{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:55:46Z","timestamp":1791388546227,"version":"4.3.3"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2022,6,9]],"date-time":"2022-06-09T00:00:00Z","timestamp":1654732800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG011466"],"award-info":[{"award-number":["R01HG011466"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01HG012069"],"award-info":[{"award-number":["U01HG012069"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5T32HG000044"],"award-info":[{"award-number":["5T32HG000044"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Stanford Genome Training Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>In silico saturation mutagenesis (ISM) is a popular approach in computational genomics for calculating feature attributions on biological sequences that proceeds by systematically perturbing each position in a sequence and recording the difference in model output. However, this method can be slow because systematically perturbing each position requires performing a number of forward passes proportional to the length of the sequence being examined.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we propose a modification of ISM that leverages the principles of compressed sensing to require only a constant number of forward passes, regardless of sequence length, when applied to models that contain operations with a limited receptive field, such as convolutions. Our method, named Yuzu, can reduce the time that ISM spends in convolution operations by several orders of magnitude and, consequently, Yuzu can speed up ISM on several commonly used architectures in genomics by over an order of magnitude. Notably, we found that Yuzu provides speedups that increase with the complexity of the convolution operation and the length of the sequence being analyzed, suggesting that Yuzu provides large benefits in realistic settings.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>We have made this tool available at https:\/\/github.com\/kundajelab\/yuzu.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac385","type":"journal-article","created":{"date-parts":[[2022,6,9]],"date-time":"2022-06-09T08:30:48Z","timestamp":1654763448000},"page":"3557-3564","source":"Crossref","is-referenced-by-count":16,"title":["Accelerating\n                    <i>in silico<\/i>\n                    saturation mutagenesis using compressed sensing"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4230-6625","authenticated-orcid":false,"given":"Jacob","family":"Schreiber","sequence":"first","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6216-2457","authenticated-orcid":false,"given":"Surag","family":"Nair","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Stanford University , Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akshay","family":"Balsubramani","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Stanford University , Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3084-2287","authenticated-orcid":false,"given":"Anshul","family":"Kundaje","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305, USA"},{"name":"Department of Computer Science, Stanford University , Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,9]]},"reference":[{"key":"2023041405370282800_","first-page":"66","author":"Ardah","year":"2019"},{"key":"2023041405370282800_","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1038\/s41588-021-00782-6","article-title":"Base-resolution models of transcription-factor binding reveal soft motif syntax","volume":"53","author":"Avsec","year":"2021","journal-title":"Nat. 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