# WSI-VQA: Interpreting Whole Slide Images by Generative Visual Question Answering

arXiv: https://arxiv.org/abs/2407.05603 · HTML: https://mlsanity.com/paper/2407.05603/

## Key facts

- Cited by 34 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 39 references that are in the map.
- First posted on arXiv 8 Jul 2024.

## Builds on (most cited first, 25 of 25)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [The Dawn of LMMs: Preliminary Explorations with GPT-4V(ision)](https://mlsanity.com/paper/2309.17421/) (2023)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering](https://mlsanity.com/paper/2305.10415/) (2023)
- [DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification](https://mlsanity.com/paper/2203.12081/) (2022)
- [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](https://mlsanity.com/paper/2303.07240/) (2023)
- [Improving Factual Completeness and Consistency of Image-to-Text Radiology Report Generation](https://mlsanity.com/paper/2010.10042/) (2020)
- [Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images](https://mlsanity.com/paper/2306.07831/) (2023)
- [Multi-Modal Masked Autoencoders for Medical Vision-and-Language Pre-Training](https://mlsanity.com/paper/2209.07098/) (2022)
- [Multiple Instance Captioning: Learning Representations from Histopathology Textbooks and Articles](https://mlsanity.com/paper/2103.05121/) (2021)
- [Towards a Visual-Language Foundation Model for Computational Pathology](https://mlsanity.com/paper/2307.12914/) (2023)
- [SlideGraph+: Whole Slide Image Level Graphs to Predict HER2Status in Breast Cancer](https://mlsanity.com/paper/2110.06042/) (2021)
- [HEROHE Challenge: assessing HER2 status in breast cancer without immunohistochemistry or in situ hybridization](https://mlsanity.com/paper/2111.04738/) (2021)

