{"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/hierarchical-grammar-induced-geometry-for","title":"Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction","arxiv_id":"2309.01788","date":"2023-09-04","proceeding":null,"authors":["Minghao Guo","Veronika Thost","Samuel W Song","Adithya Balachandran","Payel Das","Jie Chen","Wojciech Matusik"],"abstract":"The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are faced with a common challenge in practice: Labeled data are limited by the cost of manual extraction from literature and laborious experimentation. In this work, we propose a data-efficient property predictor by utilizing a learnable hierarchical molecular grammar that can generate molecules from grammar production rules. Such a grammar induces an explicit geometry of the space of molecular graphs, which provides an informative prior on molecular structural similarity. The property prediction is performed using graph neural diffusion over the grammar-induced geometry. On both small and large datasets, our evaluation shows that this approach outperforms a wide spectrum of baselines, including supervised and pre-trained graph neural networks. We include a detailed ablation study and further analysis of our solution, showing its effectiveness in cases with extremely limited data. Code is available at https://github.com/gmh14/Geo-DEG.","url_abs":"https://arxiv.org/abs/2309.01788v1","url_pdf":"https://arxiv.org/pdf/2309.01788v1.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":"hierarchical-grammar-induced-geometry-for","repo_url":"https://github.com/gmh14/geo-deg","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":"molecular-property-prediction","task_name":"Molecular Property Prediction"},{"task_slug":"property-prediction","task_name":"Property Prediction"}],"methods":[{"method_slug":"diffusion","method_name":"Diffusion"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2309.01788","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2309.01788"}},"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. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"deterministic:regex_extraction","url":"https://github.com/gmh14/Geo-DEG","reach":{"status":"ok","spdx":"MIT"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/gmh14/geo-deg","reach":{"status":"ok","spdx":"MIT"}}],"summary":{"ran_honours":2,"ran":5,"unverified":2},"by_repo_kind":{"official":{"samples":9,"ran":7,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"b822dd00427403bf","entry":"cycle_index","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/pretrain_contextpred.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/pretrain_contextpred.py","link_basis":"harvester_set","language":"python","status":"ran_honours","verification_level":1,"contract_check":"HONOURS","metamorphic_tier":"well_formed","behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"b822dd00427403bf"}},{"code_sha256_prefix":"b9e621ce8971cd48","entry":"eval","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/finetune_mutag_ptc.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/finetune_mutag_ptc.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"b9e621ce8971cd48"}},{"code_sha256_prefix":"287484b87212f47d","entry":"graph_data_obj_to_nx_simple","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/loader.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/loader.py","link_basis":"harvester_set","language":"python","status":"ran_honours","verification_level":1,"contract_check":"HONOURS","metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"287484b87212f47d"}},{"code_sha256_prefix":"7164f5ee51907055","entry":"pool_func","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/pretrain_contextpred.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/pretrain_contextpred.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"7164f5ee51907055"}},{"code_sha256_prefix":"0bd562e4c29a723d","entry":"sample","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"agent.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/agent.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"0bd562e4c29a723d"}},{"code_sha256_prefix":"fa82f5b97a3162ed","entry":"train","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/pretrain_contextpred.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/pretrain_contextpred.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"fa82f5b97a3162ed"}},{"code_sha256_prefix":"26bd6db6fc4f8df4","entry":"train","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/pretrain_deepgraphinfomax.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/pretrain_deepgraphinfomax.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"26bd6db6fc4f8df4"}},{"code_sha256_prefix":"f6e29229f7916056","entry":"eval","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/finetune.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/finetune.py","link_basis":"plan_row","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"f6e29229f7916056"}},{"code_sha256_prefix":"7a2bb855a3e02bfe","entry":"get_test_acc","repo":"gmh14/Geo-DEG","repo_kind":"official","path":"GCN/parse_result.py","file_url":"https://github.com/gmh14/Geo-DEG/blob/HEAD/GCN/parse_result.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"7a2bb855a3e02bfe"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}