Jiawen Li

Minghao Xu, Yuanfan Guo, Xuanyu Zhu et al.

Learning self-supervised image representations has been broadly studied to boost various visual understanding tasks. Existing methods typically learn a single level of image semantics like pairwise semantic similarity or image clustering patterns. However, these methods can hardly capture multiple levels of semantic information that naturally exists in an image dataset, e.g., the semantic hierarchy of "Persian cat to cat to mammal" encoded in an image database for species. It is thus unknown whether an arbitrary image self-supervised learning (SSL) approach can benefit from learning such hierarchical semantics. To answer this question, we propose a general framework for Hierarchical Image Representation Learning (HIRL). This framework aims to learn multiple semantic representations for each image, and these representations are structured to encode image semantics from fine-grained to coarse-grained. Based on a probabilistic factorization, HIRL learns the most fine-grained semantics by an off-the-shelf image SSL approach and learns multiple coarse-grained semantics by a novel semantic path discrimination scheme. We adopt six representative image SSL methods as baselines and study how they perform under HIRL. By rigorous fair comparison, performance gain is observed on all the six methods for diverse downstream tasks, which, for the first time, verifies the general effectiveness of learning hierarchical image semantics. All source code and model weights are available at https://github.com/hirl-team/HIRL

Jiawen Li, Yunqian Huang, Sheng Song et al.

The objective of this study is to develop a deep-learning based detection and diagnosis technique for carotid atherosclerosis using a portable freehand 3D ultrasound (US) imaging system. A total of 127 3D carotid artery scans were acquired using a portable 3D US system which consisted of a handheld US scanner and an electromagnetic tracking system. A U-Net segmentation network was firstly applied to extract the carotid artery on 2D transverse frame, then a novel 3D reconstruction algorithm using fast dot projection (FDP) method with position regularization was proposed to reconstruct the carotid artery volume. Furthermore, a convolutional neural network was used to classify healthy and diseased cases qualitatively. 3D volume analysis methods including longitudinal image acquisition and stenosis grade measurement were developed to obtain the clinical metrics quantitatively. The proposed system achieved sensitivity of 0.714, specificity of 0.851 and accuracy of 0.803 respectively for diagnosis of carotid atherosclerosis. The automatically measured stenosis grade illustrated good correlation (r=0.762) with the experienced expert measurement. The developed technique based on 3D US imaging can be applied to the automatic diagnosis of carotid atherosclerosis. The proposed deep-learning based technique was specially designed for a portable 3D freehand US system, which can provide more convenient carotid atherosclerosis examination and decrease the dependence on clinician's experience.

Jiawen Li, Yuxuan Chen, Hongbo Chu et al.

Histopathological whole slide images (WSIs) classification has become a foundation task in medical microscopic imaging processing. Prevailing approaches involve learning WSIs as instance-bag representations, emphasizing significant instances but struggling to capture the interactions between instances. Additionally, conventional graph representation methods utilize explicit spatial positions to construct topological structures but restrict the flexible interaction capabilities between instances at arbitrary locations, particularly when spatially distant. In response, we propose a novel dynamic graph representation algorithm that conceptualizes WSIs as a form of the knowledge graph structure. Specifically, we dynamically construct neighbors and directed edge embeddings based on the head and tail relationships between instances. Then, we devise a knowledge-aware attention mechanism that can update the head node features by learning the joint attention score of each neighbor and edge. Finally, we obtain a graph-level embedding through the global pooling process of the updated head, serving as an implicit representation for the WSI classification. Our end-to-end graph representation learning approach has outperformed the state-of-the-art WSI analysis methods on three TCGA benchmark datasets and in-house test sets. Our code is available at https://github.com/WonderLandxD/WiKG.

Yuan Zhang, Fei Xiao, Tao Huang et al.

Large vision-language models (LVLMs) have recently achieved rapid progress, exhibiting great perception and reasoning abilities concerning visual information. However, when faced with prompts in different sizes of solution spaces, LVLMs fail to always give consistent answers regarding the same knowledge point. This inconsistency of answers between different solution spaces is prevalent in LVLMs and erodes trust. To this end, we provide a multi-modal benchmark ConBench, to intuitively analyze how LVLMs perform when the solution space of a prompt revolves around a knowledge point. Based on the ConBench tool, we are the first to reveal the tapestry and get the following findings: (1) In the discriminate realm, the larger the solution space of the prompt, the lower the accuracy of the answers. (2) Establish the relationship between the discriminative and generative realms: the accuracy of the discriminative question type exhibits a strong positive correlation with its Consistency with the caption. (3) Compared to open-source models, closed-source models exhibit a pronounced bias advantage in terms of Consistency. Eventually, we ameliorate the consistency of LVLMs by trigger-based diagnostic refinement, indirectly improving the performance of their caption. We hope this paper will accelerate the research community in better evaluating their models and encourage future advancements in the consistency domain. The project is available at https://github.com/foundation-multimodal-models/ConBench.

Haoji Zhang, Xin Gu, Jiawen Li et al.

The video reasoning ability of multimodal large language models (MLLMs) is crucial for downstream tasks like video question answering and temporal grounding. While recent approaches have explored text-based chain-of-thought (CoT) reasoning for MLLMs, these methods often suffer from limited cross-modal interaction and increased hallucination, especially with longer videos or reasoning chains. To address these challenges, we propose Video Intelligence via Tool-Augmented Learning (VITAL), a novel end-to-end agentic video reasoning framework. With a visual toolbox, the model can densely sample new video frames on demand and generate multimodal CoT for precise long video reasoning. We observe that temporal grounding and question answering are mutually beneficial for video understanding tasks. Therefore, we construct two high-quality multi-task video reasoning datasets MTVR-CoT-72k for supervised fine-tuning and MTVR-RL-110k for reinforcement learning. Moreover, we propose a Difficulty-aware Group Relative Policy Optimization algorithm (DGRPO) to mitigate difficulty imbalance in multi-task reinforcement learning. Extensive experiments on 11 challenging video understanding benchmarks demonstrate the advanced reasoning ability of VITAL, outperforming existing methods in video question answering and temporal grounding tasks, especially in long video scenarios. Code is available at https://zhang9302002.github.io/thinkingwithvideos-page/.

