references.bib

@inproceedings{lee2001algorithms,
  title={Algorithms for non-negative matrix factorization},
  author={Lee, Daniel D and Seung, H Sebastian},
  booktitle={Advances in neural information processing systems},
  pages={556--562},
  year={2001}
}

@article{lee1999learning,
  title={Learning the parts of objects by non-negative matrix factorization},
  author={Lee, Daniel D and Seung, H Sebastian},
  journal={Nature},
  volume={401},
  number={6755},
  pages={788--791},
  year={1999},
  publisher={Nature Publishing Group}
}

@article{hoyer2004non,
  title={Non-negative matrix factorization with sparseness constraints},
  author={Hoyer, Patrik O},
  journal={Journal of machine learning research},
  volume={5},
  number={Nov},
  pages={1457--1469},
  year={2004}
}

@article{donoho2003does,
  title={When does non-negative matrix factorization give a correct decomposition into parts?},
  author={Donoho, David L and Stodden, Victoria C},
  year={2004},
  journal={Advances in neural information processing systems 16: proceedings of the 2003 conference},
  editor={Thrun, S and Saul, L and Sch\"{o}lkopf, B},
  publisher={MIT Press},
  location={Cambridge, Mass.}
}

@Article{gaujoux2010a,
  title = {A flexible R package for nonnegative matrix factorization},
  author = {Renaud Gaujoux and Cathal Seoighe},
  journal = {BMC Bioinformatics},
  year = {2010},
  volume = {11},
  number = {1},
  pages = {367},
  url = {http://www.biomedcentral.com/1471-2105/11/367},
  doi = {10.1186/1471-2105-11-367},
  issn = {1471-2105},
}

@Manual{gaujoux2015using,
  title = {Using the package NMF},
  author = {Renaud Gaujoux and Cathal Seoighe},
  publisher = {CRAN},
  year = {2015},
  note = {R package version 0.20.6},
  url = {http://cran.r-project.org/package=NMF},
}

@Manual{gaujoux2015the,
  title = {The package NMF: manual pages},
  author = {Renaud Gaujoux and Cathal Seoighe},
  publisher = {CRAN},
  year = {2015},
  note = {R package version 0.20.6},
  url = {http://cran.r-project.org/package=NMF},
}

@article{lee1997unsupervised,
  title={Unsupervised learning by convex and conic coding},
  author={Lee, Daniel D and Seung, H Sebastian},
  journal={Advances in neural information processing systems},
  pages={515--521},
  year={1997},
  publisher={MORGAN KAUFMANN PUBLISHERS}
}

@article{paatero1997least,
  title={Least squares formulation of robust non-negative factor analysis},
  author={Paatero, Pentti},
  journal={Chemometrics and intelligent laboratory systems},
  volume={37},
  number={1},
  pages={23--35},
  year={1997},
  publisher={Elsevier}
}


@article{nakayama1992experiencing,
  title={Experiencing and perceiving visual surfaces},
  author={Nakayama, K and Shimojo, S},
  journal={Science},
  volume={257},
  number={5075},
  pages={1357-1363},
  year={1992}
}

@article{hinton1995wake,
  title={The ``wake-sleep'' algorithm for unsupervised neural networks},
  author={Hinton, Geoffrey E and Dayan, Peter and Frey, Brendan J and Neal, Radford M},
  journal={Science},
  volume={268},
  number={5214},
  pages={1158-1161},
  year={1995},
  publisher={The American Association for the Advancement of Science}
}

@article{dempster1977maximum,
  title={Maximum likelihood from incomplete data via the EM algorithm},
  author={Dempster, Arthur P and Laird, Nan M and Rubin, Donald B},
  journal={Journal of the royal statistical society. Series B (methodological)},
  pages={1--38},
  year={1977},
  publisher={JSTOR}
}


@article{saul1997aggregate,
  title={Aggregate and mixed-order Markov models for statistical language processing},
  author={Saul, Lawrence and Pereira, Fernando},
  journal={Proceedings of the Second Conference on Empirical Methods in Natural Language Processing},
  pages={81--89},
  year={1997}
}

@manual{salton1986introduction,
  title={Introduction to modern information retrieval},
  author={Salton, Gerard and McGill, Michael J},
  year={1986},
  publisher={McGraw-Hill, New York}
}

@book{press1989numerical,
  title={Numerical recipes},
  author={Press, William H and Flannery, Brian P and Teukolsky, Saul A and Vetterling, William T and others},
  volume={3},
  year={1989},
  publisher={Cambridge University Press, Cambridge, England}
}

@book{jolliffe2002principal,
  title={Principal component analysis},
  author={Jolliffe, Ian},
  year={2002},
  publisher={Wiley Online Library}
}

@incollection{gersho1992vector,
  title={Vector Quantization I: Structure and Performance},
  author={Gersho, Allen and Gray, Robert M},
  booktitle={Vector quantization and signal compression},
  pages={309--343},
  year={1992},
  publisher={Springer}
}

