{"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/feature-selection-in-the-contrastive-analysis-1","title":"Feature Selection in the Contrastive Analysis Setting","arxiv_id":"2310.18531","date":"2023-10-27","proceeding":"NeurIPS 2023 11","authors":[],"abstract":"Contrastive analysis (CA) refers to the exploration of variations uniquely enriched in a target dataset as compared to a corresponding background dataset generated from sources of variation that are irrelevant to a given task. For example, a biomedical data analyst may wish to find a small set of genes to use as a proxy for variations in genomic data only present among patients with a given disease (target) as opposed to healthy control subjects (background). However, as of yet the problem of feature selection in the CA setting has received little attention from the machine learning community. In this work we present contrastive feature selection (CFS), a method for performing feature selection in the CA setting. We motivate our approach with a novel information-theoretic analysis of representation learning in the CA setting, and we empirically validate CFS on a semi-synthetic dataset and four real-world biomedical datasets. We find that our method consistently outperforms previously proposed state-of-the-art supervised and fully unsupervised feature selection methods not designed for the CA setting. An open-source implementation of our method is available at https://github.com/suinleelab/CFS.","url_abs":"https://arxiv.org/abs/2310.18531v1","url_pdf":"https://arxiv.org/pdf/2310.18531v1.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":"feature-selection-in-the-contrastive-analysis-1","repo_url":"https://github.com/suinleelab/cfs","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"representation-learning","task_name":"Representation Learning"},{"task_slug":"feature-selection","task_name":"feature selection"}],"methods":[{"method_slug":"feature-selection","method_name":"Feature Selection"},{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2310.18531","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2310.18531"}},"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/suinleelab/CFS","reach":{"status":"ok"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/suinleelab/cfs","reach":{"status":"ok"}}],"summary":{"ran":1},"by_repo_kind":{"listed":{"samples":1,"ran":1,"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":1,"samples":[{"code_sha256_prefix":"b1d645122832c603","entry":"CFS_SG","repo":"suinleelab/cfs","repo_kind":"listed","path":"contrastive_fs/models/CFS_SG.py","file_url":"https://github.com/suinleelab/cfs/blob/HEAD/contrastive_fs/models/CFS_SG.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"b1d645122832c603"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}