# Enhancing Spatial Reasoning in Large Language Models for Metal-Organic Frameworks Structure Prediction

arXiv: https://arxiv.org/abs/2601.09285 · HTML: https://mlsanity.com/paper/2601.09285/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 16 of its 52 references that are in the map.
- First posted on arXiv 14 Jan 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 16 of 16)

- [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)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [DeepSeek-V3 Technical Report](https://mlsanity.com/paper/2412.19437/) (2024)
- [SWIFT:A Scalable lightWeight Infrastructure for Fine-Tuning](https://mlsanity.com/paper/2408.05517/) (2024)
- [Large Language Model Alignment: A Survey](https://mlsanity.com/paper/2309.15025/) (2023)
- [Soft Adaptive Policy Optimization](https://mlsanity.com/paper/2511.20347/) (2025)
- [LLaMA-Mesh: Unifying 3D Mesh Generation with Language Models](https://mlsanity.com/paper/2411.09595/) (2024)
- [Orb: A Fast, Scalable Neural Network Potential](https://mlsanity.com/paper/2410.22570/) (2024)
- [System of Agentic AI for the Discovery of Metal-Organic Frameworks](https://mlsanity.com/paper/2504.14110/) (2025)
- [PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design](https://mlsanity.com/paper/2509.07150/) (2025)
- [Flexible MOF Generation with Torsion-Aware Flow Matching](https://mlsanity.com/paper/2505.17914/) (2025)
- [AtomWorld: A Benchmark for Evaluating Spatial Reasoning in Large Language Models on Crystalline Materials](https://mlsanity.com/paper/2510.04704/) (2025)

## Abstract (arXiv)

Metal-organic frameworks (MOFs) are porous crystalline materials with broad applications such as carbon capture and drug delivery, yet accurately predicting their 3D structures remains a significant challenge. While Large Language Models (LLMs) have shown promise in generating crystal structures, their application to MOFs is hindered by MOFs' high structural complexity arising from the large number of atoms in unit cell. Inspired by the success of block-wise paradigms in deep generative models for MOFs, we pioneer the application of LLMs in this domain by introducing MOF-LLM, the first LLM framework specifically adapted for block-level MOF structure prediction. To effectively harness LLMs for this 3D modular assembly task, our training paradigm integrates spatial-aware continual pre-training (CPT), structural supervised fine-tuning (SFT), and matching-driven reinforcement learning (RL). By incorporating explicit spatial priors and optimizing structural stability via Soft Adaptive Policy Optimization (SAPO), our approach substantially enhances the spatial reasoning in a Qwen-3 8B model for MOF structure prediction. Comprehensive experiments demonstrate that MOF-LLM achieves state-of-the-art performance with a match rate of 35.78% while exhibiting superior sampling efficiency of 0.04 seconds per structure.