# From Macro to Micro: Benchmarking Microscopic Spatial Intelligence on Molecules via Vision-Language Models

arXiv: https://arxiv.org/abs/2512.10867 · HTML: https://mlsanity.com/paper/2512.10867/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Chart understanding and anomaly detection, one of 16 directions in Multimodal LLMs / vision-language models.
- Builds on 26 of its 50 references that are in the map.
- First posted on arXiv 11 Dec 2025.

## Placed in

- Multimodal LLMs / vision-language models / [Chart understanding and anomaly detection](https://mlsanity.com/mllm/chart-understanding-and-anomaly-detection/)

## Builds on (most cited first, 26 of 26)

- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [Gemini 2.5: Pushing the Frontier with Advanced Reasoning, Multimodality, Long Context, and Next Generation Agentic Capabilities](https://mlsanity.com/paper/2507.06261/) (2025)
- [LLaVA-OneVision: Easy Visual Task Transfer](https://mlsanity.com/paper/2408.03326/) (2024)
- [MMMU: A Massive Multi-discipline Multimodal Understanding and Reasoning Benchmark for Expert AGI](https://mlsanity.com/paper/2311.16502/) (2023)
- [Video-MME: The First-Ever Comprehensive Evaluation Benchmark of Multi-modal LLMs in Video Analysis](https://mlsanity.com/paper/2405.21075/) (2024)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [SpatialVLM: Endowing Vision-Language Models with Spatial Reasoning Capabilities](https://mlsanity.com/paper/2401.12168/) (2024)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Thinking in Space: How Multimodal Large Language Models See, Remember, and Recall Spaces](https://mlsanity.com/paper/2412.14171/) (2024)
- [LLaVA-NeXT-Interleave: Tackling Multi-image, Video, and 3D in Large Multimodal Models](https://mlsanity.com/paper/2407.07895/) (2024)
- [BLINK: Multimodal Large Language Models Can See but Not Perceive](https://mlsanity.com/paper/2404.12390/) (2024)
- [MuirBench: A Comprehensive Benchmark for Robust Multi-image Understanding](https://mlsanity.com/paper/2406.09411/) (2024)
- [From Flatland to Space: Teaching Vision-Language Models to Perceive and Reason in 3D](https://mlsanity.com/paper/2503.22976/) (2025)
- [Reinforcing Spatial Reasoning in Vision-Language Models with Interwoven Thinking and Visual Drawing](https://mlsanity.com/paper/2506.09965/) (2025)
- [MindCube: Spatial Mental Modeling from Limited Views](https://mlsanity.com/paper/2506.21458/) (2025)
- [Conditional Antibody Design as 3D Equivariant Graph Translation](https://mlsanity.com/paper/2208.06073/) (2022)
- [ATOM3D: Tasks On Molecules in Three Dimensions](https://mlsanity.com/paper/2012.04035/) (2020)
- [OneThinker: All-in-one Reasoning Model for Image and Video](https://mlsanity.com/paper/2512.03043/) (2025)
- [LEGO-Puzzles: How Good Are MLLMs at Multi-Step Spatial Reasoning?](https://mlsanity.com/paper/2503.19990/) (2025)
- [Embodied-R: Collaborative Framework for Activating Embodied Spatial Reasoning in Foundation Models via Reinforcement Learning](https://mlsanity.com/paper/2504.12680/) (2025)
- [DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening](https://mlsanity.com/paper/2310.06367/) (2023)
- [Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning](https://mlsanity.com/paper/2306.01474/) (2023)
- [Structure-based drug design by denoising voxel grids](https://mlsanity.com/paper/2405.03961/) (2024)
- [Towards Foundation Models for 3D Vision: How Close Are We?](https://mlsanity.com/paper/2410.10799/) (2024)
- [An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning](https://mlsanity.com/paper/2402.12714/) (2024)

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

- [Beyond Semantic Search: Towards Referential Anchoring in Composed Image Retrieval](https://mlsanity.com/paper/2604.05393/) (2026)

## Abstract (arXiv)

This paper introduces the concept of Microscopic Spatial Intelligence (MiSI), the capability to perceive and reason about the spatial relationships of invisible microscopic entities, which is fundamental to scientific discovery. To assess the potential of Vision-Language Models (VLMs) in this domain, we propose a systematic benchmark framework MiSI-Bench. This framework features over 163,000 question-answer pairs and 587,000 images derived from approximately 4,000 molecular structures, covering nine complementary tasks that evaluate abilities ranging from elementary spatial transformations to complex relational identifications. Experimental results reveal that current state-of-the-art VLMs perform significantly below human level on this benchmark. However, a fine-tuned 7B model demonstrates substantial potential, even surpassing humans in spatial transformation tasks, while its poor performance in scientifically-grounded tasks like hydrogen bond recognition underscores the necessity of integrating explicit domain knowledge for progress toward scientific AGI. The datasets are available at https://huggingface.co/datasets/zongzhao/MiSI-bench.