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

arXiv: https://arxiv.org/abs/2603.08935 · HTML: https://mlsanity.com/paper/2603.08935/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 53 references that are in the map.
- First posted on arXiv 9 Mar 2026.

## Builds on (most cited first, 18 of 18)

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Dense Passage Retrieval for Open-Domain Question Answering](https://mlsanity.com/paper/2004.04906/) (2020)
- [Mistral 7B](https://mlsanity.com/paper/2310.06825/) (2023)
- [Billion-scale similarity search with GPUs](https://mlsanity.com/paper/1702.08734/) (2017)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Text Embeddings by Weakly-Supervised Contrastive Pre-training](https://mlsanity.com/paper/2212.03533/) (2022)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [A Study of Generative Large Language Model for Medical Research and Healthcare](https://mlsanity.com/paper/2305.13523/) (2023)
- [An Analysis of Fusion Functions for Hybrid Retrieval](https://mlsanity.com/paper/2210.11934/) (2022)
- [HISTAI: An Open-Source, Large-Scale Whole Slide Image Dataset for Computational Pathology](https://mlsanity.com/paper/2505.12120/) (2025)
- [PathologyBERT -- Pre-trained Vs. A New Transformer Language Model for Pathology Domain](https://mlsanity.com/paper/2205.06885/) (2022)
- [Computational Pathology for Accurate Prediction of Breast Cancer Recurrence: Development and Validation of a Deep Learning-based Tool](https://mlsanity.com/paper/2409.15491/) (2024)
- [Attention2Minority: A salient instance inference-based multiple instance learning for classifying small lesions in whole slide images](https://mlsanity.com/paper/2301.07700/) (2023)
- [Cross-attention-based saliency inference for predicting cancer metastasis on whole slide images](https://mlsanity.com/paper/2309.09412/) (2023)
- [RANGER: Sparsely-Gated Mixture-of-Experts with Adaptive Retrieval Re-ranking for Pathology Report Generation](https://mlsanity.com/paper/2603.04348/) (2026)
- [Learning the Language of Histopathology Images reveals Prognostic Subgroups in Invasive Lung Adenocarcinoma Patients](https://mlsanity.com/paper/2508.16742/) (2025)
- [Morphology-Aware Prognostic model for Five-Year Survival Prediction in Colorectal Cancer from H&E Whole Slide Images](https://mlsanity.com/paper/2510.14800/) (2025)

## Abstract (arXiv)

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.