nmfalgorithmlist.txt

List of NMF algorithms in this repository:

1. LRSLibrary

- NMF-MU: NMF solved by Multiplicative Updates (Lee and Seung)
	Impl: Kasper Winther Joergensen (NMF-DTU Toolbox, exact copy)
	File: lrslibrary/algorithms/nmf/NMF-DTU-Toolbox/nmf_mm.m 
- NMF-PG: NMF solved by Projected Gradient
	Impl: Chih-Jen Lin (NMF-DTU Toolbox, exact copy)
	Note: This 'clean' version contains a license note and is nicely formatted.
	File: lrslibrary/algorithms/nmf/NMF-DTU-Toolbox/nmf_cjlin.m
- NMF-ALS: NMF solved by Alternating Least Squares
	Impl: Lars Kai Hansen (NMF-DTU Toolbox, exact copy)
	File: lrslibrary/algorithms/nmf/NMF-DTU-Toolbox/nmf_als.m
- NMF-ALS-OBS: NMF solved by Alternating Least Squares with Optimal Brain Surgeon
	Impl: Kasper Winther Joergensen (NMF-DTU Toolbox, exact copy)
	File: lrslibrary/algorithms/nmf/NMF-DTU-Toolbox/nmf_alsobs.m
- PNMF: Probabilistic Non-negative Matrix Factorization
	Impl: Lars Kai Hansen (NMF-DTU Toolbox, exact copy)
	File: lrslibrary/algorithms/nmf/NMF-DTU-Toolbox/nmf_prob.m
- ManhNMF: Manhattan NMF (Guan et al. 2013)
	Impl: Naiyang Guan
	File: lrslibrary/algorithms/nmf/ManhNMF/ManhNMF.m
- NeNMF: NMF via Nesterovs Optimal Gradient Method (Guan et al. 2012)
	Impl: Naiyang Guan
	File: lrslibrary/algorithms/nmf/NeNMF/NeNMF.m
- LNMF: Spatially Localized NMF (Li et al. 2001)
	Impl: Naiyang Guan, naar Li.
	File: lrslibrary/algorithms/nmf/LNMF/LNMF.m
	Asset: DNMF - Discriminative Nonnegative Matrix Factorization ( S. Zafeiriou, A. Tefas, I. Buciu, and I. Pitas)
		Impl: Naiyang Guan
		File: lrslibrary/algorithms/nmf/LNMF/DNFM.m
	Asset: NMF - Implementation of Lee and Seung
		Impl: Jean-Philippe Brunet
		File: lrslibrary/algorithms/nmf/LNMF/NMF.m
	Asset: Fast Gradient Descent NNLS method (see NPAF.m)
		Impl: Naiyang Guan
		File: lrslibrary/algorithms/nmf/LNMF/FGD.m and lrslibrary/algorithms/nmf/LNMF/FGD_H.m
	Asset: Multiple-stepsize Fast Gradient Descent Method
		Impl: Naiyang Guan
		Files: lrslibrary/algorithms/nmf/LNMF/MFGD.m and lrslibrary/algorithms/nmf/LNMF/MFGD_H.m
- ENMF: Exact NMF (Gillis and Glineur, 2012, "on the geometric interpretation")
	Impl: N. Gillis ?
	File: lrslibrary/algorithms/nmf/ENMF/ExactNMF.m
- nmfLS2: Non-negative Matrix Factorization with sparse matrix (Ji and Eisenstein, 2013)
	Impl: Yangfeng Ji ?
	File: lrslibrary/algorithms/nmf/nmfLS2/nmfLS2.m
- Semi-NMF: Semi Non-negative Matrix Factorization
	Impl: ?
	File: lrslibrary/algorithms/nmf/Semi-NMF/seminmf.m
- Deep-Semi-NMF: Deep Semi Non-negative Matrix Factorization (Trigeorgis et al. 2014)
	Impl: ?
	File: lrslibrary/algorithms/nmf/Deep-Semi-NMF/deep_seminmf.m
- iNMF: Incremental Subspace Learning via NMF (Bucak and Gunsel, 2009)
	Impl: Serhat Bucak
	File: lrslibrary/algorithms/nmf/iNMF/inmf.m 
- DRMF: Direct Robust Matrix Factorization (Xiong et al. 2011)
	Impl: Liang Xiong
	File: lrslibrary/algorithms/nmf/DRMF/DRMF.m

