{"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/pre-training-graph-neural-networks-on-1","title":"Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck","arxiv_id":"2412.15589","date":"2024-12-20","proceeding":null,"authors":["Van Thuy Hoang","O-Joun Lee"],"abstract":"This study aims to build a pre-trained Graph Neural Network (GNN) model on molecules without human annotations or prior knowledge. Although various attempts have been proposed to overcome limitations in acquiring labeled molecules, the previous pre-training methods still rely on semantic subgraphs, i.e., functional groups. Only focusing on the functional groups could overlook the graph-level distinctions. The key challenge to build a pre-trained GNN on molecules is how to (1) generate well-distinguished graph-level representations and (2) automatically discover the functional groups without prior knowledge. To solve it, we propose a novel Subgraph-conditioned Graph Information Bottleneck, named S-CGIB, for pre-training GNNs to recognize core subgraphs (graph cores) and significant subgraphs. The main idea is that the graph cores contain compressed and sufficient information that could generate well-distinguished graph-level representations and reconstruct the input graph conditioned on significant subgraphs across molecules under the S-CGIB principle. To discover significant subgraphs without prior knowledge about functional groups, we propose generating a set of functional group candidates, i.e., ego networks, and using an attention-based interaction between the graph core and the candidates. Despite being identified from self-supervised learning, our learned subgraphs match the real-world functional groups. Extensive experiments on molecule datasets across various domains demonstrate the superiority of S-CGIB.","url_abs":"https://arxiv.org/abs/2412.15589v1","url_pdf":"https://arxiv.org/pdf/2412.15589v1.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":"pre-training-graph-neural-networks-on-1","repo_url":"https://github.com/NSLab-CUK/S-CGIB","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null},{"paper_slug":"pre-training-graph-neural-networks-on-1","repo_url":"https://github.com/nslab-cuk/halal-or-not","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"graph-neural-network","task_name":"Graph Neural Network"},{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[{"method_slug":"graph-neural-network","method_name":"Graph Neural Network"},{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2412.15589","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2412.15589"}},"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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