Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks

نویسندگان

چکیده

Deep neural networks have demonstrated improved performance at predicting the sequence specificities of DNA- and RNA-binding proteins compared to previous methods that rely on k -mers position weight matrices. To gain insights into why a DNN makes given prediction, model interpretability methods, such as attribution can be employed identify motif-like representations along sequence. Because explanations are an individual basis vary substantially across sequences, deducing generalizable trends dataset quantifying their effect size remains challenge. Here we introduce global importance analysis (GIA), method quantifies population-level putative patterns predictions. GIA provides avenue quantitatively test hypotheses interactions with other patterns, well map out specific functions network has learned. As case study, demonstrate utility computational task RNA-protein from We first convolutional network, call ResidualBind, benchmark its against RNAcompete data. Using GIA, then in addition motifs, ResidualBind learns considers number spacing, context, RNA secondary structure GC-bias.

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ژورنال

عنوان ژورنال: PLOS Computational Biology

سال: 2021

ISSN: ['1553-734X', '1553-7358']

DOI: https://doi.org/10.1371/journal.pcbi.1008925