{"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/large-scale-differentiable-causal-discovery","title":"Large-Scale Differentiable Causal Discovery of Factor Graphs","arxiv_id":"2206.07824","date":"2022-06-15","proceeding":null,"authors":["Romain Lopez","Jan-Christian Hütter","Jonathan K. Pritchard","Aviv Regev"],"abstract":"A common theme in causal inference is learning causal relationships between observed variables, also known as causal discovery. This is usually a daunting task, given the large number of candidate causal graphs and the combinatorial nature of the search space. Perhaps for this reason, most research has so far focused on relatively small causal graphs, with up to hundreds of nodes. However, recent advances in fields like biology enable generating experimental data sets with thousands of interventions followed by rich profiling of thousands of variables, raising the opportunity and urgent need for large causal graph models. Here, we introduce the notion of factor directed acyclic graphs (f-DAGs) as a way to restrict the search space to non-linear low-rank causal interaction models. Combining this novel structural assumption with recent advances that bridge the gap between causal discovery and continuous optimization, we achieve causal discovery on thousands of variables. Additionally, as a model for the impact of statistical noise on this estimation procedure, we study a model of edge perturbations of the f-DAG skeleton based on random graphs and quantify the effect of such perturbations on the f-DAG rank. This theoretical analysis suggests that the set of candidate f-DAGs is much smaller than the whole DAG space and thus may be more suitable as a search space in the high-dimensional regime where the underlying skeleton is hard to assess. We propose Differentiable Causal Discovery of Factor Graphs (DCD-FG), a scalable implementation of -DAG constrained causal discovery for high-dimensional interventional data. DCD-FG uses a Gaussian non-linear low-rank structural equation model and shows significant improvements compared to state-of-the-art methods in both simulations as well as a recent large-scale single-cell RNA sequencing data set with hundreds of genetic interventions.","url_abs":"https://arxiv.org/abs/2206.07824v2","url_pdf":"https://arxiv.org/pdf/2206.07824v2.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":"large-scale-differentiable-causal-discovery","repo_url":"https://github.com/genentech/dcdfg","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"Apache-2.0"}}],"tasks":[{"task_slug":"causal-discovery","task_name":"Causal Discovery"},{"task_slug":"causal-inference","task_name":"Causal Inference"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2206.07824","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2206.07824"}},"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/genentech/dcdfg","reach":{"status":"ok","spdx":"Apache-2.0"}}],"summary":{"unverified":3},"by_repo_kind":{"official":{"samples":3,"ran":0,"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":"a7eb2ace730425d9","entry":"bisect","repo":"genentech/dcdfg","repo_kind":"official","path":"dcdfg/utils/dag_optim.py","file_url":"https://github.com/genentech/dcdfg/blob/HEAD/dcdfg/utils/dag_optim.py","link_basis":"harvester_set","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":"a7eb2ace730425d9"}},{"code_sha256_prefix":"a6e1c78ec030ed50","entry":"is_acyclic","repo":"genentech/dcdfg","repo_kind":"official","path":"dcdfg/utils/dag_optim.py","file_url":"https://github.com/genentech/dcdfg/blob/HEAD/dcdfg/utils/dag_optim.py","link_basis":"harvester_set","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":"a6e1c78ec030ed50"}},{"code_sha256_prefix":"79f95ae8d81306ef","entry":"samesign","repo":"genentech/dcdfg","repo_kind":"official","path":"dcdfg/utils/dag_optim.py","file_url":"https://github.com/genentech/dcdfg/blob/HEAD/dcdfg/utils/dag_optim.py","link_basis":"harvester_set","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":"79f95ae8d81306ef"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}