# MAST: Motif-Augmented Diffusion with Search Tree for Spectroscopic Molecular Structure Elucidation

arXiv: https://arxiv.org/abs/2610.12067 · HTML: https://mlsanity.com/paper/2610.12067/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 54 references that are in the map.
- First posted on arXiv 8 Oct 2026.

## Builds on (most cited first, 20 of 20)

- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Scaling LLM Test-Time Compute Optimally can be More Effective than Scaling Model Parameters](https://mlsanity.com/paper/2408.03314/) (2024)
- [Decoupled Weight Decay Regularization](https://mlsanity.com/paper/1711.05101/) (2017)
- [Large Language Monkeys: Scaling Inference Compute with Repeated Sampling](https://mlsanity.com/paper/2407.21787/) (2024)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Inference Scaling Laws: An Empirical Analysis of Compute-Optimal Inference for Problem-Solving with Language Models](https://mlsanity.com/paper/2408.00724/) (2024)
- [Mulberry: Empowering MLLM with o1-like Reasoning and Reflection via Collective Monte Carlo Tree Search](https://mlsanity.com/paper/2412.18319/) (2024)
- [Accessing GPT-4 level Mathematical Olympiad Solutions via Monte Carlo Tree Self-refine with LLaMa-3 8B](https://mlsanity.com/paper/2406.07394/) (2024)
- [Mutual Reasoning Makes Smaller LLMs Stronger Problem-Solvers](https://mlsanity.com/paper/2408.06195/) (2024)
- [MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation](https://mlsanity.com/paper/2305.07508/) (2023)
- [DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra](https://mlsanity.com/paper/2502.09571/) (2025)
- [Think More, Hallucinate Less: Mitigating Hallucinations via Dual Process of Fast and Slow Thinking](https://mlsanity.com/paper/2501.01306/) (2025)
- [Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation](https://mlsanity.com/paper/2305.12347/) (2023)
- [MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra](https://mlsanity.com/paper/2502.16284/) (2025)
- [ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search](https://mlsanity.com/paper/2506.00925/) (2025)
- [DiffSpectra: Molecular Structure Elucidation from Spectra using Diffusion Models](https://mlsanity.com/paper/2507.06853/) (2025)
- [Boosting LLM's Molecular Structure Elucidation with Knowledge Enhanced Tree Search Reasoning](https://mlsanity.com/paper/2506.23056/) (2025)

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

- [Masked Diffusion Language Agents for Tool-Integrated Chemical Reasoning](https://mlsanity.com/paper/2610.13330/) (2026)

## Abstract (arXiv)

Elucidating molecular structures from spectra is a foundational problem in chemical and materials characterization, yet remains challenging due to spectral ambiguity and the vast molecular space. Although recent diffusion-based generators show strong promise for spectra-conditioned elucidation, existing methods struggle to learn robust spectra-structure relationships from limited paired data when relying solely on global spectral representation. Moreover, the repeated full sampling inference strategy incurs substantial computation overhead. To address these limitations, we propose MAST, a Motif-Augmented diffusion framework with Search Tree, for joint 2D-3D spectroscopic molecular structure elucidation. MAST introduces explicit, interpretable motif priors as intermediate evidences throughout denoising, reducing conditional ambiguity and facilitating spectra-conditioned optimization. We further cast diffusion sampling as reward-guided tree search to prioritize high-reward denoising trajectories, yielding a compact set of spectra-consistent candidates under limited budgets. On the QM9S multi-spectra benchmark, MAST achieves 94.89% exact recovery and improves 3D fidelity, while preserving high chemical validity and stability. Code is available at https://github.com/Jia040223/MAST.