Qiehe Sun, Jiawen Li, Jin Xu et al.

Due to its superior efficiency in utilizing annotations and addressing gigapixel-sized images, multiple instance learning (MIL) has shown great promise as a framework for whole slide image (WSI) classification in digital pathology diagnosis. However, existing methods tend to focus on advanced aggregators with different structures, often overlooking the intrinsic features of H\&E pathological slides. To address this limitation, we introduced two pathological priors: nuclear heterogeneity of diseased cells and spatial correlation of pathological tiles. Leveraging the former, we proposed a data augmentation method that utilizes stain separation during extractor training via a contrastive learning strategy to obtain instance-level representations. We then described the spatial relationships between the tiles using an adjacency matrix. By integrating these two views, we designed a multi-instance framework for analyzing H\&E-stained tissue images based on pathological inductive bias, encompassing feature extraction, filtering, and aggregation. Extensive experiments on the Camelyon16 breast dataset and TCGA-NSCLC Lung dataset demonstrate that our proposed framework can effectively handle tasks related to cancer detection and differentiation of subtypes, outperforming state-of-the-art medical image classification methods based on MIL. The code will be released later.

Hongbo Chu, Qiehe Sun, Jiawen Li et al.

Histopathological whole slide image (WSI) analysis with deep learning has become a research focus in computational pathology. The current paradigm is mainly based on multiple instance learning (MIL), in which approaches with Transformer as the backbone are well discussed. These methods convert WSI tasks into sequence tasks by representing patches as tokens in the WSI sequence. However, the feature complexity brought by high heterogeneity and the ultra-long sequences brought by gigapixel size makes Transformer-based MIL suffer from the challenges of high memory consumption, slow inference speed, and lack of performance. To this end, we propose a retentive MIL method called RetMIL, which processes WSI sequences through hierarchical feature propagation structure. At the local level, the WSI sequence is divided into multiple subsequences. Tokens of each subsequence are updated through a parallel linear retention mechanism and aggregated utilizing an attention layer. At the global level, subsequences are fused into a global sequence, then updated through a serial retention mechanism, and finally the slide-level representation is obtained through a global attention pooling. We conduct experiments on two public CAMELYON and BRACS datasets and an public-internal LUNG dataset, confirming that RetMIL not only achieves state-of-the-art performance but also significantly reduces computational overhead. Our code will be accessed shortly.

Ying Xiao, Shimiao Tang, Xitong Ling et al.

Liver cancer, especially hepatocellular carcinoma (HCC), imposes a substantial global disease burden. Accurate diagnosis and prognostic assessment directly influence treatment selection and patient survival, and pathological examination remains the gold standard for liver cancer diagnosis. Identifying diverse tissue components and pathological subtypes on histopathology slides is crucial for estimating postoperative recurrence risk and overall prognosis. However, most publicly available resources are still provided at the whole-slide image (WSI) level, and well-annotated datasets for fine-grained tissue component identification in liver cancer are scarce, which hinders reproducible model development and the deployment of quantitative analysis tools. To address this gap, we release HepatoBench, a patch-level image database for liver cancer with annotations for seven key tissue categories. Based on HepatoBench, we train and open-source a deep learning classification model as a tissue recognition tool. Furthermore, we train a WSI-level tumor/non-tumor segmentation model to automatically localize lesion regions across entire slides. By integrating the patch-level tissue classifier with the WSI-level segmentation model, we build HepatoQuant, an end-to-end, disease-specific regional quantification tool for liver cancer, enabling a unified workflow from WSIs to tissue composition parsing and quantitative statistics. We also open-source HepatoBench, the benchmarking protocol, and supporting tools, providing a solid foundation for automated regional quantification and fair method comparison in liver cancer pathology.

Lequan Lin, Dai Shi, Andi Han et al.

Supervised learning relies on high-quality labeled data, but obtaining such data through human annotation is both expensive and time-consuming. Recent work explores using large language models (LLMs) for annotation, but LLM-generated labels still fall short of human-level quality. To address this problem, we propose the Annotation with Critical Thinking (ACT) data pipeline, where LLMs serve not only as annotators but also as judges to critically identify potential errors. Human effort is then directed towards reviewing only the most "suspicious" cases, significantly improving the human annotation efficiency. Our major contributions are as follows: (1) ACT is applicable to a wide range of domains, including natural language processing (NLP), computer vision (CV), and multimodal understanding, by leveraging multimodal-LLMs (MLLMs). (2) Through empirical studies, we derive 7 insights on how to enhance annotation quality while efficiently reducing the human cost, and then translate these findings into user-friendly guidelines. (3) We theoretically analyze how to modify the loss function so that models trained on ACT data achieve similar performance to those trained on fully human-annotated data. Our experiments show that the performance gap can be reduced to less than 2% on most benchmark datasets while saving up to 90% of human costs.

Xitong Ling, Yuanyuan Lei, Jiawen Li et al.

Advances in optical microscopy scanning have significantly contributed to computational pathology (CPath) by converting traditional histopathological slides into whole slide images (WSIs). This development enables comprehensive digital reviews by pathologists and accelerates AI-driven diagnostic support for WSI analysis. Recent advances in foundational pathology models have increased the need for benchmarking tasks. The Camelyon series is one of the most widely used open-source datasets in computational pathology. However, the quality, accessibility, and clinical relevance of the labels have not been comprehensively evaluated. In this study, we reprocessed 1,399 WSIs and labels from the Camelyon-16 and Camelyon-17 datasets, removing low-quality slides, correcting erroneous labels, and providing expert pixel annotations for tumor regions in the previously unreleased test set. Based on the sizes of re-annotated tumor regions, we upgraded the binary cancer screening task to a four-class task: negative, micro-metastasis, macro-metastasis, and Isolated Tumor Cells (ITC). We reevaluated pre-trained pathology feature extractors and multiple instance learning (MIL) methods using the cleaned dataset, providing a benchmark that advances AI development in histopathology.

