deepNF specifications


Unique identifier OMICS_24071
Name deepNF
Software type Application/Script
Interface Command line interface
Restrictions to use None
Programming languages Python
Computer skills Advanced
Stability Stable
python, scikit-learn, numpy, keras, tensorflow, ppmi, deepnf
Maintained Yes




No version available


  • person_outline Vladimir Gligorijević
  • person_outline Meet Barot
  • person_outline Richard Bonneau

Publication for deepNF

deepNF citation


Opportunities and obstacles for deep learning in biology and medicine

PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] uctural information.An important challenge in PPI network prediction is the task of combining different networks and types of networks. Gligorijevic et al. [] developed a multimodal deep autoencoder, deepNF, to find a feature representation common among several different PPI networks. This common lower-level representation allows for the combination of various PPI data sources towards a single pre […]

deepNF institution(s)
Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA; Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, NY, USA
deepNF funding source(s)
Supported by the Simons Foundation, the NIH, the NSF and NYU for supporting this research, particularly NSF: MCB-1158273, IOS-1339362, MCB-1412232, MCB- 1355462, IOS-0922738, MCB-0929338, and NIH: 2R01GM032877-25A1.

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