Awesome-Computational-Pathology-Papers

Last updated: Jun 2025

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💡 Background

Computational pathology combines advanced imaging techniques, deep learning algorithms, and multimodal data integration to transform traditional histopathology workflows into quantitative, scalable, and precision-oriented practices. This repository collects state-of-the-art papers (most from Nature family journals, Cell Press, Science family journals, and some top-tier conferences) highlighting significant progress in pathology foundation models, multimodal generative AI, virtual staining methods, biomarker prediction, and clinical translation. These works not only drive forward precision oncology and personalized medicine but also address fundamental challenges such as model generalizability, interpretability, demographic bias, and ethical implications, reflecting the rapidly evolving landscape of AI-driven digital pathology.

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📖 Awesome list criteria

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🗂️ Contents

• Foundation Models & Feature Engineering
• Generative Models & Virtual Staining
• Multimodal LLMs & Reasoning
• Datasets & Benchmarks
• Clinical Applications & Biomarker Prediction
• 3D / Spatial-Omics & Multimodal Imaging
• Methodology, Algorithms & Bias
• Reviews, Surveys & Perspectives

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1. Pathology & Biomedical Foundation Models / Feature-Engineering

Paper	Venue	Date	Highlight	Links
UniBiomed: A Universal Foundation Model for Grounded Biomedical Image Interpretation	arXiv	Jun 2025	Cross-modal FM covering 9 imaging modalities	[PDF]
A multimodal vision foundation model for clinical dermatology	Nat. Med.	Jun 2025	Skin-imaging FM with dermatology benchmarks	[PDF]
A foundation model for generalizable cancer diagnosis & survival prediction	Nat. Commun.	Apr 2025	End-to-end prognosis from WSIs	[PDF]
Towards A Generalizable Pathology Foundation Model via Unified Knowledge Distillation	Nat. Biomed. Eng.	Apr 2025	Knowledge-distilled FM that transfers across cohorts
Foundation models for fast, label-free detection of glioma infiltration	Nature	Feb 2025	Intra-operative FM enabling real-time tumor margining
Exploring Scalable Medical Image Encoders Beyond Text Supervision	arXiv	Feb 2025	Large-scale SSL encoders for medical images
Molecular-driven Foundation Model for Oncologic Pathology	arXiv	Jan 2025	Incorporates genomics into pathology FM pre-training
A pathology foundation model for cancer diagnosis & prognosis prediction	Nature	Oct 2024	WSI FM evaluated on 20 cancer types
Multimodal Whole-Slide Foundation Model for Pathology	arXiv	Nov 2024	Joint image–text pre-training on >10 M WSI patches
A foundation model for enhancing MR images & downstream tasks	Nat. Biomed. Eng.	Oct 2024	Diffusion-based super-resolution FM for MRI
Mapping histomorphological cancer phenotypes via self-supervised learning	Nat. Commun.	Jun 2024	No-label SSL on 2.5 M slides
A foundation model for clinical-grade computational pathology & rare-cancer detection	Nat. Med.	Jun 2024	Out-of-distribution detection of <2% incidence cancers
A whole-slide foundation model from real-world data	Nature	Jun 2024	5-B-parameter FM pre-trained on hospital WSIs
RudolfV: A Foundation Model by Pathologists for Pathologists	arXiv	Jan 2024	Expert-curated pre-training corpus

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2. Generative Models & Virtual Staining

Paper	Venue	Date	Highlight	Links
PixCell: A Generative Foundation Model for Digital Histopathology Images	arXiv	Jun 2025	Diffusion FM producing 16k×16k virtual WSIs
Pixel super-resolved virtual staining of label-free tissue using diffusion models	Nat. Commun.	Jun 2025	Sub-micron resolution synthetic stains
Self-improving generative foundation model for synthetic medical image generation	Nat. Med.	Feb 2025	Continual learning diffusion FM
Generation of synthetic WSI tiles from RNA-seq via cascaded diffusion models	Nat. Biomed. Eng.	Mar 2025	Transcriptome → histology synthesis
Learned representation-guided diffusion models for large-image generation	CVPR	Jun 2024	Generates giga-pixel imagery with memory-efficient sampling
A multimodal generative AI copilot for human pathology	Nature	Jun 2024	Image-conditioned text generation for reporting
Generative models improve fairness of medical classifiers under distribution shifts	Nat. Med.	Apr 2024	Data augmentation for bias mitigation
Virtual histological staining of unlabeled autopsy tissue	Nat. Commun.	Mar 2024	First virtual staining study on post-mortem tissue

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3. Multimodal LLMs (MLLM) & Reasoning

Paper	Venue	Date	Highlight	Links
Patho-R1: A Multimodal Reinforcement Learning-Based Pathology Expert Reasoner	arXiv	May 2025	RL-tuned agent that asks & answers slide questions
ChestX-Reasoner: Advancing Radiology Foundation Models with Step-by-Step Verification	arXiv	May 2025	Chain-of-thought verification for chest CT
VisualPRM: An Effective Process Reward Model for Multimodal Reasoning	arXiv	Mar 2025	Reward-shaping for V-L reasoning tasks
InternVL3: Training & Test-time Recipes for Open-Source MMLMs	Tech report	Apr 2025	Tricks for scaling to 4096 × 4096 inputs
Mini-InternVL: 5 % Params, 90 % Performance	Tech report	Nov 2024	Lightweight MLLM for edge deployment
In-context learning enables MLLMs to classify cancer pathology images	Nat. Commun.	Aug 2024	Zero-shot WSI classification via ICL
looongLLaVA: Scaling MLLMs to 1000 Images Efficiently	arXiv	Sep 2024	Hybrid visual memory for ultra-long contexts
Quilt-LLaVA: Instruction Tuning from Histopathology Videos	CVPR	Jun 2024	Localized narrative extraction for slide QA
SlideChat: A Large V-L Assistant for Whole-Slide Images	CVPR	Oct 2024	Dialogue-centric WSI agent with 400 k Q–A pairs
Advancing Multimodal Medical Capabilities of Gemini	Tech report	May 2024	Google Gemini medical evaluation
HuatuoGPT-Vision: Injecting Medical Visual Knowledge into MLLMs	EMNLP	Sep 2024	Bilingual (CN-EN) medical-vision MLLM
A Foundational Multimodal Vision-Language AI Assistant for Human Pathology	arXiv	Dec 2023	Early large-scale slide chatbot
A Multimodal Knowledge-enhanced Whole-Slide Pathology FM	arXiv	Aug 2024	Knowledge graph joins vision tokens
Vision–language foundation model for precision oncology	Nature	Feb 2025	V-L FM predicts biomarkers & therapy response

