{"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/moltc-towards-molecular-relational-modeling","title":"MolTC: Towards Molecular Relational Modeling In Language Models","arxiv_id":"2402.03781","date":"2024-02-06","proceeding":null,"authors":["Junfeng Fang","Shuai Zhang","Chang Wu","Zhengyi Yang","Zhiyuan Liu","Sihang Li","Kun Wang","Wenjie Du","Xiang Wang"],"abstract":"Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on the textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of information underutilization, as it hinders the sharing of interaction mechanism learned across diverse datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for Molecular inTeraction prediction following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. To train MolTC efficiently, we introduce a Multi-hierarchical CoT concept to refine its training paradigm, and conduct a comprehensive Molecular Interactive Instructions dataset for the development of biochemical LLMs involving MRL. Our experiments, conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.","url_abs":"https://arxiv.org/abs/2402.03781v6","url_pdf":"https://arxiv.org/pdf/2402.03781v6.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":"moltc-towards-molecular-relational-modeling","repo_url":"https://github.com/MangoKiller/MolTC","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"relational-reasoning","task_name":"Relational Reasoning"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2402.03781","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2402.03781"}},"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":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/MangoKiller/MolTC","reach":{"status":"ok","spdx":"MIT"}}],"summary":{"ran_violates":1},"by_repo_kind":{"official":{"samples":1,"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":0,"samples":[{"code_sha256_prefix":"4cb732f513d69dfd","entry":"disabled_train","repo":"MangoKiller/MolTC","repo_kind":"official","path":"model/blip2.py","file_url":"https://github.com/MangoKiller/MolTC/blob/HEAD/model/blip2.py","link_basis":"harvester_set","language":"python","status":"ran_violates","verification_level":1,"contract_check":"VIOLATES","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"4cb732f513d69dfd"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}