{"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/evaluating-self-supervised-learning-for","title":"Evaluating Self-Supervised Learning for Molecular Graph Embeddings","arxiv_id":"2206.08005","date":"2022-06-16","proceeding":"NeurIPS 2023 11","authors":["Hanchen Wang","Jean Kaddour","Shengchao Liu","Jian Tang","Joan Lasenby","Qi Liu"],"abstract":"Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and the high cost of obtaining labels. However, GSSL methods are designed not for optimisation within a specific domain but rather for transferability across a variety of downstream tasks. This broad applicability complicates their evaluation. Addressing this challenge, we present \"Molecular Graph Representation Evaluation\" (MOLGRAPHEVAL), generating detailed profiles of molecular graph embeddings with interpretable and diversified attributes. MOLGRAPHEVAL offers a suite of probing tasks grouped into three categories: (i) generic graph, (ii) molecular substructure, and (iii) embedding space properties. By leveraging MOLGRAPHEVAL to benchmark existing GSSL methods against both current downstream datasets and our suite of tasks, we uncover significant inconsistencies between inferences drawn solely from existing datasets and those derived from more nuanced probing. These findings suggest that current evaluation methodologies fail to capture the entirety of the landscape.","url_abs":"https://arxiv.org/abs/2206.08005v3","url_pdf":"https://arxiv.org/pdf/2206.08005v3.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":"evaluating-self-supervised-learning-for","repo_url":"https://github.com/hansen7/molgrapheval","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2206.08005","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2206.08005"}},"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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