# MicroVQA++: High-Quality Microscopy Reasoning Dataset with Weakly Supervised Graphs for Multimodal Large Language Model

arXiv: https://arxiv.org/abs/2511.11407 · HTML: https://mlsanity.com/paper/2511.11407/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 17 of its 56 references that are in the map.
- First posted on arXiv 14 Nov 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- Multimodal LLMs / vision-language models / [Medical vision-language models](https://mlsanity.com/mllm/medical-vision-language-models/)

## Builds on (most cited first, 17 of 17)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [InternVL3.5: Advancing Open-Source Multimodal Models in Versatility, Reasoning, and Efficiency](https://mlsanity.com/paper/2508.18265/) (2025)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [OpenAI o1 System Card](https://mlsanity.com/paper/2412.16720/) (2024)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs](https://mlsanity.com/paper/2303.00915/) (2023)
- [MMAD: A Comprehensive Benchmark for Multimodal Large Language Models in Industrial Anomaly Detection](https://mlsanity.com/paper/2410.09453/) (2024)
- [Distractor Generation in Multiple-Choice Tasks: A Survey of Methods, Datasets, and Evaluation](https://mlsanity.com/paper/2402.01512/) (2024)
- [Open-PMC-18M: A High-Fidelity Large Scale Medical Dataset for Multimodal Representation Learning](https://mlsanity.com/paper/2506.02738/) (2025)

## Built on by (most cited first, 1 of 1)

- [NeuroQA: A Large-Scale Image-Grounded Benchmark for 3D Brain MRI Understanding](https://mlsanity.com/paper/2605.20525/) (2026)

## Abstract (arXiv)

Multimodal Large Language Models are increasingly applied to biomedical imaging, yet scientific reasoning for microscopy remains limited by the scarcity of large-scale, high-quality training data. We introduce MicroVQA++, a three-stage, large-scale and high-quality microscopy VQA corpus derived from the BIOMEDICA archive. Stage one bootstraps supervision from expert-validated figure-caption pairs sourced from peer-reviewed articles. Stage two applies HiCQA-Graph, a novel heterogeneous graph over images, captions, and QAs that fuses NLI-based textual entailment, CLIP-based vision-language alignment, and agent signals to identify and filter inconsistent samples. Stage three uses a MultiModal Large Language Model (MLLM) agent to generate multiple-choice questions (MCQ) followed by human screening. The resulting release comprises a large training split and a human-checked test split whose Bloom's level hard-sample distribution exceeds the MicroVQA benchmark. Our work delivers (i) a quality-controlled dataset that couples expert literature with graph-based filtering and human refinement; (ii) HiCQA-Graph, the first graph that jointly models (image, caption, QA) for cross-modal consistency filtering; (iii) evidence that careful data construction enables 4B-scale MLLMs to reach competitive microscopy reasoning performance (e.g., GPT-5) and achieve state-of-the-art performance among open-source MLLMs. Code and dataset will be released after the review process concludes.