{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T13:34:22Z","timestamp":1792157662134,"version":"4.4.0"},"posted":{"date-parts":[[2025,5,22]]},"group-title":"Bioinformatics","reference-count":54,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T00:00:00Z","timestamp":1747872000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R03OD038391"],"award-info":[{"award-number":["R03OD038391"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["P30CA036727"],"award-info":[{"award-number":["P30CA036727"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]},{"award":["CA036727"],"award-info":[{"award-number":["CA036727"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]},{"award":["IRG-22-146-07-IRG"],"award-info":[{"award-number":["IRG-22-146-07-IRG"]}],"id":[{"id":"https:\/\/ror.org\/02e463172","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["P20GM103427"],"award-info":[{"award-number":["P20GM103427"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy defined by aberrant clonal expansion of abnormal myeloid progenitor cells. Characterized by morphological, molecular, and genetic alterations, AML encompasses multiple distinct subtypes that would exhibit subtype-specific responses to treatment and prognosis, underscoring the critical need of accurately identifying AML subtypes for effective clinical management and tailored therapeutic approaches. Traditional wet lab approaches such as immunophenotyping, cytogenetic analysis, morphological analysis, or molecular profiling to identify AML subtypes are labor-intensive, costly, and time-consuming. To address these challenges, we propose\n                  <jats:bold>AttentionAML<\/jats:bold>\n                  , a novel attention-based deep learning framework for accurately categorizing AML subtypes based on transcriptomic profiling only. Benchmarking tests based on 1,661 AML patients suggested that AttentionAML outperformed state-of-the-art methods across all evaluated metrics (accuracy: 0.96, precision: 0.96, recall of 0.96, F1-score: 0.96, and Matthews correlation coefficient: 0.96). Furthermore, we also demonstrated the superiority of AttentionAML over conventional approaches in terms of AML patient clustering visualization and subtype-specific gene marker characterization. We believe AttentionAML will bring remarkable positive impacts on downstream AML risk stratification and personalized treatment design. To enhance its impact, a user-friendly Python package implementing AttentionAML is publicly available at\n                  <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/wan-mlab\/AttentionAML\">https:\/\/github.com\/wan-mlab\/AttentionAML<\/jats:ext-link>\n                  .\n                <\/jats:p>","DOI":"10.1101\/2025.05.20.655179","type":"posted-content","created":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T10:10:13Z","timestamp":1747908613000},"source":"Crossref","is-referenced-by-count":5,"title":["AttentionAML: An Attention-based Deep Learning Framework for Accurate Molecular Categorization of Acute Myeloid Leukemia"],"prefix":"10.64898","author":[{"given":"Lusheng","family":"Li","sequence":"first","affiliation":[{"name":"Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph D.","family":"Khoury","sequence":"additional","affiliation":[{"name":"Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jieqiong","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0661-2684","authenticated-orcid":false,"given":"Shibiao","family":"Wan","sequence":"additional","affiliation":[{"name":"Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041122591155000_2025.05.20.655179v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2014.01.031"},{"key":"2026041122591155000_2025.05.20.655179v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2016.67"},{"key":"2026041122591155000_2025.05.20.655179v1.3","unstructured":"Lagunas-Rangel FA , Ch\u00e1vez-Valencia V , G\u00f3mez-Guijosa M\u00c1 , Cortes C. Acute Myeloid Leukemia\u2014Genetic Alterations and Their Clinical Prognosis.. 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