# MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research

arXiv: https://arxiv.org/abs/2503.13399 · HTML: https://mlsanity.com/paper/2503.13399/

## Key facts

- Cited by 32 papers in the map (data through 14 Oct 2026).
- Placed in Multimodal reasoning, one of 17 directions in LLM reasoning.
- Builds on 50 of its 96 references that are in the map.
- First posted on arXiv 17 Mar 2025.

## Placed in

- LLM reasoning / [Multimodal reasoning](https://mlsanity.com/lr/multimodal-reasoning/)

## Builds on (most cited first, 30 of 50)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [GPQA: A Graduate-Level Google-Proof Q&A Benchmark](https://mlsanity.com/paper/2311.12022/) (2023)
- [MMLU-Pro: A More Robust and Challenging Multi-Task Language Understanding Benchmark](https://mlsanity.com/paper/2406.01574/) (2024)
- [MME: A Comprehensive Evaluation Benchmark for Multimodal Large Language Models](https://mlsanity.com/paper/2306.13394/) (2023)
- [MathVista: Evaluating Mathematical Reasoning of Foundation Models in Visual Contexts](https://mlsanity.com/paper/2310.02255/) (2023)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [OpenAI o1 System Card](https://mlsanity.com/paper/2412.16720/) (2024)
- [Large Language Monkeys: Scaling Inference Compute with Repeated Sampling](https://mlsanity.com/paper/2407.21787/) (2024)
- [Gemini: A Family of Highly Capable Multimodal Models](https://mlsanity.com/paper/2312.11805/) (2023)
- [Cambrian-1: A Fully Open, Vision-Centric Exploration of Multimodal LLMs](https://mlsanity.com/paper/2406.16860/) (2024)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)
- [BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs](https://mlsanity.com/paper/2303.00915/) (2023)
- [MMMU-Pro: A More Robust Multi-discipline Multimodal Understanding Benchmark](https://mlsanity.com/paper/2409.02813/) (2024)
- [PathVQA: 30000+ Questions for Medical Visual Question Answering](https://mlsanity.com/paper/2003.10286/) (2020)
- [Accelerating scientific discovery with Co-Scientist](https://mlsanity.com/paper/2502.18864/) (2025)
- [Demonstrate-Search-Predict: Composing retrieval and language models for knowledge-intensive NLP](https://mlsanity.com/paper/2212.14024/) (2022)
- [Abductive Commonsense Reasoning](https://mlsanity.com/paper/1908.05739/) (2019)
- [SciBench: Evaluating College-Level Scientific Problem-Solving Abilities of Large Language Models](https://mlsanity.com/paper/2307.10635/) (2023)
- [Capabilities of Gemini Models in Medicine](https://mlsanity.com/paper/2404.18416/) (2024)
- [MMT-Bench: A Comprehensive Multimodal Benchmark for Evaluating Large Vision-Language Models Towards Multitask AGI](https://mlsanity.com/paper/2404.16006/) (2024)
- [MuirBench: A Comprehensive Benchmark for Robust Multi-image Understanding](https://mlsanity.com/paper/2406.09411/) (2024)
- [Pixtral 12B](https://mlsanity.com/paper/2410.07073/) (2024)
- [SciCode: A Research Coding Benchmark Curated by Scientists](https://mlsanity.com/paper/2407.13168/) (2024)
- [LAB-Bench: Measuring Capabilities of Language Models for Biology Research](https://mlsanity.com/paper/2407.10362/) (2024)
- [Multimodal ArXiv: A Dataset for Improving Scientific Comprehension of Large Vision-Language Models](https://mlsanity.com/paper/2403.00231/) (2024)
- [Language agents achieve superhuman synthesis of scientific knowledge](https://mlsanity.com/paper/2409.13740/) (2024)
- [Exploring the Reasoning Abilities of Multimodal Large Language Models (MLLMs): A Comprehensive Survey on Emerging Trends in Multimodal Reasoning](https://mlsanity.com/paper/2401.06805/) (2024)
- [HelpSteer2-Preference: Complementing Ratings with Preferences](https://mlsanity.com/paper/2410.01257/) (2024)