2. NMF_APD
- AccNMF (Gillies and Glineur, 2012, "accelerated mult. up".)
	File: NMF_APD/Methods/AccNMF/RunME
- ActiveSet (Jingu Kim and Haesun Park)
	File: NMF_APD/Methods/ActiveSet/ActiveSet.m
- AloExactNMF (greedy coordinate descent)
	Impl: Hsieh and Dillon? Adapted by Khuong?
	File: NMF_APD/Methods/AloExactNMF/AloExactNMF.m
	Note: CAREFUL with this code, does not correspond to Hsieh/Dillon matlab/mex!
- AloNMF (Hsieh and Dillon? Adapted by Khuong?)
	File: NMF_APD/Methods/AloNMF/AloProject.m ? (Note: AlNMF is exactly AloExactNMF from above)
	Note: similar or same to AloExactNMF. Skip.
- FCDMNMF (Cho-Jui Hsieh and Inderjit S. Dhillon)
	File: NMF_APD/Methods/FCDMNMF/NMF_GCD
- MU (2 implementations: Brunet (copy of lrslib/LNMF version) and Ross)
	File: NMF_APD/Methods/MU/LeeNMF
- NeNMF : Guan et al, (copy of lrslib version)
	File: NMF_APD/Methods/NeNMF
- NtNMF : Dongmin Kim (and Dhillon?)
	File: NMF_APD/Methods/NtNMF/NtNMF.m
- PGNMF : Lin, Projected Gradient Methods for Nonnegative Matrix Factorization
	Impl: C.J. Lin?
	Note: This version is not as well-documented as the one in (lrslib)/NMF-DTU and does not contain license
	File: NMF_APD/Methods/PGNMF/PCLIN.m
- QNNMF : Kim, Sra and Dhillon
	Impl: Dongmin Kim (and Dhillon?)
	File: NMF_APD/Methods/QNNMF/QnNMF.m

3. nmfdtu - in its entirety included in LRSLIB

4. NMFLABSP (Cichocki et al)

- Regularized Lee-Seung NMF algorithms. Frobenius, KL or Beta-norms. Contains: 
	- EMML, 
	- ISRA, 
	- Kompass algorithm, 
	- projected pseudo-inverse.
- Projected gradient algorithms: 
	- GPCG (Gradient Projected Conjugate Gradient), 
	- PG (Projected Gradient), 
	- IPG (Interior Projected Gradient), 
	- Regularized MRNSD (Minimal Residual Norm Steepest Descent), 
	- Relaxed Hellinger, 
	- Projected pseudo-inverse.
- NMF-ALPHA : Multiplicative algorithms based on the Amari's alpha divergence.
- SMART algorithms based on the Exponentiated Gradient (EG) and various divergences.
- Second-order algorithms (mixing matrix is estimated using algorithms based on the quasi-Newton method).
- Cascade algorithms that estimate the missing matrix as a chain of matrices.

5. nmflib (Grindlay)

- Amari divergence
- Beta divergence
- Convex NMF
- Orthogonal Euclidean NMF (S. Choi)
- Sparse NMF (Virtanen)
- Sparse NMF (Eggert, Schmidt)

6. nmfpack (Hoyer)

7. nmftoolbox (Li and Ngom)

8. scattnmf (Bruna, Sprechmann, LeCun)

- demix_scatt2top: see paper Source Separation with Scattering NMF.
- note: depends on SPAMS package (see below)

9. SGNMF (Cai, He, Wu, Han)

- SGNMF: see paper Graph-regularized NMF for Data Representation

10. spams-matlab (Mairal)

- NMF: see paper Online Learning for Matrix Factorization and Sparse Coding

11. BNMF: Bayesian NMF (Mohammadiha, Smaragdis, Leijon)


TODO see
http://nimfa.biolab.si/nimfa.methods.html ? (Python) for more distance measures e.g.
or citations in
https://en.wikipedia.org/wiki/Non-negative_matrix_factorization ?
also ref
https://github.com/bioinfo-cnb ? (implementation on GPU)
http://www.cai.sk/ojs/index.php/cai/article/view/161/136 ? (implementation in C)