{"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/multimodal-contrastive-representation","title":"Multimodal Contrastive Representation Learning in Augmented Biomedical Knowledge Graphs","arxiv_id":"2501.01644","date":"2025-01-03","proceeding":null,"authors":["Tien Dang","Viet Thanh Duy Nguyen","Minh Tuan Le","Truong-Son Hy"],"abstract":"Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease relations. We introduce a novel multimodal approach that unifies embeddings from specialized Language Models (LMs) with Graph Contrastive Learning (GCL) to enhance intra-entity relationships while employing a Knowledge Graph Embedding (KGE) model to capture inter-entity relationships for effective link prediction. To address limitations in existing BKGs, we present PrimeKG++, an enriched knowledge graph incorporating multimodal data, including biological sequences and textual descriptions for each entity type. By combining semantic and relational information in a unified representation, our approach demonstrates strong generalizability, enabling accurate link predictions even for unseen nodes. Experimental results on PrimeKG++ and the DrugBank drug-target interaction dataset demonstrate the effectiveness and robustness of our method across diverse biomedical datasets. Our source code, pre-trained models, and data are publicly available at https://github.com/HySonLab/BioMedKG","url_abs":"https://arxiv.org/abs/2501.01644v1","url_pdf":"https://arxiv.org/pdf/2501.01644v1.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":"multimodal-contrastive-representation","repo_url":"https://github.com/hysonlab/biomedkg","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"contrastive-learning","task_name":"Contrastive Learning"},{"task_slug":"graph-embedding","task_name":"Graph Embedding"},{"task_slug":"knowledge-graph-embedding","task_name":"Knowledge Graph Embedding"},{"task_slug":"knowledge-graphs","task_name":"Knowledge Graphs"},{"task_slug":"link-prediction","task_name":"Link Prediction"},{"task_slug":"representation-learning","task_name":"Representation Learning"}],"methods":[{"method_slug":"contrastive-learning","method_name":"Contrastive Learning"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}