{"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/navigating-chemical-space-with-latent-flows","title":"Navigating Chemical Space with Latent Flows","arxiv_id":"2405.03987","date":"2024-05-07","proceeding":null,"authors":["Guanghao Wei","Yining Huang","Chenru Duan","Yue Song","Yuanqi Du"],"abstract":"Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and a comprehensive understanding of the vast chemical space are of great importance to molecular science and applications in drug design and materials discovery. In this paper, we propose a new framework, ChemFlow, to traverse chemical space through navigating the latent space learned by molecule generative models through flows. We introduce a dynamical system perspective that formulates the problem as learning a vector field that transports the mass of the molecular distribution to the region with desired molecular properties or structure diversity. Under this framework, we unify previous approaches on molecule latent space traversal and optimization and propose alternative competing methods incorporating different physical priors. We validate the efficacy of ChemFlow on molecule manipulation and single- and multi-objective molecule optimization tasks under both supervised and unsupervised molecular discovery settings. Codes and demos are publicly available on GitHub at https://github.com/garywei944/ChemFlow.","url_abs":"https://arxiv.org/abs/2405.03987v3","url_pdf":"https://arxiv.org/pdf/2405.03987v3.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":"navigating-chemical-space-with-latent-flows","repo_url":"https://github.com/garywei944/chemflow","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"diversity","task_name":"Diversity"},{"task_slug":"drug-design","task_name":"Drug Design"},{"task_slug":"efficient-exploration","task_name":"Efficient Exploration"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2405.03987","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2405.03987"}},"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/garywei944/ChemFlow","reach":{"status":"ok","spdx":"MIT"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/garywei944/chemflow","reach":{"status":"ok","spdx":"MIT"}}],"summary":{"ran":7,"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":"2632f545ceefa6ef","entry":"AuxClassifier","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.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":"2632f545ceefa6ef"}},{"code_sha256_prefix":"3f3fab87fe727d67","entry":"MLP","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.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":"3f3fab87fe727d67"}},{"code_sha256_prefix":"0847b98175b96a63","entry":"SinusoidalPositionEmbeddings","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.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":"0847b98175b96a63"}},{"code_sha256_prefix":"5270b12b26730833","entry":"WavePDE","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.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":"5270b12b26730833"}},{"code_sha256_prefix":"158883b1dd4ec254","entry":"WavePDEModel","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.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":"158883b1dd4ec254"}},{"code_sha256_prefix":"22d9e6138fcba0e8","entry":"WavePDEResult","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.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":"22d9e6138fcba0e8"}},{"code_sha256_prefix":"261d315ab81e63c3","entry":"normalize","repo":"garywei944/ChemFlow","repo_kind":"official","path":"src/utils/scores.py","file_url":"https://github.com/garywei944/ChemFlow/blob/HEAD/src/utils/scores.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":true,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"261d315ab81e63c3"}},{"code_sha256_prefix":"5a20550f1372e68e","entry":"Generator","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.py","link_basis":"first_harvest_node","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":"5a20550f1372e68e"}},{"code_sha256_prefix":"1b4dafcbf13d4e3f","entry":"PDE","repo":"garywei944/chemflow","repo_kind":"official","path":"src/pinn/pde/wavepde.py","file_url":"https://github.com/garywei944/chemflow/blob/HEAD/src/pinn/pde/wavepde.py","link_basis":"first_harvest_node","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":"1b4dafcbf13d4e3f"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}