Jiawen Li, Jiali Hu, Xitong Ling et al.

Foundation models trained with self-supervised learning (SSL) on large-scale histological images have significantly accelerated the development of computational pathology. These models can serve as backbones for region-of-interest (ROI) image analysis or patch-level feature extractors in whole-slide images (WSIs) based on multiple instance learning (MIL). Existing pathology foundation models (PFMs) are typically pre-trained on Hematoxylin-Eosin (H\&E) stained pathology images. However, images such as immunohistochemistry (IHC) and special stains are also frequently used in clinical practice. PFMs pre-trained mainly on H\&E-stained images may be limited in clinical applications involving these non-H\&E images. To address this issue, we propose StainNet, a collection of self-supervised foundation models specifically trained for IHC and special stains in pathology images based on the vision transformer (ViT) architecture. StainNet contains a ViT-Small and a ViT-Base model, both of which are trained using a self-distillation SSL approach on over 1.4 million patch images extracted from 20,231 publicly available IHC and special staining WSIs in the HISTAI database. To evaluate StainNet models, we conduct experiments on three in-house slide-level IHC classification tasks, three in-house ROI-level special stain and two public ROI-level IHC classification tasks to demonstrate their strong ability. We also perform ablation studies such as few-ratio learning and retrieval evaluations, and compare StainNet models with recent larger PFMs to further highlight their strengths. The StainNet model weights are available at https://github.com/WonderLandxD/StainNet.

Minxi Ouyang, Lianghui Zhu, Yaqing Bao et al.

Multimodal large models have shown great potential in automating pathology image analysis. However, current multimodal models for gastrointestinal pathology are constrained by both data quality and reasoning transparency: pervasive noise and incomplete annotations in public datasets predispose vision language models to factual hallucinations when generating diagnostic text, while the absence of explicit intermediate reasoning chains renders the outputs difficult to audit and thus less trustworthy in clinical practice. To address these issues, we construct a large scale gastrointestinal pathology dataset containing both microscopic descriptions and diagnostic conclusions, and propose a prompt argumentation strategy that incorporates lesion classification and anatomical site information. This design guides the model to better capture image specific features and maintain semantic consistency in generation. Furthermore, we employ a post training pipeline that combines supervised fine tuning with Group Relative Policy Optimization (GRPO) to improve reasoning quality and output structure. Experimental results on real world pathology report generation tasks demonstrate that our approach significantly outperforms state of the art open source and proprietary baselines in terms of generation quality, structural completeness, and clinical relevance. Our solution outperforms state of the art models with 18.7% higher clinical relevance, 32.4% improved structural completeness, and 41.2% fewer diagnostic errors, demonstrating superior accuracy and clinical utility compared to existing solutions.

Qilai Zhang, Jiawen Li, Peiran Liao et al.

The two primary types of Hematoxylin and Eosin (H&E) slides in histopathology are Formalin-Fixed Paraffin-Embedded (FFPE) and Fresh Frozen (FF). FFPE slides offer high quality histopathological images but require a labor-intensive acquisition process. In contrast, FF slides can be prepared quickly, but the image quality is relatively poor. Our task is to translate FF images into FFPE style, thereby improving the image quality for diagnostic purposes. In this paper, we propose Diffusion-FFPE, a method for FF-to-FFPE histopathological image translation using a pre-trained diffusion model. Specifically, we utilize a one-step diffusion model as the generator, which we fine-tune using LoRA adapters within an adversarial learning framework. To enable the model to effectively capture both global structural patterns and local details, we introduce a multi-scale feature fusion module that leverages two VAE encoders to extract features at different image resolutions, performing feature fusion before inputting them into the UNet. Additionally, a pre-trained vision-language model for histopathology serves as the backbone for the discriminator, enhancing model performance. Our FF-to-FFPE translation experiments on the TCGA-NSCLC dataset demonstrate that the proposed approach outperforms existing methods. The code and models are released at https://github.com/QilaiZhang/Diffusion-FFPE.

Yuanfan Guo, Minghao Xu, Jiawen Li et al.

Hierarchical semantic structures naturally exist in an image dataset, in which several semantically relevant image clusters can be further integrated into a larger cluster with coarser-grained semantics. Capturing such structures with image representations can greatly benefit the semantic understanding on various downstream tasks. Existing contrastive representation learning methods lack such an important model capability. In addition, the negative pairs used in these methods are not guaranteed to be semantically distinct, which could further hamper the structural correctness of learned image representations. To tackle these limitations, we propose a novel contrastive learning framework called Hierarchical Contrastive Selective Coding (HCSC). In this framework, a set of hierarchical prototypes are constructed and also dynamically updated to represent the hierarchical semantic structures underlying the data in the latent space. To make image representations better fit such semantic structures, we employ and further improve conventional instance-wise and prototypical contrastive learning via an elaborate pair selection scheme. This scheme seeks to select more diverse positive pairs with similar semantics and more precise negative pairs with truly distinct semantics. On extensive downstream tasks, we verify the superior performance of HCSC over state-of-the-art contrastive methods, and the effectiveness of major model components is proved by plentiful analytical studies. We build a comprehensive model zoo in Sec. D. Our source code and model weights are available at https://github.com/gyfastas/HCSC

Shiwen Ni, Jiawen Li, Hung-Yu Kao

Adversarial training has been proven to be a powerful regularization method to improve the generalization of models. However, current adversarial training methods only attack the original input sample or the embedding vectors, and their attacks lack coverage and diversity. To further enhance the breadth and depth of attack, we propose a novel masked weight adversarial training method called DropAttack, which enhances generalization of model by adding intentionally worst-case adversarial perturbations to both the input and hidden layers in different dimensions and minimize the adversarial risks generated by each layer. DropAttack is a general technique and can be adopt to a wide variety of neural networks with different architectures. To validate the effectiveness of the proposed method, we used five public datasets in the fields of natural language processing (NLP) and computer vision (CV) for experimental evaluating. We compare the proposed method with other adversarial training methods and regularization methods, and our method achieves state-of-the-art on all datasets. In addition, Dropattack can achieve the same performance when it use only a half training data compared to other standard training method. Theoretical analysis reveals that DropAttack can perform gradient regularization at random on some of the input and wight parameters of the model. Further visualization experiments show that DropAttack can push the minimum risk of the model to a lower and flatter loss landscapes. Our source code is publicly available on https://github.com/nishiwen1214/DropAttack.