## Built on by (most cited first, 30 of 32)

- [WebWatcher: Breaking New Frontier of Vision-Language Deep Research Agent](https://mlsanity.com/paper/2508.05748/) (2025)
- [Perception, Reason, Think, and Plan: A Survey on Large Multimodal Reasoning Models](https://mlsanity.com/paper/2505.04921/) (2025)
- [MIRAGE: The Illusion of Visual Understanding](https://mlsanity.com/paper/2603.21687/) (2026)
- [Intern-S1: A Scientific Multimodal Foundation Model](https://mlsanity.com/paper/2508.15763/) (2025)
- [Gemini Embedding 2: A Native Multimodal Embedding Model from Gemini](https://mlsanity.com/paper/2605.27295/) (2026)
- [LingoLoop Attack: Trapping MLLMs via Linguistic Context and State Entrapment into Endless Loops](https://mlsanity.com/paper/2506.14493/) (2025)
- [Innovator-VL: A Multimodal Large Language Model for Scientific Discovery](https://mlsanity.com/paper/2601.19325/) (2026)
- [Mirage Probes: How Vision Models Fake Visual Understanding](https://mlsanity.com/paper/2606.13870/) (2026)
- [MEDVISTAGYM: A Scalable Training Environment for Thinking with Medical Images via Tool-Integrated Reinforcement Learning](https://mlsanity.com/paper/2601.07107/) (2026)
- [MechVQA: Benchmarking and Enhancing Multimodal LLMs on Comprehensive Mechanical Drawing Understanding](https://mlsanity.com/paper/2605.30794/) (2026)
- [Domain Specific Benchmarks for Evaluating Multimodal Large Language Models](https://mlsanity.com/paper/2506.12958/) (2025)
- [SimulRAG: Simulator-based RAG for Grounding LLMs in Long-form Scientific QA](https://mlsanity.com/paper/2509.25459/) (2025)
- [UNICBench: UNIfied Counting Benchmark for MLLM](https://mlsanity.com/paper/2603.00595/) (2026)
- [MMBU: A Massive Multi-modal Biomedical Understanding Benchmark to Probe the Perception Capabilities of Vision-Language Models](https://mlsanity.com/paper/2606.06696/) (2026)
- [A Large-Scale Vision-Language Dataset Derived from Open Scientific Literature to Advance Biomedical Generalist AI](https://mlsanity.com/paper/2503.22727/) (2025)
- [EM3M: An Electron Micrograph Dataset for Microstructural Segmentation and Generation](https://mlsanity.com/paper/2508.16239/) (2025)
- [Agentic-J: An AI Agent for Biological Microscopy Image Analysis](https://mlsanity.com/paper/2606.02080/) (2026)
- [The Impact of Image Resolution on Biomedical Multimodal Large Language Models](https://mlsanity.com/paper/2510.18304/) (2025)
- [Maestro: Reinforcement Learning to Orchestrate Hierarchical Model-Skill Ensembles](https://mlsanity.com/paper/2605.22177/) (2026)
- [AWARe: Mitigating Catastrophic Forgetting via Activation-Weighted Adaptive REtention](https://mlsanity.com/paper/2608.11758/) (2026)
- [OmniScientist: An Omni-Modal Omni-Discipline AI Scientist](https://mlsanity.com/paper/2608.13558/) (2026)
- [Adapting Open-Weight MLLMs to Generate Point Prompts for Electron Microscopy Segmentation](https://mlsanity.com/paper/2609.14080/) (2026)
- [MEDSYN: Benchmarking Multi-EviDence SYNthesis in Complex Clinical Cases for Multimodal Large Language Models](https://mlsanity.com/paper/2602.21950/) (2026)
- [MicroWorld: Empowering Multimodal Large Language Models to Bridge the Microscopic Domain Gap with Multimodal Attribute Graph](https://mlsanity.com/paper/2605.10120/) (2026)
- [MatPhaseBench: A Semantics-Guided Benchmark for Materials Phase Diagrams Understanding](https://mlsanity.com/paper/2607.02934/) (2026)
- [What Transfers from Text to Vision? Capability Scaling Laws and Transfer Dynamics for VLMs](https://mlsanity.com/paper/2608.00013/) (2026)
- [VIALS: A Benchmark for Visual Interpretation of Artifacts in the Life Sciences](https://mlsanity.com/paper/2608.21357/) (2026)
- [ManGo: Manga Active Narrative Grounding Optimization](https://mlsanity.com/paper/2608.29865/) (2026)
- [Spatial Action Review: A Visual Analytics Dashboard for Auditing Language-to-Action Hand-offs in Electron Microscopy](https://mlsanity.com/paper/2609.24470/) (2026)
- [BIABench: Evaluating AI agents on real-world bioimage analysis tasks](https://mlsanity.com/paper/2609.34274/) (2026)

## Abstract (arXiv)

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology. Despite recent advances in multimodal large language models (MLLMs) for AI-assisted research, existing multimodal reasoning benchmarks only target up to college-level difficulty, while research-level benchmarks emphasize lower-level perception, falling short of the complex multimodal reasoning needed for scientific discovery. To bridge this gap, we introduce MicroVQA, a visual-question answering (VQA) benchmark designed to assess three reasoning capabilities vital in research workflows: expert image understanding, hypothesis generation, and experiment proposal. MicroVQA consists of 1,042 multiple-choice questions (MCQs) curated by biology experts across diverse microscopy modalities, ensuring VQA samples represent real scientific practice. In constructing the benchmark, we find that standard MCQ generation methods induce language shortcuts, motivating a new two-stage pipeline: an optimized LLM prompt structures question-answer pairs into MCQs; then, an agent-based `RefineBot' updates them to remove shortcuts. Benchmarking on state-of-the-art MLLMs reveal a peak performance of 53%; models with smaller LLMs only slightly underperform top models, suggesting that language-based reasoning is less challenging than multimodal reasoning; and tuning with scientific articles enhances performance. Expert analysis of chain-of-thought responses shows that perception errors are the most frequent, followed by knowledge errors and then overgeneralization errors. These insights highlight the challenges in multimodal scientific reasoning, showing MicroVQA is a valuable resource advancing AI-driven biomedical research. MicroVQA is available at https://huggingface.co/datasets/jmhb/microvqa, and project page at https://jmhb0.github.io/microvqa.