{"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/citation-needed-data-usage-and-citation","title":"[Citation needed] Data usage and citation practices in medical imaging conferences","arxiv_id":"2402.03003","date":"2024-02-05","proceeding":null,"authors":["Théo Sourget","Ahmet Akkoç","Stinna Winther","Christine Lyngbye Galsgaard","Amelia Jiménez-Sánchez","Dovile Juodelyte","Caroline Petitjean","Veronika Cheplygina"],"abstract":"Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use publicly available datasets, there is however no adopted standard for citing the datasets used in scientific papers, leading to difficulty in tracking dataset usage. In this work, we present two open-source tools we created that could help with the detection of dataset usage, a pipeline \\url{https://github.com/TheoSourget/Public_Medical_Datasets_References} using OpenAlex and full-text analysis, and a PDF annotation software \\url{https://github.com/TheoSourget/pdf_annotator} used in our study to manually label the presence of datasets. We applied both tools on a study of the usage of 20 publicly available medical datasets in papers from MICCAI and MIDL. We compute the proportion and the evolution between 2013 and 2023 of 3 types of presence in a paper: cited, mentioned in the full text, cited and mentioned. Our findings demonstrate the concentration of the usage of a limited set of datasets. We also highlight different citing practices, making the automation of tracking difficult.","url_abs":"https://arxiv.org/abs/2402.03003v2","url_pdf":"https://arxiv.org/pdf/2402.03003v2.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":"citation-needed-data-usage-and-citation","repo_url":"https://github.com/theosourget/pdf_annotator","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":{"status":"ok"}},{"paper_slug":"citation-needed-data-usage-and-citation","repo_url":"https://github.com/theosourget/public_medical_datasets_references","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":{"status":"ok"}}],"tasks":[],"methods":[{"method_slug":"focus","method_name":"Focus"},{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2402.03003","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2402.03003"}},"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/theosourget/pdf_annotator","reach":{"status":"ok"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/theosourget/public_medical_datasets_references","reach":{"status":"ok"}}],"summary":{"ran":2,"unverified":4},"by_repo_kind":{"official":{"samples":6,"ran":2,"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":6,"samples":[{"code_sha256_prefix":"da7b209e8cb4d27f","entry":"abstract_extraction","repo":"theosourget/public_medical_datasets_references","repo_kind":"official","path":"Code/usage_detection/openalex_detection.py","file_url":"https://github.com/theosourget/public_medical_datasets_references/blob/HEAD/Code/usage_detection/openalex_detection.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"da7b209e8cb4d27f"}},{"code_sha256_prefix":"8c4db14e2ec4340e","entry":"reference_extraction","repo":"theosourget/public_medical_datasets_references","repo_kind":"official","path":"Code/usage_detection/openalex_detection.py","file_url":"https://github.com/theosourget/public_medical_datasets_references/blob/HEAD/Code/usage_detection/openalex_detection.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"8c4db14e2ec4340e"}},{"code_sha256_prefix":"e44a47ab8e64ebf4","entry":"doi_to_openAlexId","repo":"theosourget/public_medical_datasets_references","repo_kind":"official","path":"Code/usage_detection/openalex_detection.py","file_url":"https://github.com/theosourget/public_medical_datasets_references/blob/HEAD/Code/usage_detection/openalex_detection.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"e44a47ab8e64ebf4"}},{"code_sha256_prefix":"7940750c803c2f70","entry":"gather_for_venue","repo":"theosourget/public_medical_datasets_references","repo_kind":"official","path":"Code/data_collection/request_dblp.py","file_url":"https://github.com/theosourget/public_medical_datasets_references/blob/HEAD/Code/data_collection/request_dblp.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"7940750c803c2f70"}},{"code_sha256_prefix":"f6ac6e72312acb07","entry":"query_openalex_by_doi","repo":"theosourget/public_medical_datasets_references","repo_kind":"official","path":"Code/data_collection/get_papers_info.py","file_url":"https://github.com/theosourget/public_medical_datasets_references/blob/HEAD/Code/data_collection/get_papers_info.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"f6ac6e72312acb07"}},{"code_sha256_prefix":"63a0486c98c3a4ad","entry":"query_openalex_by_title","repo":"theosourget/public_medical_datasets_references","repo_kind":"official","path":"Code/data_collection/get_papers_info.py","file_url":"https://github.com/theosourget/public_medical_datasets_references/blob/HEAD/Code/data_collection/get_papers_info.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"63a0486c98c3a4ad"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}