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@INPROCEEDINGS{Piroozeh:1052350,
      author       = {Piroozeh, Zohreh and Akerman, Ildem and Kesselheim, Stefan
                      and Kalinina, Olga and Bazarova, Alina},
      title        = {{I}nterpretable prediction of {DNA} replication origins in
                      {S}. cerevisiae using attention-based motif discovery},
      reportid     = {FZJ-2026-00952},
      year         = {2025},
      abstract     = {In a living cell, DNA replication begins at multiple
                      genomic sites, called replicationorigins. Identifying these
                      origins and their underlying base sequence compositionis
                      crucial for understanding replication process. Existing
                      machine learningmethods for origin prediction often require
                      labor-intensive feature engineering orlack interpretability.
                      Here, we employ DNABERT to predict yeast replication
                      originsand uncover sequence motifs by combining attention
                      maps with MEME, aclassical bioinformatics tool. Our approach
                      eliminates manual feature extractionand identifies
                      biologically relevant motifs across datasets of varying
                      complexity.This work advances interpretable machine learning
                      in genomics, offering a potentiallygeneralizable framework
                      for origin prediction and motif discovery.},
      month         = {Apr},
      date          = {2025-04-24},
      organization  = {ICLR 2025, Singapore (Singapore), 24
                       Apr 2025 - 28 Apr 2025},
      subtyp        = {Other},
      cin          = {JSC},
      cid          = {I:(DE-Juel1)JSC-20090406},
      pnm          = {5112 - Cross-Domain Algorithms, Tools, Methods Labs (ATMLs)
                      and Research Groups (POF4-511) / Helmholtz AI Consultant
                      Team FB Information (E54.303.11)},
      pid          = {G:(DE-HGF)POF4-5112 / G:(DE-Juel-1)E54.303.11},
      typ          = {PUB:(DE-HGF)24},
      doi          = {10.34734/FZJ-2026-00952},
      url          = {https://juser.fz-juelich.de/record/1052350},
}