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TF-MoDISco (Transcription Factor Motif Discovery from Importance Scores) is an algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data.
Visualizing data using t-SNE
Laurens van der Maaten and Geoffrey Hinton · 2008
Earlier work this paper cites.
The louvain method for community detection in large networks
Vincent D Blondel, Jean-Lou Guillaume, Renaud Lambiotte, and Étienne Lefebvre · 2011
Earlier work this paper cites.
Predicting the sequence specificities of dna-and rna-binding proteins by deep learning
Babak Alipanahi, Andrew Delong, Matthew T Weirauch, and Brendan J Frey · 2015
Earlier work this paper cites.
Data-Driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis
Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-Ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder, Rachel Finck, Amanda L Gedman, Ina Radtke, James R Downing, Dana Pe’er, and Garry P Nolan · 2015
Earlier work this paper cites.
Predicting effects of noncoding variants with deep learning–based sequence model
Jian Zhou and Olga G Troyanskaya · 2015
Cited alongside, same era.
Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks
David R Kelley, Jasper Snoek, and John L Rinn · 2016
Cited alongside, same era.
Deep motif: Visualizing genomic sequence classifications
Jack Lanchantin, Ritambhara Singh, Zeming Lin, and Yanjun Qi · 2016
Cited alongside, same era.
Learning important features through propagating activation differences
Avanti Shrikumar, Peyton Greenside, and Anshul Kundaje · 2017
Cited alongside, same era.
Axiomatic attribution for deep networks
Mukund Sundararajan, Ankur Taly, and Qiqi Yan · 2017
Later among the works it cites.
Deep learning at base-resolution reveals motif syntax of the cis-regulatory code
Ž Avsec, M Weilert, A Shrikumar, A Alexandari, and others · 2019
Closest in time.
GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs
Avanti Shrikumar, Eva Prakash, and Anshul Kundaje · 2019
Closest in time.
From louvain to leiden: guaranteeing well-connected communities
V A Traag, L Waltman, and N J van Eck · 2019
Closest in time.
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