Shiwen Ni, Jiawen Li, Hung-Yu Kao

Fake news on social media is a widespread and serious problem in today's society. Existing fake news detection methods focus on finding clues from Long text content, such as original news articles and user comments. This paper solves the problem of fake news detection in more realistic scenarios. Only source shot-text tweet and its retweet users are provided without user comments. We develop a novel neural network based model, \textbf{M}ulti-\textbf{V}iew \textbf{A}ttention \textbf{N}etworks (MVAN) to detect fake news and provide explanations on social media. The MVAN model includes text semantic attention and propagation structure attention, which ensures that our model can capture information and clues both of source tweet content and propagation structure. In addition, the two attention mechanisms in the model can find key clue words in fake news texts and suspicious users in the propagation structure. We conduct experiments on two real-world datasets, and the results demonstrate that MVAN can significantly outperform state-of-the-art methods by 2.5\% in accuracy on average, and produce a reasonable explanation.

Xinyi Guo, Mingyi He, Haobin Ding et al.

Implicit neural representations (INRs) encode images as neural-network weights, making image classification a problem of weight-space classifiability. A natural geometric hypothesis is that classifier feedback should make image-specific weights cluster by class in the shared-anchor coordinate. We test this hypothesis in the SIREN-based Meta Weight Transformer (MWT) regime, where end-to-end training meta-learns a shared initialization and inner-loop update schedule for fitting image-specific SIRENs. We find that this prediction fails. Exposed weight-space geometry and supervised clustering pressure do not reliably track trained-reader accuracy; clustering can even make local neighborhoods more class-consistent while making the trained reader worse. Crucially, the reader constructs rather than inherits class-aligned geometry: token-flow diagnostics show that class-aligned neighborhoods become strongly predictive of trained-reader accuracy only after late reader interactions, not in the input coordinate. We further identify the native SIREN bias column in the augmented weight token as a low-dimensional, sample-dependent causal readout route for the trained reader; targeted controls rule out generic scalar-column and marginal-distribution artifacts. The diagnosis motivates interventions that strengthen reader routing, add an explicit bias route, or use denser inner-loop fitting; under the lane-specific training conventions used here, route-directed variants often outperform the shared-anchor baseline but interact non-additively. Task-induced INR weights are classifiable not because they form raw geometric clusters, but because their class signal is routed through the reader.

Weiming Chen, Xitong Ling, Zhenyang Cai et al.

Cell-level dense prediction is central to computational pathology, but remains challenging due to fine-grained histological structures, strong domain shifts, and costly dense annotations. Existing ViT-based pathology foundation models rely on patch tokenization, which can disrupt spatial continuity and weaken local morphological details needed for cell-level prediction. To address this, we propose Masked-Diffusion Convolutional Foundation Models, termed ConvNeXt Masked-Diffusion (CMD), a self-supervised convolutional generative pretraining framework for dense pathology representation learning. CMD uses a fully convolutional ConvNeXt-UNet backbone, performs masked-diffusion pretraining in pixel space, and incorporates frozen pathology foundation model features through adaptive normalization. Experimental results demonstrate that CMD consistently outperforms existing ViT-based pathology foundation models and even surpasses state-of-the-art end-to-end segmentation methods while fine-tuning only a small number of task-specific parameters across multiple pathology dense prediction tasks. The advantage is particularly pronounced under limited annotation settings, where CMD exhibits stronger robustness and generalization ability. Our findings suggest that purely convolutional architectures can also serve as competitive pathology foundation models for cell-level dense prediction, achieving leading performance within the current ViT-dominated paradigm and providing a scalable, high-performance solution that better preserves histological structural priors for fine-grained pathology understanding.

Jiacong Wang, Zijian Kang, Haochen Wang et al.

In the field of multimodal chain-of-thought (CoT) reasoning, existing approaches predominantly rely on reasoning on pure language space, which inherently suffers from language bias and is largely confined to math or science domains. This narrow focus limits their ability to handle complex visual reasoning tasks that demand comprehensive understanding of image details. To address these limitations, this paper introduces VGR, a novel reasoning multimodal large language model (MLLM) with enhanced fine-grained visual perception capabilities. Unlike traditional MLLMs that answer the question or reasoning solely on the language space, our VGR first detects relevant regions that may help to solve problems, and then provides precise answers based on replayed image regions. To achieve this, we conduct a large-scale SFT dataset called VGR -SFT that contains reasoning data with mixed vision grounding and language deduction. The inference pipeline of VGR allows the model to choose bounding boxes for visual reference and a replay stage is introduced to integrates the corresponding regions into the reasoning process, enhancing multimodel comprehension. Experiments on the LLaVA-NeXT-7B baseline show that VGR achieves superior performance on multi-modal benchmarks requiring comprehensive image detail understanding. Compared to the baseline, VGR uses only 30\% of the image token count while delivering scores of +4.1 on MMStar, +7.1 on AI2D, and a +12.9 improvement on ChartQA.

Jiawen Li

While the Implicit Bias(or Implicit Regularization) of standard loss functions has been studied, the optimization geometry induced by discriminative metric-learning objectives remains largely unexplored.To the best of our knowledge, this paper presents an initial theoretical analysis of the implicit regularization induced by the Deep LDA,a scale invariant objective designed to minimize intraclass variance and maximize interclass distance. By analyzing the gradient flow of the loss on a L-layer diagonal linear network, we prove that under balanced initialization, the network architecture transforms standard additive gradient updates into multiplicative weight updates, which demonstrates an automatic conservation of the (2/L) quasi-norm.

