Learning latent progression states from spatial heterogeneity in uterine histopathology

Tumor progression is accompanied by changes in architecture, morphology and microenvironmental organization, yet progression-associated heterogeneity is usually compressed into static diagnostic categories in histopathology. Here we present SpaTIE, a uterus-specific computational pathology framework that learns morphology-aware representations and organizes spatial histopathological heterogeneity into progression-associated tumor states. SpaTIE was developed using 10,426 uterine hematoxylin and eosin whole-slide images and evaluated in TCGA-UCEC and TCGA-UCS cohorts. The learned representations formed morphology manifolds, supported diagnostic, molecular and survival-related prediction tasks, and localized attention to informative tumor regions. Beyond supervised prediction, SpaTIE inferred tumor-state axes from cross-sectional morphology without temporal or molecular supervision. These morphology-derived states were spatially coherent and showed associations with clinicopathological variables and survival outcomes, while not simply recapitulating staging or diagnostic labels. Integrative multi-omics analyses linked the inferred states to DNA methylation, somatic copy-number variation, mutation, RNA-seq and RPPA profiles, highlighting molecular programs related to chromatin regulation, copy-number-associated structural variation, receptor tyrosine kinase signaling, cell adhesion, extracellular-matrix remodeling and metabolic adaptation. Progression-guided virtual perturbation further prioritized molecular features coupled to the morphology-derived state organization. Together, these findings suggest that uterine histopathology contains recoverable progression-associated tumor-state information and establish SpaTIE as a framework for connecting spatial morphology with multi-omics-informed tumor-state discovery.

DeCo-MIL: Debiased Counterfactual Reasoning for Long-Tailed Whole Slide Image Analysis

Multiple instance learning (MIL) is widely used for weakly supervised whole slide image (WSI) analysis. However, under long-tailed distributions, MIL-based WSI analysis faces a nested dual long-tail: an inter-slide class long tail and an intra-slide long tail of instance-level discriminative evidence. The two long tails are coupled: tail classes have few training slides, while their limited diagnostic evidence is concentrated in a few patches and obscured by abundant within-bag redundancy. This coupling biases models toward head classes and degrades rare-class recognition. To address this, we propose DeCo-MIL for long-tailed WSI analysis, which jointly alleviates the nested dual long-tail through frequency-debiased counterfactual reasoning. For the inner long tail, DeCo-MIL clusters patches into tissue-morphology anchors, replaces each anchor with its matched normal prototype to perform a counterfactual intervention, and estimates its counterfactual contribution to the ground-truth class using class-frequency-corrected predictions. These contributions guide redundancy masking to preserve scarce discriminative instances. For the outer long tail, DeCo-MIL constructs anchor-stratified pseudo-bags from redundancy-reduced bags and combines tail-aware oversampling with consistency regularization, increasing effective supervision for tail classes while preserving tissue-morphology composition. Extensive experiments on three long-tailed WSI benchmarks demonstrate that DeCo-MIL achieves state-of-the-art performance in both tail-class recognition and overall classification.

ConRub-Med: Reinforcement Learning with Consensus Rubrics for Open-Ended Medical Question Answering

Reinforcement learning with verifiable rewards has been especially effective in mathematics and coding, where answers can be checked automatically. Many open-ended medical questions lack comparably cheap outcome verifiers: responses may be partly correct, incomplete, or contain clinically consequential errors. Rubrics written or validated by physicians offer strong clinical grounding, but involving experts in every instance is costly. Model-generated rubrics make this supervision scalable. We introduce ConRub-Med to preserve useful distinctions as rubric feedback moves from construction to policy optimization. For each prompt, three heterogeneous language models propose atomic criteria independently; a separate model reviews them, retaining only criteria with semantic support from all three generators. Three-State scoring distinguishes correct coverage, missing information, and incorrect claims. Errors receive negative rather than zero credit. When every response in a complete Group Relative Policy Optimization (GRPO) group receives the same final reward, a pairwise judge provides sequence advantages only if both candidate orders agree, without changing the scalar rewards. Groups without ties use vanilla GRPO. In a blinded study matched by question, two medical experts rate panels from the full pipeline as more clinically relevant than panels produced by one generator. Across the evaluated open models, ConRub-Med ranks first on six of nine benchmarks and achieves the highest medical and generalization averages. Using the resulting rubric dataset of 5,166 prompts, it scores $38.98 \pm 1.04$ (mean $\pm$ SD) on HealthBench-Hard, compared with InfiMed-ORBIT's 33.60 with 8,000 samples and 37.30 with 28,000.

