Learnable Token Sparsification for Efficient Gigapixel Whole Slide Image Reasoning

The processing of gigapixel whole slide images within vision language models faces a major difficulty due to an excessive number of visual tokens. Existing solutions typically rely on spatial downsampling or heuristic pruning strategies that operate without training, and these methods often discard subtle but clinically meaningful patterns because pathological evidence is scattered irregularly across the tissue. To overcome this limitation, we reformulate token reduction in whole slide images as a trainable sparsification problem, allowing the model to learn an optimal selection strategy instead of following fixed heuristics. We propose a decoupled routing architecture. To enable gradient propagation through the nondifferentiable pruning operation during training, we introduce a component called SparseLearn. This component uses a variance-preserving noise gate that regulates the information flow of each patch via a differentiable Soft Top-K operator, together with a diagonal attention denoiser that recovers perturbed representations without leaking spatial information. At inference time, the SparseLearn module is entirely discarded, and the trained scorer applies a deterministic Hard Top-K operator to keep only the highest scoring 32 tokens, incurring no extra computation. By compressing the visual sequence down to a sparse set of just 32 tokens, which represents as little as 0.78% of the original length, our framework achieves 73.32% overall accuracy on SlideBench (TCGA), consistently surpassing sampling-based baselines and general-purpose vision language models. It also demonstrates strong zero shot generalization on SlideBench (BCNB) and WSI VQA*. By resolving the visual context bottleneck and preventing the dilution of sparse diagnostic evidence, this work provides a highly efficient paradigm for end to end gigapixel whole slide image reasoning.

A unified multi-task framework enables interpretable chest radiograph analysis

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.

Beyond Surrogate Gradients: Fully Differentiable Token Pruning for Vision-Language Models

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.

XrayClaw: Cooperative-Competitive Multi-Agent Alignment for Trustworthy Chest X-ray Diagnosis

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.

From Snapshots to Symphonies: The Evolution of Protein Prediction from Static Structures to Generative Dynamics and Multimodal Interactions

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.

Multimodal Model for Computational Pathology:Representation Learning and Image Compression

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.

ZeroSense:How Vision matters in Long Context Compression

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.

TC-SSA: Token Compression via Semantic Slot Aggregation for Gigapixel Pathology Reasoning

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.

Masked Image Contrastive Learning for Efficient Visual Conceptual Pre-training

This paper proposes a scalable and straightforward pre-training paradigm for efficient visual conceptual representation called masked image contrastive learning (MiCL). Our MiCL 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 MiCL 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, MiCL learns highly semantic conceptual representations efficiently without relying on hand-crafted data augmentations or additional auxiliary modules. Empirically, MiCL 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.

A foundation model for generalizable disease diagnosis in chest X-ray images

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.