Jingyu Tang, Chaoran Chen, Jiawen Li et al.

The dark patterns, deceptive interface designs manipulating user behaviors, have been extensively studied for their effects on human decision-making and autonomy. Yet, with the rising prominence of LLM-powered GUI agents that automate tasks from high-level intents, understanding how dark patterns affect agents is increasingly important. We present a two-phase empirical study examining how agents, human participants, and human-AI teams respond to 16 types of dark patterns across diverse scenarios. Phase 1 highlights that agents often fail to recognize dark patterns, and even when aware, prioritize task completion over protective action. Phase 2 revealed divergent failure modes: humans succumb due to cognitive shortcuts and habitual compliance, while agents falter from procedural blind spots. Human oversight improved avoidance but introduced costs such as attentional tunneling and cognitive load. Our findings show neither humans nor agents are uniformly resilient, and collaboration introduces new vulnerabilities, suggesting design needs for transparency, adjustable autonomy, and oversight.

Fang Yan, Jianfeng Wu, Jiawen Li et al.

The complexity and variability inherent in high-resolution pathological images present significant challenges in computational pathology. While pathology foundation models leveraging AI have catalyzed transformative advancements, their development demands large-scale datasets, considerable storage capacity, and substantial computational resources. Furthermore, ensuring their clinical applicability and generalizability requires rigorous validation across a broad spectrum of clinical tasks. Here, we present PathOrchestra, a versatile pathology foundation model trained via self-supervised learning on a dataset comprising 300K pathological slides from 20 tissue and organ types across multiple centers. The model was rigorously evaluated on 112 clinical tasks using a combination of 61 private and 51 public datasets. These tasks encompass digital slide preprocessing, pan-cancer classification, lesion identification, multi-cancer subtype classification, biomarker assessment, gene expression prediction, and the generation of structured reports. PathOrchestra demonstrated exceptional performance across 27,755 WSIs and 9,415,729 ROIs, achieving over 0.950 accuracy in 47 tasks, including pan-cancer classification across various organs, lymphoma subtype diagnosis, and bladder cancer screening. Notably, it is the first model to generate structured reports for high-incidence colorectal cancer and diagnostically complex lymphoma-areas that are infrequently addressed by foundational models but hold immense clinical potential. Overall, PathOrchestra exemplifies the feasibility and efficacy of a large-scale, self-supervised pathology foundation model, validated across a broad range of clinical-grade tasks. Its high accuracy and reduced reliance on extensive data annotation underline its potential for clinical integration, offering a pathway toward more efficient and high-quality medical services.

Jiawen Li, Qiehe Sun, Renao Yan et al. · tsinghua

With the development of digital imaging in medical microscopy, artificial intelligent-based analysis of pathological whole slide images (WSIs) provides a powerful tool for cancer diagnosis. Limited by the expensive cost of pixel-level annotation, current research primarily focuses on representation learning with slide-level labels, showing success in various downstream tasks. However, given the diversity of lesion types and the complex relationships between each other, these techniques still deserve further exploration in addressing advanced pathology tasks. To this end, we introduce the concept of hierarchical pathological image classification and propose a representation learning called PathTree. PathTree considers the multi-classification of diseases as a binary tree structure. Each category is represented as a professional pathological text description, which messages information with a tree-like encoder. The interactive text features are then used to guide the aggregation of hierarchical multiple representations. PathTree uses slide-text similarity to obtain probability scores and introduces two extra tree specific losses to further constrain the association between texts and slides. Through extensive experiments on three challenging hierarchical classification datasets: in-house cryosectioned lung tissue lesion identification, public prostate cancer grade assessment, and public breast cancer subtyping, our proposed PathTree is consistently competitive compared to the state-of-the-art methods and provides a new perspective on the deep learning-assisted solution for more complex WSI classification.

Marta Andronic, Jiawen Li, George A. Constantinides

Standard deep neural network inference involves the computation of interleaved linear maps and nonlinear activation functions. Prior work for ultra-low latency implementations has hardcoded these operations inside FPGA lookup tables (LUTs). However, FPGA LUTs can implement a much greater variety of functions. In this paper, we propose a novel approach to training DNNs for FPGA deployment using multivariate polynomials as the basic building block. Our method takes advantage of the flexibility offered by the soft logic, hiding the polynomial evaluation inside the LUTs with minimal overhead. By using polynomial building blocks, we achieve the same accuracy using considerably fewer layers of soft logic than by using linear functions, leading to significant latency and area improvements. LUT-based implementations also face a significant challenge: the LUT size grows exponentially with the number of inputs. Prior work relies on a priori fixed sparsity, with results heavily dependent on seed selection. To address this, we propose a structured pruning strategy using a bespoke hardware-aware group regularizer that encourages a particular sparsity pattern that leads to a small number of inputs per neuron. We demonstrate the effectiveness of PolyLUT on three tasks: network intrusion detection, jet identification at the CERN Large Hadron Collider, and MNIST.

Yuxuan Chen, Jiawen Li, Huijuan Shi et al.

Bone metastasis analysis is a significant challenge in pathology and plays a critical role in determining patient quality of life and treatment strategies. The microenvironment and specific tissue structures are essential for pathologists to predict the primary bone cancer origins and primary bone cancer subtyping. By digitizing bone tissue sections into whole slide images (WSIs) and leveraging deep learning to model slide embeddings, this analysis can be enhanced. However, tumor metastasis involves complex multivariate interactions with diverse bone tissue structures, which traditional WSI analysis methods such as multiple instance learning (MIL) fail to capture. Moreover, graph neural networks (GNNs), limited to modeling pairwise relationships, are hard to represent high-order biological associations. To address these challenges, we propose a dynamic hypergraph neural network (DyHG) that overcomes the edge construction limitations of traditional graph representations by connecting multiple nodes via hyperedges. A low-rank strategy is used to reduce the complexity of parameters in learning hypergraph structures, while a Gumbel-Softmax-based sampling strategy optimizes the patch distribution across hyperedges. An MIL aggregator is then used to derive a graph-level embedding for comprehensive WSI analysis. To evaluate the effectiveness of DyHG, we construct two large-scale datasets for primary bone cancer origins and subtyping classification based on real-world bone metastasis scenarios. Extensive experiments demonstrate that DyHG significantly outperforms state-of-the-art (SOTA) baselines, showcasing its ability to model complex biological interactions and improve the accuracy of bone metastasis analysis.

