{"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/benchmarking-fish-dataset-and-evaluation","title":"Benchmarking Fish Dataset and Evaluation Metric in Keypoint Detection -- Towards Precise Fish Morphological Assessment in Aquaculture Breeding","arxiv_id":"2405.12476","date":"2024-05-21","proceeding":null,"authors":["Weizhen Liu","Jiayu Tan","Guangyu Lan","Ao Li","Dongye Li","Le Zhao","Xiaohui Yuan","Nanqing Dong"],"abstract":"Accurate phenotypic analysis in aquaculture breeding necessitates the quantification of subtle morphological phenotypes. Existing datasets suffer from limitations such as small scale, limited species coverage, and inadequate annotation of keypoints for measuring refined and complex morphological phenotypes of fish body parts. To address this gap, we introduce FishPhenoKey, a comprehensive dataset comprising 23,331 high-resolution images spanning six fish species. Notably, FishPhenoKey includes 22 phenotype-oriented annotations, enabling the capture of intricate morphological phenotypes. Motivated by the nuanced evaluation of these subtle morphologies, we also propose a new evaluation metric, Percentage of Measured Phenotype (PMP). It is designed to assess the accuracy of individual keypoint positions and is highly sensitive to the phenotypes measured using the corresponding keypoints. To enhance keypoint detection accuracy, we further propose a novel loss, Anatomically-Calibrated Regularization (ACR), that can be integrated into keypoint detection models, leveraging biological insights to refine keypoint localization. Our contributions set a new benchmark in fish phenotype analysis, addressing the challenges of precise morphological quantification and opening new avenues for research in sustainable aquaculture and genetic studies. Our dataset and code are available at https://github.com/WeizhenLiuBioinform/Fish-Phenotype-Detect.","url_abs":"https://arxiv.org/abs/2405.12476v2","url_pdf":"https://arxiv.org/pdf/2405.12476v2.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":"benchmarking-fish-dataset-and-evaluation","repo_url":"https://github.com/weizhenliubioinform/fish-phenotype-detect","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"keypoint-detection","task_name":"Keypoint Detection"}],"methods":[{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2405.12476","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2405.12476"}},"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/WeizhenLiuBioinform/Fish-Phenotype-Detect","reach":null}],"summary":{"ran":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"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":1,"samples":[{"code_sha256_prefix":"dadb32ccb813263c","entry":"KpLoss","repo":"WeizhenLiuBioinform/Fish-Phenotype-Detect","repo_kind":"official","path":"fish_ACR/train_utils/loss.py","file_url":"https://github.com/WeizhenLiuBioinform/Fish-Phenotype-Detect/blob/HEAD/fish_ACR/train_utils/loss.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":"dadb32ccb813263c"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}