Pretraining Multiple Instance Learning Networks with Multi-Teacher Distillation from Pathology Slide Foundation Models

Multiple instance learning (MIL) has become the main paradigm for whole-slide image (WSI) analysis in computational pathology. However, existing MIL aggregators are still typically trained from scratch for each downstream task, relying on limited slide-level labels to learn both aggregation mechanisms and downstream discriminative representations simultaneously. As a result, they often suffer from unstable optimization, overfitting, and limited transferability. Similar to pretrained ResNet and Vision Transformer models in natural image learning, MIL also requires reusable pretrained initialization. However, high-quality slide-level pretraining data remain scarce, and MIL models are usually lightweight and weakly supervised, making large-scale pretraining difficult in practice. To address this challenge, we propose a distillation-based pretraining framework for MIL, which leverages two slide-level foundation models, TITAN and CARE, as teachers to transfer their representational knowledge into a diverse set of MIL architectures. To effectively balance supervision from different teachers, we further introduce an angular dispersion normalized distillation loss. The distilled weights are then used as initialization for downstream adaptation. We conduct systematic evaluations on 15 benchmark datasets under both linear probing and full-parameter fine-tuning, and further validate its advantages in few-shot scenarios. Experimental results show that pretraining generally improves MIL aggregators over from scratch training, especially in linear-probing and few-shot settings, while maintaining the computational efficiency of lightweight MIL models. Code is available at https://github.com/fu0201/MIL_Pretrained.

ALICE: Learning a General-Purpose Pathology Foundation Model from Vision, Vision-Language, and Slide-Level Experts

Foundation models are reshaping computational pathology, yet their capabilities remain shaped by pretraining objectives, data sources, and spatial scales, fragmenting complementary expertise across separate backbones. Here we present ALICE, a unified foundation model trained through multi-stage agglomerative distillation that sequentially distills eight vision-only, vision-language, and slide-level teacher models into dedicated modules of a single backbone. ALICE is pretrained on 24,985,184 tile-level pathology images and 155,604 high-resolution images, and evaluated across 21 task scenarios, 96 downstream tasks, and 48 data sources, spanning region-of-interest tissue analysis, vision-language multimodal evaluation, and whole-slide clinical assessment. In all three evaluation settings, ALICE achieved the best average rank among task-matched pathology foundation models. These results demonstrate that agglomerative distillation can consolidate complementary capabilities from specialized models into a unified backbone for broad computational pathology applications. The model is available at https://github.com/WonderLandxD/ALICE.

From Knowing to Doing: A Memory-Controlled Benchmark for LLM Trading Agents on Stock Markets

Evaluating whether large language model (LLM) agents can profit in capital markets is increasingly framed as end-to-end trading: place an agent in a historical market, let it trade, and measure portfolio returns. This setup is vulnerable to two evaluation failures. First, long backtests often overlap with the knowledge cutoffs of frontier LLMs, allowing memorized tickers, dates, prices, and market narratives to substitute for investment reasoning. Second, raw returns are a noisy proxy for stock-selection ability, since positive performance may come from market beta, style exposure, or favorable regimes rather than genuine alpha. We introduce KTD-Fin (Knowing-To-Doing Financial Benchmark), an end-to-end stock-market trading benchmark that addresses both issues. KTD-Fin uses a data-side masking protocol to anonymize key identifiers and calendar information consistently across prompts and tools, separating historical market memory from investment decision-making. It also incorporates a Barra-style performance attribution framework that decomposes portfolio returns into market, style, and stock-selection alpha components. Across ten frontier LLM agents evaluated on the Chinese CSI300 over a 2024--2026 window, masking substantially changes agent rationales, pushing them towards anonymized factor-based reasoning. Attribution analysis further shows that LLM agents' cumulative returns under leakage-controlled evaluation are largely explained by passive market and style exposure, with limited evidence of persistent stock-selection alpha. These findings suggest that financial LLM benchmarks should evaluate not only whether an agent makes money, but also whether the source of returns reflects transferable investment skill. We release KTD-Fin as a reproducible template for leakage-controlled and attribution-aware evaluation of LLM trading agents.

