Lijian Xu

Lijian Xu, Ziyu Ni, Xinglong Liu et al.

While multimodal deep learning has advanced medical imaging analysis, existing black-box systems \textcolor{black}{may remain confined to isolated tasks, often overlooking} the trust-sensitive nature of clinical diagnosis as a multi-task process. We propose IMT-CXR (Interpretable Multi-task Transformer for Chest X-ray Analysis), a framework that emulates radiologists' diagnostic workflow through three evidence-driven stages: 1) Disease recognition; 2) Attribute characterization (e.g., size, location, severity quantification); 3) Evidence-integrated report generation with traceable decision pathways. The framework employs a unified transformer architecture optimized via medical-domain instruction tuning, sequentially executing four clinical tasks: multi-label disease classification, lesion localization, anatomical segmentation, and radiology report generation. Experimental validation demonstrates competitive performance on ten CXR benchmarks under direct inference and fine-tuning settings. In a blinded evaluation of 160 historical reports from four medical centers, three radiologists rated 66\% of AI-generated reports as comparable to or surpassing original clinical reports in diagnostic clarity, highlighting the framework's translational potential. By establishing traceable diagnostic pathways from anatomical findings to conclusions, this work bridges the gap between AI technical metrics and clinical utility, advancing trustworthy AI systems in medical imaging.

Landi He, Mingde Yao, Shawn Young et al.

Visual token pruning reduces the computational cost of Vision-Language Models (VLMs) by removing redundant visual tokens. Existing methods typically rely on Gumbel-Softmax to approximate discrete selection during training. However, the optimization is driven by surrogate gradients rather than the true selection process, leading to unreliable learning of token importance. In this paper, we propose DiffPrune, which reformulates pruning as continuous control of token information instead of discrete selection learning. Specifically, we introduce an Information Throttler that modulates each token using variance-preserving noise conditioned on importance scores, where higher scores induce less information suppression during training. This design directly operates on token representations, naturally providing a fully differentiable optimization path for learning token importance. At inference, tokens are removed via hard thresholding on the learned scores. Across ten VLM benchmarks, DiffPrune retains 96.5% of full-model accuracy while accelerating LLM prefill by 2.85x, with only 0.69 ms of inference overhead.

Xiaoyu Yang, Lijian Xu, Hao Sun et al.

Visual grounding (VG) occupies a pivotal position in multi-modality vision-language models. In this study, we propose ViLaM, a large multi-modality model, that supports multi-tasks of VG using the cycle training strategy, with abundant interaction instructions. The cycle training between referring expression generation (REG) and referring expression comprehension (REC) is introduced. It enhances the consistency between visual location and referring expressions, and addresses the need for high-quality, multi-tasks VG datasets. Moreover, multi-tasks of VG are promoted in our model, contributed by the cycle training strategy. The multi-tasks in REC encompass a range of granularities, from region-level to pixel-level, which include referring bbox detection, referring keypoints detection, and referring image segmentation. In REG, referring region classification determines the fine-grained category of the target, while referring region captioning generates a comprehensive description. Meanwhile, all tasks participate in the joint training, synergistically enhancing one another and collectively improving the overall performance of the model. Furthermore, leveraging the capabilities of large language models, ViLaM extends a wide range of instructions, thereby significantly enhancing its generalization and interaction potentials. Extensive public datasets corroborate the superior capabilities of our model in VG with muti-tasks. Additionally, validating its robust generalization, ViLaM is validated under open-set and few-shot scenarios. Especially in the medical field, our model demonstrates cross-domain robust generalization capabilities. Furthermore, we contribute a VG dataset, especially with multi-tasks. To support and encourage the community focused on VG, we have made both the dataset and our code public: https://github.com/AnonymGiant/ViLaM.

