# SpectraLLM: Uncovering the Ability of LLMs for Molecular Structure Elucidation from Multi-Spectral Data

arXiv: https://arxiv.org/abs/2508.08441 · HTML: https://mlsanity.com/paper/2508.08441/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 93 references that are in the map.
- First posted on arXiv 4 Aug 2025.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation](https://mlsanity.com/paper/1406.1078/) (2014)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [On the Properties of Neural Machine Translation: Encoder-Decoder Approaches](https://mlsanity.com/paper/1409.1259/) (2014)
- [A Survey on Visual Transformer](https://mlsanity.com/paper/2012.12556/) (2020)
- [Transformer in Transformer](https://mlsanity.com/paper/2103.00112/) (2021)
- [An Introduction to Convolutional Neural Networks](https://mlsanity.com/paper/1511.08458/) (2015)
- [A Survey of Convolutional Neural Networks: Analysis, Applications, and Prospects](https://mlsanity.com/paper/2004.02806/) (2020)
- [Retrosynthetic reaction prediction using neural sequence-to-sequence models](https://mlsanity.com/paper/1706.01643/) (2017)
- [Spectral Representations for Convolutional Neural Networks](https://mlsanity.com/paper/1506.03767/) (2015)
- [MassSpecGym: A benchmark for the discovery and identification of molecules](https://mlsanity.com/paper/2410.23326/) (2024)
- [DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra](https://mlsanity.com/paper/2502.09571/) (2025)
- [Unraveling Molecular Structure: A Multimodal Spectroscopic Dataset for Chemistry](https://mlsanity.com/paper/2407.17492/) (2024)
- [MolTC: Towards Molecular Relational Modeling In Language Models](https://mlsanity.com/paper/2402.03781/) (2024)
- [Accurate and efficient structure elucidation from routine one-dimensional NMR spectra using multitask machine learning](https://mlsanity.com/paper/2408.08284/) (2024)
- [MutaGAN: A Seq2seq GAN Framework to Predict Mutations of Evolving Protein Populations](https://mlsanity.com/paper/2008.11790/) (2020)

## Built on by (most cited first, 3 of 3)

- [General Intelligence-based Fragmentation (GIF): A framework for peak-labeled spectra simulation](https://mlsanity.com/paper/2511.09571/) (2025)
- [S3C-LLM: Skill-Code Guided Agentic Language Models for Spectrum-to-Structure Elucidation](https://mlsanity.com/paper/2608.30910/) (2026)
- [MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure?](https://mlsanity.com/paper/2610.12522/) (2026)

## Abstract (arXiv)

Automated molecular structure elucidation remains challenging, as existing approaches often depend on pre-compiled databases or restrict themselves to single spectroscopic modalities. Here we introduce SpectraLLM, a large language model that performs end-to-end structure prediction by reasoning over one or multiple spectra. Unlike conventional spectrum-to-structure pipelines, SpectraLLM represents both continuous (IR, Raman, UV-Vis, NMR) and discrete (MS) modalities in a shared language space, enabling it to capture substructural patterns that are complementary across different spectral types. We pretrain and fine-tune the model on small-molecule domains and evaluate it on four public benchmark datasets. SpectraLLM achieves state-of-the-art performance, substantially surpassing single-modality baselines. Moreover, it demonstrates strong robustness in unimodal settings and further improves prediction accuracy when jointly reasoning over diverse spectra, establishing a scalable paradigm for language-based spectroscopic analysis. Code is available at https://github.com/OPilgrim/SpectraLLM.