Bridging SFT and RL: Dynamic Policy Optimization for Robust Reasoning

Post-training paradigms for Large Language Models (LLMs), primarily Supervised Fine-Tuning (SFT) and Reinforcement Learning (RL), face a fundamental dilemma: SFT provides stability (low variance) but suffers from high fitting bias, while RL enables exploration (low bias) but grapples with high gradient variance. Existing unified optimization strategies often employ naive loss weighting, overlooking the statistical conflict between these distinct gradient signals. In this paper, we provide a rigorous theoretical analysis of this bias-variance trade-off and propose \textbf{DYPO} (Dynamic Policy Optimization), a unified framework designed to structurally mitigate this conflict. DYPO integrates three core components: (1) a \textit{Group Alignment Loss (GAL)} that leverages intrinsic group dynamics to significantly reduce RL gradient variance; (2) a \textit{Multi-Teacher Distillation} mechanism that corrects SFT fitting bias via diverse reasoning paths; and (3) a \textit{Dynamic Exploitation-Exploration Gating} mechanism that adaptively arbitrates between stable SFT and exploratory RL based on reward feedback. Theoretical analysis confirms that DYPO linearly reduces fitting bias and minimizes overall variance. Extensive experiments demonstrate that DYPO significantly outperforms traditional sequential pipelines, achieving an average improvement of 4.8\% on complex reasoning benchmarks and 13.3\% on out-of-distribution tasks. Our code is publicly available at https://github.com/Tocci-Zhu/DYPO.

GloPath: An Entity-Centric Foundation Model for Glomerular Lesion Assessment and Clinicopathological Insights

Glomerular pathology is central to the diagnosis and prognosis of renal diseases, yet the heterogeneity of glomerular morphology and fine-grained lesion patterns remain challenging for current AI approaches. We present GloPath, an entity-centric foundation model trained on over one million glomeruli extracted from 14,049 renal biopsy specimens using multi-scale and multi-view self-supervised learning. GloPath addresses two major challenges in nephropathology: glomerular lesion assessment and clinicopathological insights discovery. For lesion assessment, GloPath was benchmarked across three independent cohorts on 52 tasks, including lesion recognition, grading, few-shot classification, and cross-modality diagnosis-outperforming state-of-the-art methods in 42 tasks (80.8%). In the large-scale real-world study, it achieved an ROC-AUC of 91.51% for lesion recognition, demonstrating strong robustness in routine clinical settings. For clinicopathological insights, GloPath systematically revealed statistically significant associations between glomerular morphological parameters and clinical indicators across 224 morphology-clinical variable pairs, demonstrating its capacity to connect tissue-level pathology with patient-level outcomes. Together, these results position GloPath as a scalable and interpretable platform for glomerular lesion assessment and clinicopathological discovery, representing a step toward clinically translatable AI in renal pathology.

To What Extent Do Token-Level Representations from Pathology Foundation Models Improve Dense Prediction?

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

HookMIL: Revisiting Context Modeling in Multiple Instance Learning for Computational Pathology

Multiple Instance Learning (MIL) has enabled weakly supervised analysis of whole-slide images (WSIs) in computational pathology. However, traditional MIL approaches often lose crucial contextual information, while transformer-based variants, though more expressive, suffer from quadratic complexity and redundant computations. To address these limitations, we propose HookMIL, a context-aware and computationally efficient MIL framework that leverages compact, learnable hook tokens for structured contextual aggregation. These tokens can be initialized from (i) key-patch visual features, (ii) text embeddings from vision-language pathology models, and (iii) spatially grounded features from spatial transcriptomics-vision models. This multimodal initialization enables Hook Tokens to incorporate rich textual and spatial priors, accelerating convergence and enhancing representation quality. During training, Hook tokens interact with instances through bidirectional attention with linear complexity. To further promote specialization, we introduce a Hook Diversity Loss that encourages each token to focus on distinct histopathological patterns. Additionally, a hook-to-hook communication mechanism refines contextual interactions while minimizing redundancy. Extensive experiments on four public pathology datasets demonstrate that HookMIL achieves state-of-the-art performance, with improved computational efficiency and interpretability. Codes are available at https://github.com/lingxitong/HookMIL.