{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:35Z","timestamp":1772138075241,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,5,29]],"date-time":"2025-05-29T00:00:00Z","timestamp":1748476800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2018-06169"],"award-info":[{"award-number":["2018-06169"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001729","name":"Swedish Foundation for Strategic Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001729","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Nanopores are highly sensitive sensors that have achieved commercial success in DNA\/RNA sequencing, with potential applications in protein sequencing and biomarker identification. Solid-state nanopores, in particular, face challenges such as instability and low signal-to-noise ratios, which lead scientists to adopt data-driven methods for nanopore signal analysis, although data acquisition remains restrictive.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We address this data scarcity by augmenting the training samples with traces that emulate Brownian motion effects, based on dynamic models in the literature. We apply this method to a publicly available dataset of a classification task containing nanopore reads of DNA with encoded barcodes. A neural network named QuipuNet was previously published for this dataset, and we demonstrate that our augmentation method produces a noticeable increase in QuipuNet\u2019s accuracy. Furthermore, we introduce a novel neural network named YupanaNet, which achieves greater accuracy (95.8%) than QuipuNet (94.6%) on the same dataset. YupanaNet benefits from both the enhanced generalization provided by Brownian motion data augmentation and the incorporation of novel architectures, including skip connections and a soft attention mask.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code and data are available at: https:\/\/github.com\/JavierKipen\/browDataAug.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf323","type":"journal-article","created":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T07:31:59Z","timestamp":1748331119000},"source":"Crossref","is-referenced-by-count":0,"title":["Brownian motion data augmentation: a method to push neural network performance on nanopore sensors"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6753-8548","authenticated-orcid":false,"given":"Javier","family":"Kipen","sequence":"first","affiliation":[{"name":"Division of Information Science and Engineering, Kungliga Tekniska H\u00f6gskolan , Stockholm 114 28,","place":["Sweden"]}]},{"given":"Joakim","family":"Jald\u00e9n","sequence":"additional","affiliation":[{"name":"Division of Information Science and Engineering, Kungliga Tekniska H\u00f6gskolan , Stockholm 114 28,","place":["Sweden"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,29]]},"reference":[{"key":"2025070408280221000_btaf323-B1","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/nnano.2016.50","article-title":"Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores","volume":"11","author":"Bell","year":"2016","journal-title":"Nat 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