{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/unifying-molecular-and-textual","title":"Unifying Molecular and Textual Representations via Multi-task Language Modelling","arxiv_id":"2301.12586","date":"2023-01-29","proceeding":null,"authors":["Dimitrios Christofidellis","Giorgio Giannone","Jannis Born","Ole Winther","Teodoro Laino","Matteo Manica"],"abstract":"The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains. Our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.","url_abs":"https://arxiv.org/abs/2301.12586v2","url_pdf":"https://arxiv.org/pdf/2301.12586v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"unifying-molecular-and-textual","repo_url":"https://github.com/gt4sd/multitask_text_and_chemistry_t5","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"language-modelling","task_name":"Language Modelling"},{"task_slug":"molecule-captioning","task_name":"Molecule Captioning"},{"task_slug":"multi-task-learning","task_name":"Multi-Task Learning"},{"task_slug":"text-based-de-novo-molecule-generation","task_name":"Text-based de novo Molecule Generation"},{"task_slug":"scientific-discovery","task_name":"scientific discovery"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[{"leaderboard":"/sota/molecule-captioning-on-chebi-20","task":"Molecule Captioning","dataset":"ChEBI-20","model":"Text+Chem T5-augm-Base","rank_in_archive_order":6,"of":33,"metrics":{"BLEU-2":"62.5","BLEU-4":"54.2","METEOR":"64.8","ROUGE-1":"68.2","ROUGE-2":"54.3","ROUGE-L":"62.2"},"uses_additional_data":false},{"leaderboard":"/sota/molecule-captioning-on-chebi-20","task":"Molecule Captioning","dataset":"ChEBI-20","model":"Text+Chem T5-Base","rank_in_archive_order":19,"of":33,"metrics":{"BLEU-2":"58","BLEU-4":"49","METEOR":"60.4","ROUGE-1":"64.7","ROUGE-2":"49.8","ROUGE-L":"58.6"},"uses_additional_data":false},{"leaderboard":"/sota/molecule-captioning-on-chebi-20","task":"Molecule Captioning","dataset":"ChEBI-20","model":"Text+Chem T5-augm-Small","rank_in_archive_order":23,"of":33,"metrics":{"BLEU-2":"56.0","BLEU-4":"47.0","METEOR":"58.8","ROUGE-1":"63.8","ROUGE-2":"48.8","ROUGE-L":"58"},"uses_additional_data":false},{"leaderboard":"/sota/molecule-captioning-on-chebi-20","task":"Molecule Captioning","dataset":"ChEBI-20","model":"Text+Chem T5-Small","rank_in_archive_order":24,"of":33,"metrics":{"BLEU-2":"55.3","BLEU-4":"46.2","METEOR":"58.3","ROUGE-1":"63.3","ROUGE-2":"48.1","ROUGE-L":"57.4"},"uses_additional_data":false},{"leaderboard":"/sota/text-based-de-novo-molecule-generation-on","task":"Text-based de novo Molecule Generation","dataset":"ChEBI-20","model":"Text+Chem T5-augm base","rank_in_archive_order":7,"of":20,"metrics":{"BLEU":"85.3","Exact Match":"32.2","Frechet ChemNet Distance (FCD)":".05","Levenshtein":"16.87","MACCS FTS":"90.1","Morgan FTS":"75.7","Parameter Count":"220000000","RDK FTS":"81.6","Validity":"94.3"},"uses_additional_data":false},{"leaderboard":"/sota/text-based-de-novo-molecule-generation-on","task":"Text-based de novo Molecule Generation","dataset":"ChEBI-20","model":"Text+Chem T5-augm small","rank_in_archive_order":11,"of":20,"metrics":{"BLEU":"81.5","Exact Match":"19.1","Frechet ChemNet Distance (FCD)":"0.06","Levenshtein":"21.78","MACCS FTS":"86.4","Morgan FTS":"67.2","Parameter Count":"60000000","RDK FTS":"74.4","Validity":"95.1"},"uses_additional_data":false},{"leaderboard":"/sota/text-based-de-novo-molecule-generation-on","task":"Text-based de novo Molecule Generation","dataset":"ChEBI-20","model":"Text+Chem T5 base","rank_in_archive_order":18,"of":20,"metrics":{"BLEU":"75","Exact Match":"21.2","Frechet ChemNet Distance (FCD)":"0.061","Levenshtein":"27.39","MACCS FTS":"87.4","Morgan FTS":"69.7","Parameter Count":"220000000","RDK FTS":"76.7","Validity":"79.2"},"uses_additional_data":false},{"leaderboard":"/sota/text-based-de-novo-molecule-generation-on","task":"Text-based de novo Molecule Generation","dataset":"ChEBI-20","model":"Text+Chem T5 small","rank_in_archive_order":19,"of":20,"metrics":{"BLEU":"73.9","Exact Match":"15.7","Frechet ChemNet Distance (FCD)":"0.066","Levenshtein":"28.54","MACCS FTS":"85.9","Morgan FTS":"66","Parameter Count":"60000000","RDK FTS":"73.6","Validity":"77.6"},"uses_additional_data":false}],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2301.12586","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}