{"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/a-deep-learning-classifier-for-local-ancestry","title":"A deep learning classifier for local ancestry inference","arxiv_id":"2011.02081","date":"2020-11-04","proceeding":null,"authors":["Matthew Aguirre","Jan Sokol","Guhan Venkataraman","Alexander Ioannidis"],"abstract":"Local ancestry inference (LAI) identifies the ancestry of each segment of an individual's genome and is an important step in medical and population genetic studies of diverse cohorts. Several techniques have been used for LAI, including Hidden Markov Models and Random Forests. Here, we formulate the LAI task as an image segmentation problem and develop a new LAI tool using a deep convolutional neural network with an encoder-decoder architecture. We train our model using complete genome sequences from 982 unadmixed individuals from each of five continental ancestry groups, and we evaluate it using simulated admixed data derived from an additional 279 individuals selected from the same populations. We show that our model is able to learn admixture as a zero-shot task, yielding ancestry assignments that are nearly as accurate as those from the existing gold standard tool, RFMix.","url_abs":"https://arxiv.org/abs/2011.02081v1","url_pdf":"https://arxiv.org/pdf/2011.02081v1.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":"a-deep-learning-classifier-for-local-ancestry","repo_url":"https://github.com/maguirre1/deepLAI","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"tf","reach":null}],"tasks":[{"task_slug":"decoder","task_name":"Decoder"},{"task_slug":"deep-learning","task_name":"Deep Learning"},{"task_slug":"image-segmentation","task_name":"Image Segmentation"},{"task_slug":"semantic-segmentation","task_name":"Semantic Segmentation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2011.02081","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2011.02081"}},"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/maguirre1/deepLAI","reach":null}],"summary":{"unverified":1},"by_repo_kind":{"official":{"samples":1,"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":"9d0762b543258832","entry":"segnet","repo":"maguirre1/deepLAI","repo_kind":"official","path":"model/segnet.py","file_url":"https://github.com/maguirre1/deepLAI/blob/HEAD/model/segnet.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":"9d0762b543258832"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}