Jiawen Li, Anwar PP Abdul Majeed, Pascal Lefevre

This paper first proposes the Halfway Escape Optimization (HEO) algorithm, a quantum-inspired metaheuristic designed to address general optimization problems. The HEO mimics the effects between quantum such as tunneling, entanglement. After the introduction to the HEO mechansims, the study presents a comprehensive evaluation of HEO's performance against extensively-used optimization algorithms, including Particle Swarm Optimization (PSO), Genetic Algorithm (GA), Artificial Fish Swarm Algorithm (AFSA), Grey Wolf Optimizer (GWO), and Quantum behaved Particle Swarm Optimization (QPSO). The primary analysis encompasses 14 benchmark functions with dimension 30, demonstrating HEO's effectiveness and adaptability in navigating general optimization problems. The test of HEO in Pressure Vessel Design and Tubular Column Design also infers its feasibility and potential in real-time applications. Further validation of HEO in Osmancik-97 and Cammeo Rice Classification achieves a higher accuracy record.

Weiming Chen, Xitong Ling, Xidong Wang et al.

Pathology foundation models (PFMs) have rapidly advanced and are becoming a common backbone for downstream clinical tasks, offering strong transferability across tissues and institutions. However, for dense prediction (e.g., segmentation), practical deployment still lacks a clear, reproducible understanding of how different PFMs behave across datasets and how adaptation choices affect performance and stability. We present PFM-DenseBench, a large-scale benchmark for dense pathology prediction, evaluating 17 PFMs across 18 public segmentation datasets. Under a unified protocol, we systematically assess PFMs with multiple adaptation and fine-tuning strategies, and derive insightful, practice-oriented findings on when and why different PFMs and tuning choices succeed or fail across heterogeneous datasets. We release containers, configs, and dataset cards to enable reproducible evaluation and informed PFM selection for real-world dense pathology tasks. Project Website: https://m4a1tastegood.github.io/PFM-DenseBench

Rongjun Chen, Chengsi Yao, Jinchang Ren et al.

Text-image alignment constitutes a foundational challenge in multimedia content understanding, where effective modeling of cross-modal semantic correspondences critically enhances retrieval system performance through joint embedding space optimization. Given the inherent difference in information entropy between texts and images, conventional approaches often show an imbalance in the mutual retrieval of these two modalities. To address this particular challenge, we propose to use the open semantic knowledge of Large Language Model (LLM) to fill for the entropy gap and reproduce the alignment ability of humans in these tasks. Our entropy-enhancing alignment is achieved through a two-step process: 1) a new prompt template that does not rely on explicit knowledge in the task domain is designed to use LLM to enhance the polysemy description of the text modality. By analogy, the information entropy of the text modality relative to the visual modality is increased; 2) A hypergraph adapter is used to construct multilateral connections between the text and image modalities, which can correct the positive and negative matching errors for synonymous semantics in the same fixed embedding space, whilst reducing the noise caused by open semantic entropy by mapping the reduced dimensions back to the original dimensions. Comprehensive evaluations on the Flickr30K and MS-COCO benchmarks validate the superiority of our Open Semantic Hypergraph Adapter (OS-HGAdapter), showcasing 16.8\% (text-to-image) and 40.1\% (image-to-text) cross-modal retrieval gains over existing methods while establishing new state-of-the-art performance in semantic alignment tasks.

Jiawen Li, Pascal Lefevre, Anwar Pp Abdul Majeed

Based on Stochastic Gradient Descent (SGD), the paper introduces two optimizers, named Interpolational Accelerating Gradient Descent (IAGD) as well as Noise-Regularized Stochastic Gradient Descent (NRSGD). IAGD leverages second-order Newton Interpolation to expedite the convergence process during training, assuming relevancy in gradients between iterations. To avoid over-fitting, NRSGD incorporates a noise regularization technique that introduces controlled noise to the gradients during the optimization process. Comparative experiments of this research are conducted on the CIFAR-10, and CIFAR-100 datasets, benchmarking different CNNs(Convolutional Neural Networks) with IAGD and NRSGD against classical optimizers in Keras Package. Results demonstrate the potential of those two viable improvement methods in SGD, implicating the effectiveness of the advancements.

Yizhi Wang, Li Chen, Qiang Huang et al.

Cervical cancer remains a major malignancy, necessitating extensive and complex histopathological assessments and comprehensive support tools. Although deep learning shows promise, these models still lack accuracy and generalizability. General foundation models offer a broader reach but remain limited in capturing subspecialty-specific features and task adaptability. We introduce the Cervical Subspecialty Pathology (CerS-Path) diagnostic system, developed through two synergistic pretraining stages: self-supervised learning on approximately 190 million tissue patches from 140,000 slides to build a cervical-specific feature extractor, and multimodal enhancement with 2.5 million image-text pairs, followed by integration with multiple downstream diagnostic functions. Supporting eight diagnostic functions, including rare cancer classification and multimodal Q&A, CerS-Path surpasses prior foundation models in scope and clinical applicability. Comprehensive evaluations demonstrate a significant advance in cervical pathology, with prospective testing on 3,173 cases across five centers maintaining 99.38% screening sensitivity and excellent generalizability, highlighting its potential for subspecialty diagnostic translation and cervical cancer screening.

Jiawen Li, Zheng Ning, Yuan Tian et al.

