MApLe: Multi-instance Alignment of Diagnostic Reports and Large Medical Images

Pathology reports are structured, multi-granular documents encoding diagnostic conclusions, histological grades, and ancillary test results across one or more anatomical sites; yet existing pathology vision-language models (VLMs) reduce this output to a flat label or free-form text. We present HiPath, a lightweight VLM framework built on frozen UNI2 and Qwen3 backbones that treats structured report prediction as its primary training objective. Three trainable modules totalling 15M parameters address complementary aspects of the problem: a Hierarchical Patch Aggregator (HiPA) for multi-image visual encoding, Hierarchical Contrastive Learning (HiCL) for cross-modal alignment via optimal transport, and Slot-based Masked Diagnosis Prediction (Slot-MDP) for structured diagnosis generation. Trained on 749K real-world Chinese pathology cases from three hospitals, HiPath achieves 68.9% strict and 74.7% clinically acceptable accuracy with a 97.3% safety rate, outperforming all baselines under the same frozen backbone. Cross-hospital evaluation confirms generalisation with only a 3.4pp drop in strict accuracy while maintaining 97.1% safety.

Recent advances in large-scale foundation models have enabled strong generalization across a wide range of clinical and research tasks in magnetic resonance imaging (MRI). However, existing vision-language MRI models remain limited in anatomy-specific localization and pathology-aware representation, particularly in real-world settings. We introduce A4-MR, a 3D vision-language foundation model trained on approximately 50,000 MRI studies comprising 491,000 series, roughly half of which are paired with radiology reports. A4-MR is designed to: (1) learn anatomy localization through large-scale pretraining with noisy labels; (2) align image and text representations at the anatomical level; and (3) learn distinct representations of healthy and abnormal anatomy. Across a diverse set of downstream tasks, A4-MR outperforms existing foundation models, including a +1.7 AUROC improvement over MedSigLIP for abnormality detection. Using a frozen encoder, A4-MR also surpasses an end-to-end task-specific MedNeXt model for knee segmentation by +1.4 Dice and performs comparably to the best task-specific model for abdominal organ segmentation on AMOS, within 0.4 Dice. Finally, without anatomical prompts, A4-MR localizes 3D anatomy comparably to MedSAM2 provided with ground-truth bounding boxes. Together, these results demonstrate that anatomy-level multimodal alignment and abnormality-aware representation learning can enable a single MRI foundation model to support localization, segmentation, and pathology-related tasks.

Recent radiology-adapted vision-language models have achieved strong performance on standard report generation benchmarks, yet their robustness and generalization remain constrained by imperfect alignment and correlation between visual and textual features. Existing methods connect image and text either implicitly through autoregressive report supervision or explicitly through contrastive learning. However, autoregressive supervision alone is insufficient to establish reliable image-text alignment, while contrastive learning can push apart unpaired reports that describe related pathologies simply because they are not paired with the same image. This is problematic in radiology, where different reports may share compatible pathology semantics rather than being true negatives. As a result, the learned representation may fail to organize images and reports around shared pathology concepts, causing the decoder to rely on pretrained language priors and generate clinically plausible reports that are not fully supported by radiographic evidence. To address this issue, we propose PALM, a pathology-aware alignment framework for radiology report generation. Instead of directly matching each image-report pair while separating all others, PALM aligns visual and textual features through shared pathology prototypes. These prototypes provide a clinically meaningful bridge between radiographic evidence and textual findings, allowing cases with similar pathology semantics to move toward common concepts without separating compatible cases. In addition, we introduce Masked Evidence Modeling to strengthen the image encoder sensitivity to local radiographic evidence by learning semantic changes caused by masked image regions. Experiments on MIMIC-CXR, IU X-Ray, and MIMIC-ABN show that PALM consistently improves both report generation and abnormality-focused robustness.