Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2603.08935

PathoScribe: Transforming Pathology Data into a Living Library with a Unified LLM-Driven Framework for Semantic Retrieval and Clinical Integration

Abdul Rehman Akbar·Samuel Wales-McGrath·Alejadro Levya·Lina Gokhale·Rajendra Singh·Wei Chen·Anil Parwani·Muhammad Khalid Khan Niazi
View original source ↗Read source document ↗Export metadata ↓

Abstract

Pathology underpins modern diagnosis and cancer care, yet its most valuable asset, the accumulated experience encoded in millions of narrative reports, remains largely inaccessible. Although institutions are rapidly digitizing pathology workflows, storing data without effective mechanisms for retrieval and reasoning risks transforming archives into a passive data repository, where institutional knowledge exists but cannot meaningfully inform patient care. True progress requires not only digitization, but the ability for pathologists to interrogate prior similar cases in real time while evaluating a new diagnostic dilemma. We present PathoScribe, a unified retrieval-augmented large language model (LLM) framework designed to transform static pathology archives into a searchable, reasoning-enabled living library. PathoScribe enables natural language case exploration, automated cohort construction, clinical question answering, immunohistochemistry (IHC) panel recommendation, and prompt-controlled report transformation within a single architecture. Evaluated on 70,000 multi-institutional surgical pathology reports, PathoScribe achieved perfect Recall@10 for natural language case retrieval and demonstrated high-quality retrieval-grounded reasoning (mean reviewer score 4.56/5). Critically, the system operationalized automated cohort construction from free-text eligibility criteria, assembling research-ready cohorts in minutes (mean 9.2 minutes) with 91.3% agreement to human reviewers and no eligible cases incorrectly excluded, representing orders-of-magnitude reductions in time and cost compared to traditional manual chart review. This work establishes a scalable foundation for converting digital pathology archives from passive storage systems into active clinical intelligence platforms.

Explore related subjects

cs.CVcs.AIcs.CLcs.DLcs.IR

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Abdul Rehman Akbar, Samuel Wales-McGrath, Alejadro Levya, Lina Gokhale, Rajendra Singh, Wei Chen, Anil Parwani, Muhammad Khalid Khan Niazi. 2026-03-11. PathoScribe: Transforming Pathology Data into a Living Library with a Unified LLM-Driven Framework for Semantic Retrieval and Clinical Integration. https://arxiv.org/abs/2603.08935

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

SSP-GNN: Learning to Track via Bilevel Optimization

We propose a graph-based tracking formulation for multi-object tracking (MOT) where target detections contain kinematic information and re-identification features (attributes). Our method applies a successive shortest paths (SSP) algorithm to a tracking graph defined over a batch of frames. The edge costs in this tracking graph are computed via a message-passing network, a graph neural network (GNN) variant. The parameters of the GNN, and hence, the tracker, are learned end-to-end on a training set of example ground-truth tracks and detections. Specifically, learning takes the form of bilevel optimization guided by our novel loss function. We evaluate our algorithm on simulated scenarios to understand its sensitivity to scenario aspects and model hyperparameters. Across varied scenario complexities, our method compares favorably to a strong baseline.

cs.CV↗
arXiv2026

AdaptiveCDM: Source-Free Few-Shot Domain Adaptation for Cell Detection in Microscopic Images

Cross-domain cell detection for microscopic images suffers from performance degradation due to distribution shifts across imaging domains. Unsupervised Domain Adaptation (UDA) strategies, attempt to overcome domain sift without requiring annotated data from target. However, requirement of availability of annotated data from the source domain and large-size data from target domain are both challenging limitations for realistic scenarios. This is especially true in medical imaging, where privacy requirements might prevent access to annotated source data, and costly data acquisition restricts extensive sampling of the target domain. To address these challenges, we propose AdaptiveCDM, a modular framework for Source-Free Few-Shot Domain Adaptive Object Detection (SF-FSDAOD) setting, that adapts a pretrained source model using only few labeled target images without accessing source data. AdaptiveCDM combines Resolution-Aware Augmentation (RAug) and Category-Aware Representation Learning (CARL). RAug alleviates the scarcity and class imbalance by augmenting instance balanced training examples, while preserving the scale fidelity and morphological properties of cellular structures. CARL enhances discriminative representation learning by encouraging class-consistent proposals, improving both localization and classification. We also introduce two competitive baselines for proposed setting: Faster-FreeShot and MT-FreeShot. Our approach achieves 40.4/43.4 mAP0.5 on M5 and 67.1/75.5 mAP0.5 on Raabin-WBC under 2-/5-shot adaptation. Despite using only a few labeled target images and no source data, AdaptiveCDM achieves competitive or superior performance compared with SOTA methods under their respective supervision settings. Ablations and qualitative analyses further substantiate the contribution of each component and the effectiveness of AdaptiveCDM in low-data regimes. Code/models will be available.

cs.CV↗
arXiv2026

Uncertainty-Weighted Fusion of Image and Synthetic Event for Video Anomaly Detection

Most existing video anomaly detectors rely on RGB frames alone, which limit their ability to capture abrupt or transient motion cues that are critical for identifying anomalous events. We propose Uncertainty Weighted Image Event Fusion (IEF-VAD), a framework that integrates complementary RGB and synthetic motion information through a principled weighting mechanism. The method models the high variance and heavy tailed characteristics of synthetic motion cues with a Student's t likelihood, computes value level inverse variance weights using a Laplace approximation to prevent the image modality from overshadowing motion information, and performs iterative refinement to suppress residual cross modal noise. This formulation provides a more balanced and reliable fusion process compared to cross attention or gating based approaches that often suffer from modality dominance. Without requiring an event camera or frame level annotations, IEF-VAD achieves new state of the art performance on multiple real world anomaly detection benchmarks and remains stable under degradation applied to individual modalities. The results indicate that extracting and integrating complementary motion cues is an effective direction for robust video understanding across diverse environments.

cs.CV↗