{"entity": "researcher", "timestamp": "2026-08-22T07:48:17.180Z", "family": "Dai", "given": "Shubin", "initials": "S", "orcid": "0000-0001-6680-0500", "affiliations": [", Changsha, China."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f4835d5b16a400b9dd9aaff8a8d49f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f4835d5b16a400b9dd9aaff8a8d49f7"}}, "publications": [{"entity": "publication", "iuid": "82fcc044a9424abea9804a6b4242c8a5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/82fcc044a9424abea9804a6b4242c8a5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/82fcc044a9424abea9804a6b4242c8a5"}}, "title": "Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.", "authors": [{"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Axelsson", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-0273-9306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c60c73df0c445b38aabb5e91a118a2b.json"}}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Mohanakrishnan Kaimal", "given": "Jayasankar", "initials": "J"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Dai", "given": "Shubin", "initials": "S", "orcid": "0000-0001-6680-0500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f4835d5b16a400b9dd9aaff8a8d49f7.json"}}, {"family": "Makarov", "given": "Ilya S", "initials": "IS"}, {"family": "Ostankovich", "given": "Vladislav", "initials": "V", "orcid": "0000-0001-7020-8825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3a24a4ce6254b1aa5ee0ffc987b3b45.json"}}, {"family": "Xu", "given": "Yang", "initials": "Y"}, {"family": "Benhamou", "given": "Eric", "initials": "E"}, {"family": "Henkel", "given": "Christof", "initials": "C", "orcid": "0000-0002-2913-3662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2560edfc894b48b4849f28173e580861.json"}}, {"family": "Solovyev", "given": "Roman A", "initials": "RA", "orcid": "0000-0003-0312-452X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6aee06b530294a58b87b0e0c40aa316d.json"}}, {"family": "Bani\u0107", "given": "Nikola", "initials": "N"}, {"family": "Bo\u0161njak", "given": "Vito", "initials": "V", "orcid": "0000-0003-3786-0592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14fb5bfa316e4fb48cb6afc00ccbb2dc.json"}}, {"family": "Bo\u0161njak", "given": "Ana", "initials": "A", "orcid": "0000-0002-3425-8363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58a2bdb9d5b94686a57238eddc685730.json"}}, {"family": "Mili\u010devi\u0107", "given": "Andrija", "initials": "A", "orcid": "0000-0001-7148-7651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffd8bc851170484c85db3c7699c3c49d.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "19", "issue": "10", "pages": "1221-1229", "issn-l": "1548-7091"}, "abstract": "While spatial proteomics by fluorescence imaging has quickly become an essential discovery tool for researchers, fast and scalable methods to classify and embed single-cell protein distributions in such images are lacking. Here, we present the design and analysis of the results from the competition Human Protein Atlas - Single-Cell Classification hosted on the Kaggle platform. This represents a crowd-sourced competition to develop machine learning models trained on limited annotations to label single-cell protein patterns in fluorescent images. The particular challenges of this competition include class imbalance, weak labels and multi-label classification, prompting competitors to apply a wide range of approaches in their solutions. The winning models serve as the first subcellular omics tools that can annotate single-cell locations, extract single-cell features and capture cellular dynamics.", "doi": "10.1038/s41592-022-01606-z", "pmid": "36175767", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9550622"}, {"db": "pii", "key": "10.1038/s41592-022-01606-z"}], "notes": [], "created": "2026-08-20T09:02:51.438Z", "modified": "2026-08-20T09:02:51.797Z"}, {"entity": "publication", "iuid": "03d08ef75f714ba79b4cd3439ed53961", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/03d08ef75f714ba79b4cd3439ed53961.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/03d08ef75f714ba79b4cd3439ed53961"}}, "title": "Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d6d89bd3a43eab43eee98539ed4ad.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Dai", "given": "Shubin", "initials": "S", "orcid": "0000-0001-6680-0500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f4835d5b16a400b9dd9aaff8a8d49f7.json"}}, {"family": "Lan", "given": "Jun", "initials": "J"}, {"family": "Jinmo", "given": "Park", "initials": "P"}, {"family": "Galib", "given": "Shaikat M", "initials": "SM", "orcid": "0000-0002-8192-578X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d73568f63e9c4f4f8687af3846410d38.json"}}, {"family": "Henkel", "given": "Christof", "initials": "C"}, {"family": "Hwang", "given": "Kevin", "initials": "K"}, {"family": "Poplavskiy", "given": "Dmytro", "initials": "D"}, {"family": "Tunguz", "given": "Bojan", "initials": "B"}, {"family": "Wolfinger", "given": "Russel D", "initials": "RD"}, {"family": "Gu", "given": "Yinzheng", "initials": "Y"}, {"family": "Li", "given": "Chuanpeng", "initials": "C", "orcid": "0000-0003-1804-9032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51bfd11cec9f44b6a905026c542ac798.json"}}, {"family": "Xie", "given": "Jinbin", "initials": "J"}, {"family": "Buslov", "given": "Dmitry", "initials": "D"}, {"family": "Fironov", "given": "Sergei", "initials": "S"}, {"family": "Kiselev", "given": "Alexander", "initials": "A"}, {"family": "Panchenko", "given": "Dmytro", "initials": "D", "orcid": "0000-0001-5454-5661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246b23ea5e3241c596c68ebc747a153e.json"}}, {"family": "Cao", "given": "Xuan", "initials": "X", "orcid": "0000-0001-7241-7188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1362c170d9bb4dfeaf7c07189b468ee2.json"}}, {"family": "Wei", "given": "Runmin", "initials": "R", "orcid": "0000-0001-7707-0160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/24edd83eaee941cbb07feecf5aff3f07.json"}}, {"family": "Wu", "given": "Yuanhao", "initials": "Y", "orcid": "0000-0001-9800-8235", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a8f35c0ae5d4685888e65f72322b4fb.json"}}, {"family": "Zhu", "given": "Xun", "initials": "X", "orcid": "0000-0001-9097-7824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ef45320edf54750b45df077b9ddb9d0.json"}}, {"family": "Tseng", "given": "Kuan-Lun", "initials": "KL", "orcid": "0000-0001-8382-9241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c92f097647814f62be7db381e248da16.json"}}, {"family": "Gao", "given": "Zhifeng", "initials": "Z"}, {"family": "Ju", "given": "Cheng", "initials": "C", "orcid": "0000-0001-7585-6266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3a65861c99344e4bd7e0dd80194f02e.json"}}, {"family": "Yi", "given": "Xiaohan", "initials": "X"}, {"family": "Zheng", "given": "Hongdong", "initials": "H"}, {"family": "Kappel", "given": "Constantin", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2020-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "17", "issue": "1", "pages": "115", "issn-l": "1548-7091"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41592-019-0699-x", "pmid": "31822866", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41592-019-0699-x"}], "notes": [], "created": "2026-08-20T09:02:25.124Z", "modified": "2026-08-20T09:02:25.632Z"}]}