{"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/product-manifold-representations-for-learning","title":"Product Manifold Representations for Learning on Biological Pathways","arxiv_id":"2401.15478","date":"2024-01-27","proceeding":null,"authors":["Daniel McNeela","Frederic Sala","Anthony Gitter"],"abstract":"Machine learning models that embed graphs in non-Euclidean spaces have shown substantial benefits in a variety of contexts, but their application has not been studied extensively in the biological domain, particularly with respect to biological pathway graphs. Such graphs exhibit a variety of complex network structures, presenting challenges to existing embedding approaches. Learning high-quality embeddings for biological pathway graphs is important for researchers looking to understand the underpinnings of disease and train high-quality predictive models on these networks. In this work, we investigate the effects of embedding pathway graphs in non-Euclidean mixed-curvature spaces and compare against traditional Euclidean graph representation learning models. We then train a supervised model using the learned node embeddings to predict missing protein-protein interactions in pathway graphs. We find large reductions in distortion and boosts on in-distribution edge prediction performance as a result of using mixed-curvature embeddings and their corresponding graph neural network models. However, we find that mixed-curvature representations underperform existing baselines on out-of-distribution edge prediction performance suggesting that these representations may overfit to the training graph topology. We provide our Mixed-Curvature Product Graph Convolutional Network code at https://github.com/mcneela/Mixed-Curvature-GCN and our pathway analysis code at https://github.com/mcneela/Mixed-Curvature-Pathways.","url_abs":"https://arxiv.org/abs/2401.15478v2","url_pdf":"https://arxiv.org/pdf/2401.15478v2.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":"product-manifold-representations-for-learning","repo_url":"https://github.com/mcneela/mixed-curvature-gcn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"Apache-2.0"}},{"paper_slug":"product-manifold-representations-for-learning","repo_url":"https://github.com/mcneela/mixed-curvature-pathways","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"graph-neural-network","task_name":"Graph Neural Network"},{"task_slug":"graph-representation-learning","task_name":"Graph Representation Learning"},{"task_slug":"representation-learning","task_name":"Representation Learning"}],"methods":[{"method_slug":"gcn","method_name":"GCN"},{"method_slug":"graph-neural-network","method_name":"Graph Neural Network"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2401.15478","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2401.15478"}},"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. 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