{"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/motifpiece-a-data-driven-approach-for","title":"MotifPiece: A Data-Driven Approach for Effective Motif Extraction and Molecular Representation Learning","arxiv_id":"2312.15387","date":"2023-12-24","proceeding":null,"authors":["Zhaoning Yu","Hongyang Gao"],"abstract":"Motif extraction is an important task in motif based molecular representation learning. Previously, machine learning approaches employing either rule-based or string-based techniques to extract motifs. Rule-based approaches may extract motifs that aren't frequent or prevalent within the molecular data, which can lead to an incomplete understanding of essential structural patterns in molecules. String-based methods often lose the topological information inherent in molecules. This can be a significant drawback because topology plays a vital role in defining the spatial arrangement and connectivity of atoms within a molecule, which can be critical for understanding its properties and behavior. In this paper, we develop a data-driven motif extraction technique known as MotifPiece, which employs statistical measures to define motifs. To comprehensively evaluate the effectiveness of MotifPiece, we introduce a heterogeneous learning module. Our model shows an improvement compared to previously reported models. Additionally, we demonstrate that its performance can be further enhanced in two ways: first, by incorporating more data to aid in generating a richer motif vocabulary, and second, by merging multiple datasets that share enough motifs, allowing for cross-dataset learning.","url_abs":"https://arxiv.org/abs/2312.15387v1","url_pdf":"https://arxiv.org/pdf/2312.15387v1.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":"motifpiece-a-data-driven-approach-for","repo_url":"https://github.com/zhaoningyu1996/motifpiece","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"representation-learning","task_name":"Representation Learning"},{"task_slug":"molecular-representation","task_name":"molecular representation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}