Large language models (LLMs) enable end-users to delegate complex tasks to autonomous agents through natural language. However, prompt-based interaction faces critical limitations: Users often struggle to specify procedural requirements for tasks, especially those that don't have a factually correct solution but instead rely on personal preferences, such as posting social media content or planning a trip. Additionally, a ''successful'' prompt for one task may not be reusable or generalizable across similar tasks. We present ALLOY, a system inspired by classical HCI theories on Programming by Demonstration (PBD), but extended to enhance adaptability in creating LLM-based web agents. ALLOY enables users to express procedural preferences through natural demonstrations rather than prompts, while making these procedures transparent and editable through visualized workflows that can be generalized across task variations. In a study with 12 participants, ALLOY's demonstration--based approach outperformed prompt-based agents and manual workflows in capturing user intent and procedural preferences in complex web tasks. Insights from the study also show how demonstration--based interaction complements the traditional prompt-based approach.

Mingxi Fu, Xitong Ling, Yuxuan Chen et al.

Accurate classification of Whole Slide Images (WSIs) and Regions of Interest (ROIs) is a fundamental challenge in computational pathology. While mainstream approaches often adopt Multiple Instance Learning (MIL), they struggle to capture the spatial dependencies among tissue structures. Graph Neural Networks (GNNs) have emerged as a solution to model inter-instance relationships, yet most rely on static graph topologies and overlook the physical spatial positions of tissue patches. Moreover, conventional attention mechanisms lack specificity, limiting their ability to focus on structurally relevant regions. In this work, we propose a novel GNN framework with deformable attention for pathology image analysis. We construct a dynamic weighted directed graph based on patch features, where each node aggregates contextual information from its neighbors via attention-weighted edges. Specifically, we incorporate learnable spatial offsets informed by the real coordinates of each patch, enabling the model to adaptively attend to morphologically relevant regions across the slide. This design significantly enhances the contextual field while preserving spatial specificity. Our framework achieves state-of-the-art performance on four benchmark datasets (TCGA-COAD, BRACS, gastric intestinal metaplasia grading, and intestinal ROI classification), demonstrating the power of deformable attention in capturing complex spatial structures in WSIs and ROIs.

Jiawen Li, Jiang Guo, Yuanzhe Li et al.

Metamaterials are artificially engineered structures that manipulate electromagnetic waves, having optical properties absent in natural materials. Recently, machine learning for the inverse design of metamaterials has drawn attention. However, the highly nonlinear relationship between the metamaterial structures and optical behaviour, coupled with fabrication difficulties, poses challenges for using machine learning to design and manufacture complex metamaterials. Herein, we propose a general framework that implements customised spectrum-to-shape and size parameters to address one-to-many metamaterial inverse design problems using conditional diffusion models. Our method exhibits superior spectral prediction accuracy, generates a diverse range of patterns compared to other typical generative models, and offers valuable prior knowledge for manufacturing through the subsequent analysis of the diverse generated results, thereby facilitating the experimental fabrication of metamaterial designs. We demonstrate the efficacy of the proposed method by successfully designing and fabricating a free-form metamaterial with a tailored selective emission spectrum for thermal camouflage applications.

Yuxuan Chen, Jiawen Li, Jiali Hu et al.

With the rapid advancement of pathology foundation models (FMs), the representation learning of whole slide images (WSIs) attracts increasing attention. Existing studies develop high-quality patch feature extractors and employ carefully designed aggregation schemes to derive slide-level representations. However, mainstream weakly supervised slide representation learning methods, primarily based on multiple instance learning (MIL), are tailored to specific downstream tasks, which limits their generalizability. To address this issue, some studies explore unsupervised slide representation learning. However, these approaches focus solely on the visual modality of patches, neglecting the rich semantic information embedded in textual data. In this work, we propose ProAlign, a cross-modal unsupervised slide representation learning framework. Specifically, we leverage a large language model (LLM) to generate descriptive text for the prototype types present in a WSI, introducing patch-text contrast to construct initial prototype embeddings. Furthermore, we propose a parameter-free attention aggregation strategy that utilizes the similarity between patches and these prototypes to form unsupervised slide embeddings applicable to a wide range of downstream tasks. Extensive experiments on four public datasets show that ProAlign outperforms existing unsupervised frameworks and achieves performance comparable to some weakly supervised models.

Xitong Ling, Yifeng Ping, Jiawen Li et al.

Multiple Instance Learning (MIL) plays a significant role in computational pathology, enabling weakly supervised analysis of Whole Slide Image (WSI) datasets. The field of WSI analysis is confronted with a severe long-tailed distribution problem, which significantly impacts the performance of classifiers. Long-tailed distributions lead to class imbalance, where some classes have sparse samples while others are abundant, making it difficult for classifiers to accurately identify minority class samples. To address this issue, we propose an ensemble learning method based on MIL, which employs expert decoders with shared aggregators and consistency constraints to learn diverse distributions and reduce the impact of class imbalance on classifier performance. Moreover, we introduce a multimodal distillation framework that leverages text encoders pre-trained on pathology-text pairs to distill knowledge and guide the MIL aggregator in capturing stronger semantic features relevant to class information. To ensure flexibility, we use learnable prompts to guide the distillation process of the pre-trained text encoder, avoiding limitations imposed by specific prompts. Our method, MDE-MIL, integrates multiple expert branches focusing on specific data distributions to address long-tailed issues. Consistency control ensures generalization across classes. Multimodal distillation enhances feature extraction. Experiments on Camelyon+-LT and PANDA-LT datasets show it outperforms state-of-the-art methods.

