{"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/assigning-species-information-to","title":"Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework","arxiv_id":"2205.03853","date":"2022-05-08","proceeding":null,"authors":["Ling Luo","Chih-Hsuan Wei","Po-Ting Lai","Qingyu Chen","Rezarta Islamaj Doğan","Zhiyong Lu"],"abstract":"The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or identifier by a text-mining algorithm. Existing methods typically rely on heuristic rules based on gene and species co-occurrence in the article, but their accuracy is suboptimal. We therefore developed a high-performance method, using a novel deep learning-based framework, to classify whether there is a relation between a gene and a species. Instead of the traditional binary classification framework in which all possible pairs of genes and species in the same article are evaluated, we treat the problem as a sequence-labeling task such that only a fraction of the pairs needs to be considered. Our benchmarking results show that our approach obtains significantly higher performance compared to that of the rule-based baseline method for the species assignment task (from 65.8% to 81.3% in accuracy). The source code and data for species assignment are freely available at https://github.com/ncbi/SpeciesAssignment.","url_abs":"https://arxiv.org/abs/2205.03853v1","url_pdf":"https://arxiv.org/pdf/2205.03853v1.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":"assigning-species-information-to","repo_url":"https://github.com/ncbi/speciesassignment","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"tf","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"binary-classification","task_name":"Binary Classification"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}