## Built on by (most cited first, 30 of 34)

- [SlideChat: A Large Vision-Language Assistant for Whole-Slide Pathology Image Understanding](https://mlsanity.com/paper/2410.11761/) (2024)
- [WSI-LLaVA: A Multimodal Large Language Model for Whole Slide Image](https://mlsanity.com/paper/2412.02141/) (2024)
- [CPath-Omni: A Unified Multimodal Foundation Model for Patch and Whole Slide Image Analysis in Computational Pathology](https://mlsanity.com/paper/2412.12077/) (2024)
- [CPathAgent: An Agent-based Foundation Model for Interpretable High-Resolution Pathology Image Analysis Mimicking Pathologists' Diagnostic Logic](https://mlsanity.com/paper/2505.20510/) (2025)
- [A New Era in Computational Pathology: A Survey on Foundation and Vision-Language Models](https://mlsanity.com/paper/2408.14496/) (2024)
- [Multi-Modal Foundation Models for Computational Pathology: A Survey](https://mlsanity.com/paper/2503.09091/) (2025)
- [Cost-effective Instruction Learning for Pathology Vision and Language Analysis](https://mlsanity.com/paper/2407.17734/) (2024)
- [Navigating Gigapixel Pathology Images with Large Multimodal Models](https://mlsanity.com/paper/2511.19652/) (2025)
- [PathNavigate: A Training-Free Pathology Agent with Surprise-Guided Scan and Shared Slide Memory for Whole-Slide Image VQA](https://mlsanity.com/paper/2605.23559/) (2026)
- [Efficient Whole Slide Pathology VQA via Token Compression](https://mlsanity.com/paper/2507.14497/) (2025)
- [Content Generation Models in Computational Pathology: A Comprehensive Survey on Methods, Applications, and Challenges](https://mlsanity.com/paper/2505.10993/) (2025)
- [Act Like a Pathologist: Tissue-Aware Whole Slide Image Reasoning](https://mlsanity.com/paper/2603.00667/) (2026)
- [Beyond Pixel Simulation: Pathology Image Generation via Diagnostic Semantic Tokens and Prototype Control](https://mlsanity.com/paper/2512.21058/) (2025)
- [QCAgent: An agentic framework for quality-controllable pathology report generation from whole slide image](https://mlsanity.com/paper/2603.01647/) (2026)
- [ChatEXAONEPath: An Expert-level Multimodal Large Language Model for Histopathology Using Whole Slide Images](https://mlsanity.com/paper/2504.13023/) (2025)
- [MLLM-HWSI: A Multimodal Large Language Model for Hierarchical Whole Slide Image Understanding](https://mlsanity.com/paper/2603.23067/) (2026)
- [Enhancing Pathological VLMs with Cross-scale Reasoning](https://mlsanity.com/paper/2606.17412/) (2026)
- [PathSelect: Sequential Token Selection for Whole Slide Pathology](https://mlsanity.com/paper/2607.23631/) (2026)
- [The Impact of Image Resolution on Biomedical Multimodal Large Language Models](https://mlsanity.com/paper/2510.18304/) (2025)
- [CTIS-QA: Clinical Template-Informed Slide-level Question Answering for Pathology](https://mlsanity.com/paper/2601.01769/) (2026)
- [PathMem: Toward Cognition-Aligned Memory Transformation for Pathology MLLMs](https://mlsanity.com/paper/2603.09943/) (2026)
- [Towards Clinically Interpretable Ophthalmic VQA via Spatially-Grounded Lesion Evidence](https://mlsanity.com/paper/2605.22414/) (2026)
- [Auditing Data Leakage in Whole-Slide Image Multimodal Benchmarks](https://mlsanity.com/paper/2607.12278/) (2026)
- [Agentic Visual Reasoning in Whole-Slide Pathology Images via Active Perception](https://mlsanity.com/paper/2608.08648/) (2026)
- [SlideBank: A Persistent Hierarchical Evidence Bank for Consistent Whole-Slide Reasoning](https://mlsanity.com/paper/2609.00342/) (2026)
- [Efficient and Comprehensive Feature Extraction in Large Vision-Language Model for Pathology Analysis](https://mlsanity.com/paper/2412.09521/) (2024)
- [VGAT: A Cancer Survival Analysis Framework Transitioning from Generative Visual Question Answering to Genomic Reconstruction](https://mlsanity.com/paper/2503.19367/) (2025)
- [PathReasoning: A multimodal reasoning agent for query-based ROI navigation on whole-slide images](https://mlsanity.com/paper/2511.21902/) (2025)
- [Bayesian Integration of Nonlinear Incomplete Clinical Data](https://mlsanity.com/paper/2602.01924/) (2026)
- [PBSBench: A Multi-Level Vision-Language Framework and Benchmark for Hematopathology Whole Slide Image Interpretation](https://mlsanity.com/paper/2604.17570/) (2026)

## Abstract (arXiv)

Whole slide imaging is routinely adopted for carcinoma diagnosis and prognosis. Abundant experience is required for pathologists to achieve accurate and reliable diagnostic results of whole slide images (WSI). The huge size and heterogeneous features of WSIs make the workflow of pathological reading extremely time-consuming. In this paper, we propose a novel framework (WSI-VQA) to interpret WSIs by generative visual question answering. WSI-VQA shows universality by reframing various kinds of slide-level tasks in a question-answering pattern, in which pathologists can achieve immunohistochemical grading, survival prediction, and tumor subtyping following human-machine interaction. Furthermore, we establish a WSI-VQA dataset which contains 8672 slide-level question-answering pairs with 977 WSIs. Besides the ability to deal with different slide-level tasks, our generative model which is named Wsi2Text Transformer (W2T) outperforms existing discriminative models in medical correctness, which reveals the potential of our model to be applied in the clinical scenario. Additionally, we also visualize the co-attention mapping between word embeddings and WSIs as an intuitive explanation for diagnostic results. The dataset and related code are available at https://github.com/cpystan/WSI-VQA.