Lei Miao, Lijian Xu

Today's fixed-cycle traffic signaling is highly suboptimal and aggravates traffic congestion and waste of energy in urban areas. In addition, it offers no quality-of-service guarantee and makes travel time prediction extremely hard. While existing traffic light control research primarily focuses on improving the average wait time of cars, we study in this paper how traffic light scheduling affects the worst-case wait time. In particular, we derive the time a car spends at an intersection in the best-case and the worst-case, respectively. Using the theoretical results, we propose a simple but effective controller and run simulation to verify its performance. The result shows that it works much better than fixed-cycle controllers in both light and heavy traffic scenarios.

Zhuo Chen, Shawn Young, Lijian Xu

The application of large vision-language models to computational pathology holds great promise for diagnostic assistants but faces a critical computational bottleneck: the gigapixel scale of Whole Slide Images (WSIs). A single WSI typically contains over 105 patches, creating sequence lengths that exceed the constraints of standard Transformer architectures. Existing solutions often resort to spatial sampling, which risks discarding diagnostically critical evidence. To address this, we propose TC-SSA (Token Compression via Semantic Slot Aggregation), a learnable token compression framework that aggregates patch features into a fixed number of semantic slots. A gated routing module assigns patches to slots using sparse Top-2 routing, followed by weighted aggregation, enabling global slide coverage under a strict token budget. The resulting representation retains diagnostically relevant information while reducing the number of visual tokens to 1.7% of the original sequence. On the SlideBench(TCGA), our model achieves 78.34% overall accuracy and 77.14% on the diagnosis subset, outperforming sampling-based baselines under comparable token budgets. The method also generalizes to MIL classification, reaching AUC of 95.83% on TCGA-BRCA, 98.27% on TCGA-NSCLC and 79.80% on PANDA. These results suggest that learnable semantic aggregation provides an effective trade-off between efficiency and diagnostic performance for gigapixel pathology reasoning.

Lijian Xu, Hao Sun, Ziyu Ni et al.

Medicine is inherently multimodal and multitask, with diverse data modalities spanning text, imaging. However, most models in medical field are unimodal single tasks and lack good generalizability and explainability. In this study, we introduce MedViLaM, a unified vision-language model towards a generalist model for medical data that can flexibly encode and interpret various forms of medical data, including clinical language and imaging, all using the same set of model weights. To facilitate the creation of such multi-task model, we have curated MultiMedBench, a comprehensive pretaining dataset and benchmark consisting of several distinct tasks, i.e., continuous question-answering, multi-label disease classification, disease localization, generation and summarization of radiology reports. MedViLaM demonstrates strong performance across all MultiMedBench tasks, frequently outpacing other generalist models by a significant margin. Additionally, we present instances of zero-shot generalization to new medical concepts and tasks, effective transfer learning across different tasks, and the emergence of zero-shot medical reasoning.

Lijian Xu, Ziyu Ni, Xinglong Liu et al.

The emergence of multi-modal deep learning models has made significant impacts on clinical applications in the last decade. However, the majority of models are limited to single-tasking, without considering disease diagnosis is indeed a multi-task procedure. Here, we demonstrate a unified transformer model specifically designed for multi-modal clinical tasks by incorporating customized instruction tuning. We first compose a multi-task training dataset comprising 13.4 million instruction and ground-truth pairs (with approximately one million radiographs) for the customized tuning, involving both image- and pixel-level tasks. Thus, we can unify the various vision-intensive tasks in a single training framework with homogeneous model inputs and outputs to increase clinical interpretability in one reading. Finally, we demonstrate the overall superior performance of our model compared to prior arts on various chest X-ray benchmarks across multi-tasks in both direct inference and finetuning settings. Three radiologists further evaluate the generated reports against the recorded ones, which also exhibit the enhanced explainability of our multi-task model.

Yonghan Gao, Zehong Chen, Lijian Xu et al.

