{"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/trident-tri-modal-molecular-representation","title":"TRIDENT: Tri-Modal Molecular Representation Learning with Taxonomic Annotations and Local Correspondence","arxiv_id":"2506.21028","date":"2025-06-26","proceeding":null,"authors":["Feng Jiang","Mangal Prakash","Hehuan Ma","Jianyuan Deng","Yuzhi Guo","Amina Mollaysa","Tommaso Mansi","Rui Liao","Junzhou Huang"],"abstract":"Molecular property prediction aims to learn representations that map chemical structures to functional properties. While multimodal learning has emerged as a powerful paradigm to learn molecular representations, prior works have largely overlooked textual and taxonomic information of molecules for representation learning. We introduce TRIDENT, a novel framework that integrates molecular SMILES, textual descriptions, and taxonomic functional annotations to learn rich molecular representations. To achieve this, we curate a comprehensive dataset of molecule-text pairs with structured, multi-level functional annotations. Instead of relying on conventional contrastive loss, TRIDENT employs a volume-based alignment objective to jointly align tri-modal features at the global level, enabling soft, geometry-aware alignment across modalities. Additionally, TRIDENT introduces a novel local alignment objective that captures detailed relationships between molecular substructures and their corresponding sub-textual descriptions. A momentum-based mechanism dynamically balances global and local alignment, enabling the model to learn both broad functional semantics and fine-grained structure-function mappings. TRIDENT achieves state-of-the-art performance on 11 downstream tasks, demonstrating the value of combining SMILES, textual, and taxonomic functional annotations for molecular property prediction.","url_abs":"https://arxiv.org/abs/2506.21028v1","url_pdf":"https://arxiv.org/pdf/2506.21028v1.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":[],"tasks":[{"task_slug":"molecular-property-prediction","task_name":"Molecular Property Prediction"},{"task_slug":"property-prediction","task_name":"Property Prediction"},{"task_slug":"representation-learning","task_name":"Representation Learning"},{"task_slug":"molecular-representation","task_name":"molecular representation"}],"methods":[{"method_slug":"align","method_name":"ALIGN"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2506.21028","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2506.21028"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"deterministic:regex_extraction","url":"https://github.com/uta-smile/TRIDENT","reach":null}],"summary":{"ran":1,"unverified":1},"by_repo_kind":{"found_in_text":{"samples":2,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":2,"samples":[{"code_sha256_prefix":"7526c0cbabab5d07","entry":"GRAM3ModalLoss","repo":"uta-smile/TRIDENT","repo_kind":"found_in_text","path":"models.py","file_url":"https://github.com/uta-smile/TRIDENT/blob/HEAD/models.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":"invariant","behaviour_fingerprint":true,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"7526c0cbabab5d07"}},{"code_sha256_prefix":"6ab038430b7b71dd","entry":"MultiModalContrastiveModel","repo":"uta-smile/TRIDENT","repo_kind":"found_in_text","path":"models.py","file_url":"https://github.com/uta-smile/TRIDENT/blob/HEAD/models.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"6ab038430b7b71dd"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}