anomaly detection. In this paper, to alleviate this issue, we introduce the semantic space of healthy anatomy in the process of modeling healthy-data distribution. More precisely, we view the couple of segmentation and synthesis as a special Autoencoder, and propose a novel cycle translation framework with a journey of 'image->semantic->image'. Experimental results on the BraTS and ISLES databases show that the proposed approach achieves significantly superior performance compared to several prior methods and segments the anomalies more accurately.

Yunlong Zhang, Changxing Jing, Huangxing Lin et al.

Domain adaptation (DA) aims to transfer knowledge from a label-rich and related domain (source domain) to a label-scare domain (target domain). Pseudo-labeling has recently been widely explored and used in DA. However, this line of research is still confined to the inaccuracy of pseudo-labels. In this paper, we reveal an interesting observation that the target samples belonging to the classes with larger domain shift are easier to be misclassified compared with the other classes. These classes are called hard class, which deteriorates the performance of DA and restricts the applications of DA. We propose a novel framework, called Hard Class Rectification Pseudo-labeling (HCRPL), to alleviate the hard class problem from two aspects. First, as is difficult to identify the target samples as hard class, we propose a simple yet effective scheme, named Adaptive Prediction Calibration (APC), to calibrate the predictions of the target samples according to the difficulty degree for each class. Second, we further consider that the predictions of target samples belonging to the hard class are vulnerable to perturbations. To prevent these samples to be misclassified easily, we introduce Temporal-Ensembling (TE) and Self-Ensembling (SE) to obtain consistent predictions. The proposed method is evaluated in both unsupervised domain adaptation (UDA) and semi-supervised domain adaptation (SSDA). The experimental results on several real-world cross-domain benchmarks, including ImageCLEF, Office-31 and Office-Home, substantiates the superiority of the proposed method.

Chi Wang, Dong Liu, Yifeng Wei et al.

A software system has been developed for the DArk Matter Particle Explorer (DAMPE) mission, a satellite-based experiment. The DAMPE software is mainly written in C++ and steered using Python script. This article presents an overview of the DAMPE offline software, including the major architecture design and specific implementation for simulation, calibration and reconstruction. The whole system has been successfully applied to DAMPE data analysis, based on which some results from simulation and beam test experiments are obtained and presented.