@book{kullback1997information,
  title={Information theory and statistics},
  author={Kullback, Solomon},
  year={1997},
  publisher={Courier Corporation}
}

@article{kullback1951information,
  title={On information and sufficiency},
  author={Kullback, Solomon and Leibler, Richard A},
  journal={The annals of mathematical statistics},
  volume={22},
  number={1},
  pages={79--86},
  year={1951},
  publisher={JSTOR}
}


@article{mcculloch1943logical,
  title={A logical calculus of the ideas immanent in nervous activity},
  author={McCulloch, Warren S and Pitts, Walter},
  journal={The bulletin of mathematical biophysics},
  volume={5},
  number={4},
  pages={115--133},
  year={1943},
  publisher={Springer}
}

@book{hebb2005organization,
  title={The organization of behavior: A neuropsychological theory},
  author={Hebb, Donald Olding},
  year={2005},
  publisher={Psychology Press}
}


@article{cauchy1847methode,
  title={M{\'e}thode g{\'e}n{\'e}rale pour la r{\'e}solution des systemes d’{\'e}quations simultan{\'e}es},
  author={Cauchy, Augustin},
  journal={Comp. Rend. Sci. Paris},
  volume={25},
  number={1847},
  pages={536--538},
  year={1847}
}


@phdthesis{straeter1971extension,
  title={On the extension of the Davidon-Broyden class of rank one, quasi-Newton minimization methods to an infinite dimensional Hilbert space with applications to optimal control problems},
  author={Straeter, Terry Anthony},
  year={1971},
  school={North Carolina State University at Raleigh.}
}


@book{hestenes1952methods,
  title={Methods of conjugate gradients for solving linear systems},
  author={Hestenes, Magnus Rudolph and Stiefel, Eduard},
  volume={49},
  year={1952},
  publisher={NBS}
}

@book{friedman2001elements,
  title={The elements of statistical learning},
  author={Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
  volume={1},
  year={2001},
  publisher={Springer series in statistics Springer, Berlin}
}

@book{cichocki2009nonnegative,
  title={Nonnegative matrix and tensor factorizations: applications to exploratory multi-way data analysis and blind source separation},
  author={Cichocki, Andrzej and Zdunek, Rafal and Phan, Anh Huy and Amari, Shun-ichi},
  year={2009},
  publisher={John Wiley \& Sons}
}


@article{pascual2006nonsmooth,
  title={Nonsmooth nonnegative matrix factorization (nsNMF)},
  author={Pascual-Montano, Alberto and Carazo, Jose Maria and Kochi, Kieko and Lehmann, Dietrich and Pascual-Marqui, Roberto D},
  journal={IEEE transactions on pattern analysis and machine intelligence},
  volume={28},
  number={3},
  pages={403--415},
  year={2006},
  publisher={IEEE}
}

@inproceedings{badea2008extracting,
  title={Extracting gene expression profiles common to colon and pancreatic adenocarcinoma using simultaneous nonnegative matrix factorization.},
  author={Badea, Liviu},
  booktitle={Pacific Symposium on Biocomputing},
  volume={290},
  number={13},
  pages={279--290},
  year={2008},
  organization={Citeseer}
}


@article{kim2007sparse,
  title={Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis},
  author={Kim, Hyunsoo and Park, Haesun},
  journal={Bioinformatics},
  volume={23},
  number={12},
  pages={1495--1502},
  year={2007},
  publisher={Oxford University Press}
}


@article{marchini2013fastica,
  title={fastICA: FastICA algorithms to perform ICA and Projection Pursuit},
  author={Marchini, JL and Heaton, C and Ripley, BD},
  journal={R package version},
  pages={1--2},
  year={2013}
}




@article{boutsidis2008svd,
  title={SVD based initialization: A head start for nonnegative matrix factorization},
  author={Boutsidis, Christos and Gallopoulos, Efstratios},
  journal={Pattern Recognition},
  volume={41},
  number={4},
  pages={1350--1362},
  year={2008},
  publisher={Elsevier}
}


@article{brunet2004metagenes,
  title={Metagenes and molecular pattern discovery using matrix factorization},
  author={Brunet, Jean-Philippe and Tamayo, Pablo and Golub, Todd R and Mesirov, Jill P},
  journal={Proceedings of the national academy of sciences},
  volume={101},
  number={12},
  pages={4164--4169},
  year={2004},
  publisher={National Acad Sciences}
}


@article{hutchins2008position,
  title={Position-dependent motif characterization using non-negative matrix factorization},
  author={Hutchins, Lucie N and Murphy, Sean M and Singh, Priyam and Graber, Joel H},
  journal={Bioinformatics},
  volume={24},
  number={23},
  pages={2684--2690},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{frigyesi2008non,
  title={Non-negative matrix factorization for the analysis of complex gene expression data: identification of clinically relevant tumor subtypes},
  author={Frigyesi, Attila and H{\"o}glund, Mattias},
  journal={Cancer informatics},
  volume={6},
  year={2008},
  publisher={Libertas Academica Ltd.}
}