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4. Datasets & Benchmarks

Paper	Venue	Date	Highlight	Links
MedBookVQA: A Systematic & Comprehensive Medical VQA Benchmark	arXiv	Jun 2025	2 M Q–A pairs from open-access textbooks
PathBench: A Comparison Benchmark for Pathology Foundation Models	arXiv	May 2025	12 tasks, 30 + FMs, oncology-oriented
MEDTRINITY-25M: A Large-Scale Multimodal Dataset with Multigranular Annotations	ICLR	Feb 2025	25 M image-text pairs across 17 organs
PHARAOH: A Crowdsourcing Platform for Histology Phenotyping	Nat. Commun.	Jan 2025	50 k expert-verified ROI labels
HEST-1k: A Dataset for Spatial Transcriptomics & Histology	NeurIPS	Dec 2024	1 k paired ST–WSI samples
RadGenome-Chest CT: A Grounded V-L Dataset	arXiv	Apr 2024	Combines ROI boxes & genetic markers
WSI-VQA: Interpreting Whole-Slide Images by Generative VQA	ECCV	Jul 2024	8 k high-res slide questions

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5. Clinical Applications & Biomarker Prediction

Paper	Venue	Date	Highlight	Links
Deep learning using histological images for gene-mutation prediction in lung cancer	The Lancet	Jan 2025	Multi-centre mutation prediction study
Prediction of recurrence risk in endometrial cancer with multimodal DL	Nat. Med.	Jul 2024	Combines WSI & clinical data
Histopathologic DL classifier for platinum-response in ovarian cancer	Nat. Commun.	May 2024	Treatment-response predictor
Prediction of tumor origin in cancers of unknown primary	Nat. Med.	Apr 2024	Cytology images beat DNA panels
ANORAK improves histopathological grading of lung adenocarcinoma	Nat. Cancer	Feb 2024	AI-augmented grading workflow
Population-level digital histologic biomarker for breast-cancer prognosis	Nat. Med.	Jan 2024	1 M patient registry validation
A vision–language foundation model for precision oncology	Nature	Feb 2025	(see FM table)

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6. 3D / Spatial-Omics & Multimodal Imaging

Paper	Venue	Date	Highlight	Links
AI-driven 3D Spatial Transcriptomics	arXiv	Feb 2025	Generates 3-D ST volumes from serial sections
An end-to-end workflow for nondestructive 3-D pathology	Nat. Protocols	Apr 2024	Clears, images & analyses thick tissue

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7. Methodology, Algorithms & Bias

Paper	Venue	Date	Highlight	Links
Do Multiple Instance Learning Models Transfer?	ICML	Jun 2025	Large-scale MIL transferability study
Vision Transformers Need Registers	ICLR	Jun 2024	Architectural tweak boosting ViT convergence
Demographic bias of expert-level V-L foundation models in medical imaging	Sci. Adv.	Mar 2025	Finds systematic under-performance on minorities
Demographic bias in misdiagnosis by computational pathology models	Nat. Med.	Feb 2024	Patient-level bias audit across 4 cohorts

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8. Reviews, Surveys & Perspectives

Paper	Venue	Date	Highlight	Links
Artificial intelligence in digital pathology — time for a reality check	Nat. Rev. Clin. Oncol.	Apr 2025	Critical appraisal of deployment hurdles
Foundation Models – A Panacea for AI in Pathology?	arXiv	Feb 2025	Opportunities & pitfalls of pathology FMs
Multi-Modal Foundation Models for Computational Pathology: A Survey	arXiv	Mar 2025	Catalogues 60 + MLLM/FMs
Generative Models in Computational Pathology: A Comprehensive Survey	arXiv	May 2025	End-to-end review of diffusion & GANs
A Survey of Pathology Foundation Models: Progress & Future Directions	IJCAI	Apr 2025	Taxonomy & benchmark summary
Data-Centric Foundation Models in Computational Healthcare	arXiv	Nov 2024	Argues for data-quality over model size
A Guide to AI for Cancer Researchers	Nat. Rev. Cancer	Jun 2024	Plain-language intro for oncologists
A New Era in Computational Pathology: Survey on FM & V-L Models	arXiv	Sep 2024	Early holistic survey
A systematic review on MLLMs in computational pathology	arXiv	Jan 2025	Focused on slide-level V-L models
A Clinical Benchmark of Public Self-Supervised Pathology FMs	Nat. Commun.	Apr 2025	Head-to-head evaluation of 15 SSL models
Multimodal Generative AI for Medical Image Interpretation (Perspective)	Nature	Mar 2025	Outlook on Gen-AI regulators & ethics

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🧑‍💻 Contributing

If you would like to contribute, please read the contribution guidelines and submit a pull request. If you find some ignored papers, feel free to create pull requests, or open issues. Contributions in any form to make this list more comprehensive are welcome. 📣📣📣