{"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/chest-imagenome-dataset-for-clinical","title":"Chest ImaGenome Dataset for Clinical Reasoning","arxiv_id":"2108.00316","date":"2021-07-31","proceeding":null,"authors":["Joy T. Wu","Nkechinyere N. Agu","Ismini Lourentzou","Arjun Sharma","Joseph A. Paguio","Jasper S. Yao","Edward C. Dee","William Mitchell","Satyananda Kashyap","Andrea Giovannini","Leo A. Celi","Mehdi Moradi"],"abstract":"Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global \"weak\" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe $242,072$ images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) $1,256$ combinations of relation annotations between $29$ CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over $670,000$ localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from $500$ unique patients.","url_abs":"https://arxiv.org/abs/2108.00316v1","url_pdf":"https://arxiv.org/pdf/2108.00316v1.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":"chest-imagenome-dataset-for-clinical","repo_url":"https://github.com/LourentzouTBD/ChestImaGenomeChangeDetection","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"anatomy","task_name":"Anatomy"}],"methods":[],"datasets_introduced":[{"slug":"chest-imagenome","name":"Chest ImaGenome","full_name":""}],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2108.00316","atlas_url":"https://app.syntology.ai/?focus=2108.00316","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2108.00316"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+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/LourentzouTBD/ChestImaGenomeChangeDetection","reach":{"status":"ok","spdx":"MIT"}}],"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":"a0d52457fbfb9ccc","entry":"split_dataset","repo":"LourentzouTBD/ChestImaGenomeChangeDetection","repo_kind":"official","path":"data.py","file_url":"https://github.com/LourentzouTBD/ChestImaGenomeChangeDetection/blob/HEAD/data.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":"a0d52457fbfb9ccc"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}