@article{paatero1994positive,
  title={Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values},
  author={Paatero, Pentti and Tapper, Unto},
  journal={Environmetrics},
  volume={5},
  number={2},
  pages={111--126},
  year={1994},
  publisher={Wiley Online Library}
}

@article{vavasis2009complexity,
  title={On the complexity of nonnegative matrix factorization},
  author={Vavasis, Stephen A},
  journal={SIAM Journal on Optimization},
  volume={20},
  number={3},
  pages={1364--1377},
  year={2009},
  publisher={SIAM}
}

@inproceedings{arora2013practical,
  title={A Practical Algorithm for Topic Modeling with Provable Guarantees.},
  author={Arora, Sanjeev and Ge, Rong and Halpern, Yonatan and Mimno, David M and Moitra, Ankur and Sontag, David and Wu, Yichen and Zhu, Michael},
  booktitle={ICML (2)},
  pages={280--288},
  year={2013}
}

@article{wild2004improving,
  title={Improving non-negative matrix factorizations through structured initialization},
  author={Wild, Stefan and Curry, James and Dougherty, Anne},
  journal={Pattern recognition},
  volume={37},
  number={11},
  pages={2217--2232},
  year={2004},
  publisher={Elsevier}
}


@article{xue2008clustering,
  title={Clustering-based initialization for non-negative matrix factorization},
  author={Xue, Yun and Tong, Chong Sze and Chen, Ying and Chen, Wen-Sheng},
  journal={Applied Mathematics and Computation},
  volume={205},
  number={2},
  pages={525--536},
  year={2008},
  publisher={Elsevier}
}

@article{berry2007algorithms,
  title={Algorithms and applications for approximate nonnegative matrix factorization},
  author={Berry, Michael W and Browne, Murray and Langville, Amy N and Pauca, V Paul and Plemmons, Robert J},
  journal={Computational statistics \& data analysis},
  volume={52},
  number={1},
  pages={155--173},
  year={2007},
  publisher={Elsevier}
}

@inproceedings{chu2004optimality,
  title={Optimality, computation, and interpretation of nonnegative matrix factorizations},
  author={Chu, Moody and Diele, Fasma and Plemmons, Robert and Ragni, Stefania},
  booktitle={SIAM Journal on Matrix Analysis},
  year={2004},
  organization={Citeseer}
}

@article{finesso2006nonnegative,
  title={Nonnegative matrix factorization and I-divergence alternating minimization},
  author={Finesso, Lorenzo and Spreij, Peter},
  journal={Linear Algebra and its Applications},
  volume={416},
  number={2-3},
  pages={270--287},
  year={2006},
  publisher={Elsevier}
}

@article{zhang2008pattern,
  title={Pattern expression nonnegative matrix factorization: algorithm and applications to blind source separation},
  author={Zhang, Junying and Wei, Le and Feng, Xuerong and Ma, Zhen and Wang, Yue},
  journal={Computational intelligence and neuroscience},
  volume={2008},
  year={2008},
  publisher={Hindawi Publishing Corporation}
}

@book{smilde2005multi,
  title={Multi-way analysis: applications in the chemical sciences},
  author={Smilde, Age and Bro, Rasmus and Geladi, Paul},
  year={2005},
  publisher={John Wiley \& Sons}
}

@article{langville2014algorithms,
  title={Algorithms, initializations, and convergence for the nonnegative matrix factorization},
  author={Langville, Amy N and Meyer, Carl D and Albright, Russell and Cox, James and Duling, David},
  journal={arXiv preprint arXiv:1407.7299},
  year={2014}
}

@article{jeter1981note,
  title={A note on nonnegative rank factorizations},
  author={Jeter, MW and Pye, WC},
  journal={Linear Algebra and its Applications},
  volume={38},
  pages={171--173},
  year={1981},
  publisher={Elsevier}
}

@inproceedings{xu2003document,
  title={Document clustering based on non-negative matrix factorization},
  author={Xu, Wei and Liu, Xin and Gong, Yihong},
  journal={Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval},
  pages={267--273},
  year={2003},
  organization={ACM}
}


@inproceedings{hofmann1999probabilistic,
  title={Probabilistic latent semantic indexing},
  author={Hofmann, Thomas},
  booktitle={Proceedings of the 22nd annual international ACM SIGIR conference on Research and development in information retrieval},
  pages={50--57},
  year={1999},
  organization={ACM}
}

@manual{gaujoux2014introduction,
  title={An introduction to NMF package},
  author={Gaujoux, Renaud},
  year={2014},
  booktitle={ }
}

@inproceedings{cichocki2007hierarchical,
  title={Hierarchical ALS algorithms for nonnegative matrix and 3D tensor factorization},
  author={Cichocki, Andrzej and Zdunek, Rafal and Amari, Shun-ichi},
  booktitle={International Conference on Independent Component Analysis and Signal Separation},
  pages={169--176},
  year={2007},
  organization={Springer}
}