Developing ChemMLLM as a multimodal large language model for chemistry
Source abstract
Abstract
Recent years have seen rapid progress in multimodal large language models (MLLMs) in the field of chemistry. However, chemical MLLMs capable of handling cross-modal understanding and generation remain underexplored. To fill this gap, we propose ChemMLLM, a unified chemical MLLM for molecule understanding and generation. In this work, we design five types of multimodal tasks across text, molecular simplified molecular input line entry system (SMILES) strings, and images and curate the datasets. We benchmark ChemMLLM against a range of general leading MLLMs, chemical LLMs, and specialized models on these tasks. Experimental results demonstrate the feasibility of a unified multimodal interface. Our work extends the capabilities of chemical MLLMs to the realm of image generation, demonstrating the feasibility of unifying multiple cross-modal chemical tasks within a single mode l and enabling more intuitive, visual human-artificial intelligence (AI) interaction.
Source: openalex_inverted_index · Quality: baseline
Research context
OpenAlex topics: Machine Learning in Materials Science · Biomedical Text Mining and Ontologies · Computational Drug Discovery Methods
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (57)
Show source-provided references
1. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules10.1021/ci00057a005 ↗
2. MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation10.1021/acs.jcim.2c01480 ↗
3. Multi-modal molecule structure–text model for text-based retrieval and editing10.1038/s42256-023-00759-6 ↗
4. Translation between molecules and natural language
5. Enhancing activity prediction models in drug discovery with the ability to understand human language
6. A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals10.1038/s41467-022-28494-3 ↗
7. Molfm: A multimodal molecular foundation model
8. InstructMol: Multi-modal integration for building a versatile and reliable molecular assistant in drug discovery
9. Learning multi-view molecular representations with structured and unstructured knowledge
10. Unified molecule-text language model with discrete token representation
11. BioT5: Enriching cross-modal integration in biology with chemical knowledge and natural language associations
12. BioT5+: Towards generalized biological understanding with IUPAC integration and multitask tuning. In: Findings of the Association for Computational Linguistics
13. KG-Predict: A knowledge graph computational framework for drug repurposing10.1016/j.jbi.2022.104133 ↗
14. A foundation model for cliniciancentered drug repurposing10.1038/s41591-024-03233-x ↗
15. HGTDR: Advancing drug repurposing with heterogeneous graph transformers10.1093/bioinformatics/btae349 ↗
16. Chemvlm: Exploring the power of multimodal large language models in chemistry area
17. Image-based generation for molecule design with SketchMol10.1038/s42256-025-00982-3 ↗
18. Chemprop: a machine learning package for chemical property prediction10.1021/acs.jcim.3c01250 ↗
19. Automated 3D pre-training for molecular property prediction
20. Hierarchical graph tokenization for molecule-language alignment
21. Developing ChemDFM as a large language foundation model for chemistry
22. ChemDFM-X: towards large multimodal model for chemistry10.1007/s11432-024-4243-0 ↗
23. Chemllm: A chemical large languagemodel
24. Learning phrase representations using RNN encoder-decoder for statistical machine translation
25. Computer vision in chemistry: Automatic titration10.1021/acs.jchemed.1c00810 ↗
26. BLEU: a method for automatic evaluation of machine translation
27. Rouge: A package for automatic evaluation of summaries
28. Banerjee S., Lavie A. METEOR: An automatic metric for MT evaluation with improved correlation with human judgments. In: Proceedings of the ACL Workshop on Intrinsic and Extrinsic Evaluation Measures for Machine Translation and/or Summarization. Ann Arbor, MI: Association for Computational Linguistics; 2005. p. 65–72.
29. Qwen-VL: A Frontier Large Vision-Language Model with Versatile Abilities
30. InternVL: Scaling up vision foundation models and aligning for generic visual-linguistic tasks
31. Visual instruction tuning10.52202/075280-1516 ↗
32. OpenAI. GPT-4o: Our most advanced AI model. OpenAI. 2024.
33. an efficient and accurate method for detecting marker genes among many subtypes10.1093/bioadv/vbac037 ↗
34. Chemception: a deep neural network with minimal chemistry knowledge matches the performance of expert-developed QSAR/QSPR models
35. DECIMER: towards deep learning for chemical image recognition10.1186/s13321-020-00469-w ↗
36. MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design
37. Therapeutics Data Commons: Machine learning datasets and tasks for drug discovery and development
38. Automatic molecule optimization using copy & refine strategy
39. ChemGAN challenge for drug discovery: can AI reproduce natural chemical diversity?
40. Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
41. Extended-Connectivity Fingerprints10.1021/ci100050t ↗
42. Hierarchical generation of molecular graphs using structural motifs
43. Chemformer: a pre-trained transformer for computational chemistry10.1088/2632-2153/ac3ffb ↗
44. Lumina-mGPT: Flexible photorealistic autoregressive text-to-image generation10.1007/s11263-026-02795-2 ↗
45. Chameleon: Mixed-modal early-fusion foundation models
46. Taming transformers for high-resolution image synthesis
47. Neural discrete representation learning
48. Image-to-image translation with conditional adversarial networks
49. The unreasonable effectiveness of deep features as a perceptual metric
50. Anderson · 1987
51. Neural machine translation of rare words with subword units
52. Palm: Scaling language modeling with pathways
53. Landrum, G. (2006). RDKit: Open-source cheminformatics.
54. Adam: A method for stochastic optimization
55. Mol-Instructions: A large-scale biomolecular instruction dataset for large language models
56. PubChem in 2021: new data content and improved web interfaces10.1093/nar/gkaa971 ↗
57. Software, O. S. (2023). OpenEye Toolkits Documentation.