Jiawen Li, Jiali Hu, Qiehe Sun et al. · tsinghua

The emergence of foundation models in computational pathology has transformed histopathological image analysis, with whole slide imaging (WSI) diagnosis being a core application. Traditionally, weakly supervised fine-tuning via multiple instance learning (MIL) has been the primary method for adapting foundation models to WSIs. However, in this work we present a key experimental finding: a simple nonlinear mapping strategy combining mean pooling and a multilayer perceptron, called SiMLP, can effectively adapt patch-level foundation models to slide-level tasks without complex MIL-based learning. Through extensive experiments across diverse downstream tasks, we demonstrate the superior performance of SiMLP with state-of-the-art methods. For instance, on a large-scale pan-cancer classification task, SiMLP surpasses popular MIL-based methods by 3.52%. Furthermore, SiMLP shows strong learning ability in few-shot classification and remaining highly competitive with slide-level foundation models pretrained on tens of thousands of slides. Finally, SiMLP exhibits remarkable robustness and transferability in lung cancer subtyping. Overall, our findings challenge the conventional MIL-based fine-tuning paradigm, demonstrating that a task-agnostic representation strategy alone can effectively adapt foundation models to WSI analysis. These insights offer a unique and meaningful perspective for future research in digital pathology, paving the way for more efficient and broadly applicable methodologies.

Jiawen Li, Tian Guan, Qingxin Xia et al.

Foundation models have revolutionized the paradigm of digital pathology, as they leverage general-purpose features to emulate real-world pathological practices, enabling the quantitative analysis of critical histological patterns and the dissection of cancer-specific signals. However, these static general features constrain the flexibility and pathological relevance in the ever-evolving needs of clinical applications, hindering the broad use of the current models. Here we introduce PathFiT, a dynamic feature learning method that can be effortlessly plugged into various pathology foundation models to unlock their adaptability. Meanwhile, PathFiT performs seamless implementation across diverse pathology applications regardless of downstream specificity. To validate PathFiT, we construct a digital pathology benchmark with over 20 terabytes of Internet and real-world data comprising 28 H\&E-stained tasks and 7 specialized imaging tasks including Masson's Trichrome staining and immunofluorescence images. By applying PathFiT to the representative pathology foundation models, we demonstrate state-of-the-art performance on 34 out of 35 tasks, with significant improvements on 23 tasks and outperforming by 10.20% on specialized imaging tasks. The superior performance and versatility of PathFiT open up new avenues in computational pathology.

Zetian Mao, Chuan-Shen Hu, Jiawen Li et al.

Message passing neural networks have demonstrated significant efficacy in predicting molecular interactions. Introducing equivariant vectorial representations augments expressivity by capturing geometric data symmetries, thereby improving model accuracy. However, two-body bond vectors in opposition may cancel each other out during message passing, leading to the loss of directional information on their shared node. In this study, we develop Equivariant N-body Interaction Networks (ENINet) that explicitly integrates l = 1 equivariant many-body interactions to enhance directional symmetric information in the message passing scheme. We provided a mathematical analysis demonstrating the necessity of incorporating many-body equivariant interactions and generalized the formulation to $N$-body interactions. Experiments indicate that integrating many-body equivariant representations enhances prediction accuracy across diverse scalar and tensorial quantum chemical properties.

Shiwen Ni, Jiawen Li, Hung-Yu Kao

It is difficult for humans to distinguish the true and false of rumors, but current deep learning models can surpass humans and achieve excellent accuracy on many rumor datasets. In this paper, we investigate whether deep learning models that seem to perform well actually learn to detect rumors. We evaluate models on their generalization ability to out-of-domain examples by fine-tuning BERT-based models on five real-world datasets and evaluating against all test sets. The experimental results indicate that the generalization ability of the models on other unseen datasets are unsatisfactory, even common-sense rumors cannot be detected. Moreover, we found through experiments that models take shortcuts and learn absurd knowledge when the rumor datasets have serious data pitfalls. This means that simple modifications to the rumor text based on specific rules will lead to inconsistent model predictions. To more realistically evaluate rumor detection models, we proposed a new evaluation method called paired test (PairT), which requires models to correctly predict a pair of test samples at the same time. Furthermore, we make recommendations on how to better create rumor dataset and evaluate rumor detection model at the end of this paper.

Shiwen Ni, Jiawen Li, Hung-Yu Kao

With the development of social media, social communication has changed. While this facilitates people's communication and access to information, it also provides an ideal platform for spreading rumors. In normal or critical situations, rumors will affect people's judgment and even endanger social security. However, natural language is high-dimensional and sparse, and the same rumor may be expressed in hundreds of ways on social media. As such, the robustness and generalization of the current rumor detection model are put into question. We proposed a novel \textbf{h}ierarchical \textbf{a}dversarial \textbf{t}raining method for \textbf{r}umor \textbf{d}etection (HAT4RD) on social media. Specifically, HAT4RD is based on gradient ascent by adding adversarial perturbations to the embedding layers of post-level and event-level modules to deceive the detector. At the same time, the detector uses stochastic gradient descent to minimize the adversarial risk to learn a more robust model. In this way, the post-level and event-level sample spaces are enhanced, and we have verified the robustness of our model under a variety of adversarial attacks. Moreover, visual experiments indicate that the proposed model drifts into an area with a flat loss landscape, leading to better generalization. We evaluate our proposed method on three public rumors datasets from two commonly used social platforms (Twitter and Weibo). Experiment results demonstrate that our model achieves better results than state-of-the-art methods.

Yudianto Sujana, Jiawen Li, Hung-Yu Kao

Social media platforms such as Twitter have become a breeding ground for unverified information or rumors. These rumors can threaten people's health, endanger the economy, and affect the stability of a country. Many researchers have developed models to classify rumors using traditional machine learning or vanilla deep learning models. However, previous studies on rumor detection have achieved low precision and are time consuming. Inspired by the hierarchical model and multitask learning, a multiloss hierarchical BiLSTM model with an attenuation factor is proposed in this paper. The model is divided into two BiLSTM modules: post level and event level. By means of this hierarchical structure, the model can extract deep in-formation from limited quantities of text. Each module has a loss function that helps to learn bilateral features and reduce the training time. An attenuation fac-tor is added at the post level to increase the accuracy. The results on two rumor datasets demonstrate that our model achieves better performance than that of state-of-the-art machine learning and vanilla deep learning models.