{"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/cell-morphology-guided-small-molecule","title":"Cell Morphology-Guided Small Molecule Generation with GFlowNets","arxiv_id":"2408.05196","date":"2024-08-09","proceeding":null,"authors":["Stephen Zhewen Lu","Ziqing Lu","Ehsan Hajiramezanali","Tommaso Biancalani","Yoshua Bengio","Gabriele Scalia","Michał Koziarski"],"abstract":"High-content phenotypic screening, including high-content imaging (HCI), has gained popularity in the last few years for its ability to characterize novel therapeutics without prior knowledge of the protein target. When combined with deep learning techniques to predict and represent molecular-phenotype interactions, these advancements hold the potential to significantly accelerate and enhance drug discovery applications. This work focuses on the novel task of HCI-guided molecular design. Generative models for molecule design could be guided by HCI data, for example with a supervised model that links molecules to phenotypes of interest as a reward function. However, limited labeled data, combined with the high-dimensional readouts, can make training these methods challenging and impractical. We consider an alternative approach in which we leverage an unsupervised multimodal joint embedding to define a latent similarity as a reward for GFlowNets. The proposed model learns to generate new molecules that could produce phenotypic effects similar to those of the given image target, without relying on pre-annotated phenotypic labels. We demonstrate that the proposed method generates molecules with high morphological and structural similarity to the target, increasing the likelihood of similar biological activity, as confirmed by an independent oracle model.","url_abs":"https://arxiv.org/abs/2408.05196v1","url_pdf":"https://arxiv.org/pdf/2408.05196v1.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":"cell-morphology-guided-small-molecule","repo_url":"https://github.com/thematrixmaster/omics-guided-gfn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"Apache-2.0"}}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2408.05196","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2408.05196"}},"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":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/thematrixmaster/omics-guided-gfn","reach":{"status":"ok","spdx":"Apache-2.0"}}],"summary":{"ran":3,"unverified":10},"by_repo_kind":{"official":{"samples":13,"ran":3,"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":"54936394beb9f240","entry":"get_active_assay_cols","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/utils.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/utils.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"54936394beb9f240"}},{"code_sha256_prefix":"29b3d9a2a4428f17","entry":"load_run","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_num_modes_over_trajs.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_num_modes_over_trajs.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"29b3d9a2a4428f17"}},{"code_sha256_prefix":"b6e0ab7839b75db7","entry":"load_sm_run","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_oracle_hist.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_oracle_hist.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"b6e0ab7839b75db7"}},{"code_sha256_prefix":"8c3564ce41ecc062","entry":"compute_num_modes","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_num_modes_over_trajs.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_num_modes_over_trajs.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"8c3564ce41ecc062"}},{"code_sha256_prefix":"84b1f70fe2f28daa","entry":"compute_rew_thresh","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_num_modes_over_trajs.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_num_modes_over_trajs.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"84b1f70fe2f28daa"}},{"code_sha256_prefix":"14c5f28b5c28ecbb","entry":"compute_rew_thresh","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_oracle_hist.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_oracle_hist.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"14c5f28b5c28ecbb"}},{"code_sha256_prefix":"d257b6ddb4daf66e","entry":"load_run","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/compute_max_tanimoto_sim.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/compute_max_tanimoto_sim.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"d257b6ddb4daf66e"}},{"code_sha256_prefix":"79a72ec80eecdf67","entry":"load_run","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_main.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_main.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"79a72ec80eecdf67"}},{"code_sha256_prefix":"e5f14c7ec00729a6","entry":"load_run","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_oracle_hist.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_oracle_hist.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"e5f14c7ec00729a6"}},{"code_sha256_prefix":"a223c9ddde2baeee","entry":"load_run","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_umap.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_umap.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"a223c9ddde2baeee"}},{"code_sha256_prefix":"1147f62a9cb2ddd4","entry":"merge","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plot_main.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plot_main.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"1147f62a9cb2ddd4"}},{"code_sha256_prefix":"db648b3524c8c8b4","entry":"smooth","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plotting.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plotting.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"db648b3524c8c8b4"}},{"code_sha256_prefix":"d99d5b1c131f02db","entry":"smooth_ci","repo":"thematrixmaster/omics-guided-gfn","repo_kind":"official","path":"vis/plotting.py","file_url":"https://github.com/thematrixmaster/omics-guided-gfn/blob/HEAD/vis/plotting.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"d99d5b1c131f02db"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}