Recent visual-text compression (VTC) methods, typified by DeepSeek-OCR, report impressive high token compression ratios for long-context modeling tasks by leveraging text-to-image rendering. However, existing evaluation protocols heavily rely on downstream task performance. Such evaluation metrics fail to accurately measure text preservation due to the strong inherent linguistic priors of Multimodal Large Language Models (MLLMs). In this work, we introduce a new evaluation framework that decouples MLLMs' capabilities to faithfully assess VTC quality. Within this framework, we further introduce the ZeroSense Benchmark to ensure low semantic correlation of testing samples. By eliminating contextual dependencies, our benchmark guarantees that the evaluation results are purely reflective of VTC quality, unaffected by the semantic inference capabilities of downstream models. Extensive experiments across multiple datasets demonstrate that VTC quality and downstream task accuracy diverge significantly, highlighting the necessity of our decoupled evaluation framework.

Landi He, Xiaoyu Yang, Lijian Xu

Visual tokens dominate inference cost in vision-language models (VLMs), yet many carry redundant information. Existing pruning methods alleviate this but typically rely on attention magnitude or similarity scores. We reformulate visual token pruning as capacity constrained communication: given a fixed budget K, the model must allocate limited bandwidth to maximally preserve visual information. We propose AutoSelect, which attaches a lightweight Scorer and Denoiser to a frozen VLM and trains with only the standard next token prediction loss, without auxiliary objectives or extra annotations. During training, a variance preserving noise gate modulates each token's information flow according to its predicted importance so that gradients propagate through all tokens; a diagonal attention Denoiser then recovers the perturbed representations. At inference, only the Scorer and a hard top-K selection remain, adding negligible latency. On ten VLM benchmarks, AutoSelect retains 96.5% of full model accuracy while accelerating LLM prefill by 2.85x with only 0.69 ms overhead, and transfers to different VLM backbones without architecture-specific tuning. Code is available at https://github.com/MedHK23/AutoSelect.

Xiaoyu Yang, Lijian Xu, Hongsheng Li et al.

This paper proposes a scalable and straightforward pre-training paradigm for efficient visual conceptual representation called occluded image contrastive learning (OCL). Our OCL approach is simple: we randomly mask patches to generate different views within an image and contrast them among a mini-batch of images. The core idea behind OCL consists of two designs. First, masked tokens have the potential to significantly diminish the conceptual redundancy inherent in images, and create distinct views with substantial fine-grained differences on the semantic concept level instead of the instance level. Second, contrastive learning is adept at extracting high-level semantic conceptual features during the pre-training, circumventing the high-frequency interference and additional costs associated with image reconstruction. Importantly, OCL learns highly semantic conceptual representations efficiently without relying on hand-crafted data augmentations or additional auxiliary modules. Empirically, OCL demonstrates high scalability with Vision Transformers, as the ViT-L/16 can complete pre-training in 133 hours using only 4 A100 GPUs, achieving 85.8\% accuracy in downstream fine-tuning tasks. Code is available at https://anonymous.4open.science/r/OLRS/.

Shawn Young, Lijian Xu

Chest X-ray (CXR) interpretation is a fundamental yet complex clinical task that increasingly relies on artificial intelligence for automation. However, traditional monolithic models often lack the nuanced reasoning required for trustworthy diagnosis, frequently leading to logical inconsistencies and diagnostic hallucinations. While multi-agent systems offer a potential solution by simulating collaborative consultations, existing frameworks remain susceptible to consensus-based errors when instantiated by a single underlying model. This paper introduces XrayClaw, a novel framework that operationalizes multi-agent alignment through a sophisticated cooperative-competitive architecture. XrayClaw integrates four specialized cooperative agents to simulate a systematic clinical workflow, alongside a competitive agent that serves as an independent auditor. To reconcile these distinct diagnostic pathways, we propose Competitive Preference Optimization, a learning objective that penalizes illogical reasoning by enforcing mutual verification between analytical and holistic interpretations. Extensive empirical evaluations on the MS-CXR-T, MIMIC-CXR, and CheXbench benchmarks demonstrate that XrayClaw achieves state-of-the-art performance in diagnostic accuracy, clinical reasoning fidelity, and zero-shot domain generalization. Our results indicate that XrayClaw effectively mitigates cumulative hallucinations and enhances the overall reliability of automated CXR diagnosis, establishing a new paradigm for trustworthy medical imaging analysis.

