{"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/evaluating-histopathology-transfer-learning","title":"Evaluating histopathology transfer learning with ChampKit","arxiv_id":"2206.06862","date":"2022-06-14","proceeding":null,"authors":["Jakub R. Kaczmarzyk","Tahsin M. Kurc","Shahira Abousamra","Rajarsi Gupta","Joel H. Saltz","Peter K. Koo"],"abstract":"Histopathology remains the gold standard for diagnosis of various cancers. Recent advances in computer vision, specifically deep learning, have facilitated the analysis of histopathology images for various tasks, including immune cell detection and microsatellite instability classification. The state-of-the-art for each task often employs base architectures that have been pretrained for image classification on ImageNet. The standard approach to develop classifiers in histopathology tends to focus narrowly on optimizing models for a single task, not considering the aspects of modeling innovations that improve generalization across tasks. Here we present ChampKit (Comprehensive Histopathology Assessment of Model Predictions toolKit): an extensible, fully reproducible benchmarking toolkit that consists of a broad collection of patch-level image classification tasks across different cancers. ChampKit enables a way to systematically document the performance impact of proposed improvements in models and methodology. ChampKit source code and data are freely accessible at https://github.com/kaczmarj/champkit .","url_abs":"https://arxiv.org/abs/2206.06862v1","url_pdf":"https://arxiv.org/pdf/2206.06862v1.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":"evaluating-histopathology-transfer-learning","repo_url":"https://github.com/kaczmarj/champkit","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"Apache-2.0"}}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"cell-detection","task_name":"Cell Detection"},{"task_slug":"classification","task_name":"General Classification"},{"task_slug":"image-classification","task_name":"Image Classification"},{"task_slug":"medical-image-classification","task_name":"Medical Image Classification"},{"task_slug":"transfer-learning","task_name":"Transfer Learning"},{"task_slug":"image-classification","task_name":"image-classification"}],"methods":[{"method_slug":"base","method_name":"BASE"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2206.06862","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2206.06862"}},"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/kaczmarj/champkit","reach":{"status":"ok","spdx":"Apache-2.0"}}],"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":"dcef9cbdadfea711","entry":"run_all_evaluations","repo":"kaczmarj/champkit","repo_kind":"official","path":"run_all_evaluations.py","file_url":"https://github.com/kaczmarj/champkit/blob/HEAD/run_all_evaluations.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":"dcef9cbdadfea711"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}