Jingzhi Chen, Lijian Xu

The protein folding problem has been fundamentally transformed by artificial intelligence, evolving from static structure prediction toward the modeling of dynamic conformational ensembles and complex biomolecular interactions. This review systematically examines the paradigm shift in AI driven protein science across five interconnected dimensions: unified multimodal representations that integrate sequences, geometries, and textual knowledge; refinement of static prediction through MSA free architectures and all atom complex modeling; generative frameworks, including diffusion models and flow matching, that capture conformational distributions consistent with thermodynamic ensembles; prediction of heterogeneous interactions spanning protein ligand, protein nucleic acid, and protein protein complexes; and functional inference of fitness landscapes, mutational effects, and text guided property prediction. We critically analyze current bottlenecks, including data distribution biases, limited mechanistic interpretability, and the disconnect between geometric metrics and biophysical reality, while identifying future directions toward physically consistent generative models, multimodal foundation architectures, and experimental closed loop systems. This methodological transformation marks artificial intelligence's transition from a structural analysis tool into a universal simulator capable of understanding and ultimately rewriting the dynamic language of life.

Peihang Wu, Zehong Chen, Lijian Xu

Whole slide imaging (WSI) has transformed digital pathology by enabling computational analysis of gigapixel histopathology images. Recent foundation model advances have accelerated progress in computational pathology, facilitating joint reasoning across pathology images, clinical reports, and structured data. Despite this progress, challenges remain: the extreme resolution of WSIs creates computational hurdles for visual learning; limited expert annotations constrain supervised approaches; integrating multimodal information while preserving biological interpretability remains difficult; and the opacity of modeling ultra-long visual sequences hinders clinical transparency. This review comprehensively surveys recent advances in multimodal computational pathology. We systematically analyze four research directions: (1) self-supervised representation learning and structure-aware token compression for WSIs; (2) multimodal data generation and augmentation; (3) parameter-efficient adaptation and reasoning-enhanced few-shot learning; and (4) multi-agent collaborative reasoning for trustworthy diagnosis. We specifically examine how token compression enables cross-scale modeling and how multi-agent mechanisms simulate a pathologist's "Chain of Thought" across magnifications to achieve uncertainty-aware evidence fusion. Finally, we discuss open challenges and argue that future progress depends on unified multimodal frameworks integrating high-resolution visual data with clinical and biomedical knowledge to support interpretable and safe AI-assisted diagnosis.

Wangyu Feng, Shawn Young, Lijian Xu

Self-supervised learning (SSL) has emerged as a powerful paradigm for Chest X-ray (CXR) analysis under limited annotations. Yet, existing SSL strategies remain suboptimal for medical imaging. Masked image modeling allocates substantial computation to reconstructing high-frequency background details with limited diagnostic value. Contrastive learning, on the other hand, often depends on aggressive augmentations that risk altering clinically meaningful structures. We introduce Semantic-Partitioned Contrastive Learning (S-PCL), an efficient pre-training framework tailored for CXR representation learning. Instead of reconstructing pixels or relying on heavy augmentations, S-PCL randomly partitions patch tokens from a single CXR into two non-overlapping semantic subsets. Each subset provides a complementary but incomplete view. The encoder must maximize agreement between these partitions, implicitly inferring global anatomical layout and local pathological cues from partial evidence. This semantic partitioning forms an internal bottleneck that enforces long-range dependency modeling and structural coherence. S-PCL eliminates the need for hand-crafted augmentations, auxiliary decoders, and momentum encoders. The resulting architecture is streamlined, computationally efficient, and easy to scale. Extensive experiments on large-scale CXR benchmarks, including ChestX-ray14, CheXpert, RSNA Pneumonia and SIIM-ACR Pneumothorax, show that S-PCL achieves competitive performance while attaining the lowest GFLOPs and superior accuracy among existing SSL approaches.

Lijian Xu, Ziyu Ni, Hao Sun et al.

Medical artificial intelligence (AI) is revolutionizing the interpretation of chest X-ray (CXR) images by providing robust tools for disease diagnosis. However, the effectiveness of these AI models is often limited by their reliance on large amounts of task-specific labeled data and their inability to generalize across diverse clinical settings. To address these challenges, we introduce CXRBase, a foundational model designed to learn versatile representations from unlabelled CXR images, facilitating efficient adaptation to various clinical tasks. CXRBase is initially trained on a substantial dataset of 1.04 million unlabelled CXR images using self-supervised learning methods. This approach allows the model to discern meaningful patterns without the need for explicit labels. After this initial phase, CXRBase is fine-tuned with labeled data to enhance its performance in disease detection, enabling accurate classification of chest diseases. CXRBase provides a generalizable solution to improve model performance and alleviate the annotation workload of experts to enable broad clinical AI applications from chest imaging.

Shawn Young, Xingyu Zeng, Lijian Xu

This paper investigates the fundamental relationship between model capacity and the minimal number of visual tokens required to preserve image semantics. Inspired by the Minimum Description Length principle, we reinterpret image tokens as vectors in a visual semantic space and define the intrinsic semantic complexity of an image as the smallest set of basis vectors needed to span this space. Building on this perspective, we propose Orthogonal Filtering, a lightweight module that adaptively clusters redundant tokens into a compact set of orthogonal bases. Through extensive experiments across a range of ViT models, we reveal a consistent token, model scaling law: larger models require significantly fewer tokens to span visual semantic space. Besides, we also contribute a visual long-context dataset.

Ziyu Ni, Linda Wei, Lijian Xu et al.

Local hemodynamic forces play an important role in determining the functional significance of coronary arterial stenosis and understanding the mechanism of coronary disease progression. Computational fluid dynamics (CFD) have been widely performed to simulate hemodynamics non-invasively from coronary computed tomography angiography (CCTA) images. However, accurate computational analysis is still limited by the complex construction of patient-specific modeling and time-consuming computation. In this work, we proposed an end-to-end deep learning framework, which could predict the coronary artery hemodynamics from CCTA images. The model was trained on the hemodynamic data obtained from 3D simulations of synthetic and real datasets. Extensive experiments demonstrated that the predicted hemdynamic distributions by our method agreed well with the CFD-derived results. Quantitatively, the proposed method has the capability of predicting the fractional flow reserve with an average error of 0.5\% and 2.5\% for the synthetic dataset and real dataset, respectively. Particularly, our method achieved much better accuracy for the real dataset compared to PointNet++ with the point cloud input. This study demonstrates the feasibility and great potential of our end-to-end deep learning method as a fast and accurate approach for hemodynamic analysis.

Xiaoyu Yang, Lijian Xu, Simon Yu et al.

Segmentation of the coronary artery is an important task for the quantitative analysis of coronary computed tomography angiography (CCTA) images and is being stimulated by the field of deep learning. However, the complex structures with tiny and narrow branches of the coronary artery bring it a great challenge. Coupled with the medical image limitations of low resolution and poor contrast, fragmentations of segmented vessels frequently occur in the prediction. Therefore, a geometry-based cascaded segmentation method is proposed for the coronary artery, which has the following innovations: 1) Integrating geometric deformation networks, we design a cascaded network for segmenting the coronary artery and vectorizing results. The generated meshes of the coronary artery are continuous and accurate for twisted and sophisticated coronary artery structures, without fragmentations. 2) Different from mesh annotations generated by the traditional marching cube method from voxel-based labels, a finer vectorized mesh of the coronary artery is reconstructed with the regularized morphology. The novel mesh annotation benefits the geometry-based segmentation network, avoiding bifurcation adhesion and point cloud dispersion in intricate branches. 3) A dataset named CCA-200 is collected, consisting of 200 CCTA images with coronary artery disease. The ground truths of 200 cases are coronary internal diameter annotations by professional radiologists. Extensive experiments verify our method on our collected dataset CCA-200 and public ASOCA dataset, with a Dice of 0.778 on CCA-200 and 0.895 on ASOCA, showing superior results. Especially, our geometry-based model generates an accurate, intact and smooth coronary artery, devoid of any fragmentations of segmented vessels.