Nmf (models.nmf)

class nimfa.models.nmf.Nmf(params)

Bases: object

This class defines a common interface / model to handle NMF models in a generic way.

It contains definitions of the minimum set of generic methods that are used in common computations and matrix factorizations. Besides it contains some quality and performance measures about factorizations.

rank

Factorization rank

V

Target matrix, the matrix for the MF method to estimate. The columns of target matrix V are called samples, the rows of target matrix V are called features. Some algorithms (e. g. multiple NMF) specify more than one target matrix. In that case target matrices are passed as tuples. Internally, additional attributes with names following Vn pattern are created, where n is the consecutive index of target matrix. Zero index is omitted (there are V, V1, V2, V3, etc. matrices and then H, H1, H2, etc. and W, W1, W2, etc. respectively - depends on the algorithm).

seed

Method to seed the computation of a factorization

method

The algorithm to use to perform MF on target matrix

n_run

The number of runs of the algorithm

n_iter

The number of iterations performed

final_obj

Final value (of the last performed iteration) of the objective function

callback

A callback function that is called after each run if performing multiple runs

options

Runtime / algorithm specific options

max_iter

Maximum number of factorization iterations

min_residuals

Minimal required improvement of the residuals from the previous iteration

test_conv

Indication how often convergence test is done.

basis()

Return the matrix of basis vectors. See NMF specific model.

coef(idx=None)

Return the matrix of mixture coefficients. See NMF specific model.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

connectivity(H=None, idx=None)

Compute the connectivity matrix for the samples based on their mixture coefficients.

The connectivity matrix C is a symmetric matrix which shows the shared membership of the samples: entry C_ij is 1 iff sample i and sample j belong to the same cluster, 0 otherwise. Sample assignment is determined by its largest metagene expression value.

Return connectivity matrix.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

consensus(idx=None)

Compute consensus matrix as the mean connectivity matrix across multiple runs of the factorization. It has been proposed by [Brunet2004] to help visualize and measure the stability of the clusters obtained by NMF.

Tracking of matrix factors across multiple runs must be enabled for computing consensus matrix. For results of a single NMF run, the consensus matrix reduces to the connectivity matrix.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

coph_cor(idx=None)

Compute cophenetic correlation coefficient of consensus matrix, generally obtained from multiple NMF runs.

The cophenetic correlation coefficient is measure which indicates the dispersion of the consensus matrix and is based on the average of connectivity matrices. It measures the stability of the clusters obtained from NMF. It is computed as the Pearson correlation of two distance matrices: the first is the distance between samples induced by the consensus matrix; the second is the distance between samples induced by the linkage used in the reordering of the consensus matrix [Brunet2004].

Return real number. In a perfect consensus matrix, cophenetic correlation equals 1. When the entries in consensus matrix are scattered between 0 and 1, the cophenetic correlation is < 1. We observe how this coefficient changes as factorization rank increases. We select the first rank, where the magnitude of the cophenetic correlation coefficient begins to fall [Brunet2004].

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model :param:`idx` is always None.

dim(idx=None)

Return triple containing the dimension of the target matrix and matrix factorization rank.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

dispersion(idx=None)

Compute dispersion coefficient of consensus matrix

Dispersion coefficient [Park2007] measures the reproducibility of clusters obtained from multiple NMF runs.

Return the real value in [0,1]. Dispersion is 1 for a perfect consensus matrix and has value in [0,0] for a scattered consensus matrix.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In standard NMF model or nonsmooth NMF model idx is always None.

distance(metric='euclidean', idx=None)

Return the loss function value. See NMF specific model.

Parameters:

• distance (str with values ‘euclidean’ or ‘kl’) – Specify distance metric to be used. Possible are Euclidean and Kullback-Leibler (KL) divergence. Strictly, KL is not a metric.
• idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

entropy(membership=None, idx=None)

Compute the entropy of the NMF model given a priori known groups of samples [Park2007].

The entropy is a measure of performance of a clustering method in recovering classes defined by a list a priori known (true class labels).

Return the real number. The smaller the entropy, the better the clustering performance.

Parameters:

• membership (list) – Specify known class membership for each sample.
• idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

estimate_rank(rank_range=[30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], n_run=10, idx=0, what='all')

Choosing factorization parameters carefully is vital for success of a factorization. However, the most critical parameter is factorization rank. This method tries different values for ranks, performs factorizations, computes some quality measures of the results and chooses the best value according to [Brunet2004] and [Hutchins2008].

Note

The process of rank estimation can be lengthy.

Note

Matrix factors are tracked during rank estimation. This is needed for computing cophenetic correlation coefficient.

Return a dict (keys are values of rank from range, values are `dict`s of measures) of quality measures for each value in rank’s range. This can be passed to the visualization model, from which estimated rank can be established.

Parameters:

• rank_range (list or tuple like range of int) – Range of factorization ranks to try. Default is range(30, 51).
• n_run (int) – The number of runs to be performed for each value in range. Default is 10.
• what (list or tuple like of str) –

  Specify quality measures of the results computed for each rank. By default, summary of the fitted factorization model is computed. Instead, user can supply list of strings that matches some of the following quality measures:

  • sparseness
  • rss
  • evar
  • residuals
  • connectivity
  • dispersion
  • cophenetic
  • consensus
  • euclidean
  • kl

• idx (str or int) – Name of the matrix (coefficient) matrix. Used only in the multiple NMF model. Default is 0 (first coefficient matrix).

evar(idx=None)

Compute the explained variance of the NMF estimate of the target matrix.

This measure can be used for comparing the ability of models for accurately reproducing the original target matrix. Some methods specifically aim at minimizing the RSS and maximizing the explained variance while others not, which one should note when using this measure.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

fitted(idx=None)

Compute the estimated target matrix according to the NMF model. See NMF specific model.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

predict(what='samples', prob=False, idx=None)

Compute the dominant basis components. The dominant basis component is computed as the row index for which the entry is the maximum within the column.

If prob is not specified, list is returned which contains computed index for each sample (feature). Otherwise tuple is returned where first element is a list as specified before and second element is a list of associated probabilities, relative contribution of the maximum entry within each column.

Parameters:

• what (str) – Specify target for dominant basis components computation. Two values are possible, ‘samples’ or ‘features’. When what=’samples’ is specified, dominant basis component for each sample is determined based on its associated entries in the mixture coefficient matrix (H). When what=’features’ computation is performed on the transposed basis matrix (W.T).
• prob (bool equivalent) – Specify dominant basis components probability inclusion.
• idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

purity(membership=None, idx=None)

Compute the purity given a priori known groups of samples [Park2007].

The purity is a measure of performance of a clustering method in recovering classes defined by a list a priori known (true class labels).

Return the real number in [0,1]. The larger the purity, the better the clustering performance.

Parameters:

• membership (list) – Specify known class membership for each sample.
• idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

residuals(idx=None)

Compute residuals between the target matrix and its NMF estimate. See NMF specific model.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

rss(idx=None)

Compute Residual Sum of Squares (RSS) between NMF estimate and target matrix [Hutchins2008].

This measure can be used to estimate optimal factorization rank. [Hutchins2008] suggested to choose the first value where the RSS curve presents an inflection point. [Frigyesi2008] suggested to use the smallest value at which the decrease in the RSS is lower than the decrease of the RSS obtained from random data.

RSS tells us how much of the variation in the dependent variables our model did not explain.

Return real value.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In factorizations following standard NMF model or nonsmooth NMF model idx is always None.

score_features(idx=None)

Score features in terms of their specificity to the basis vectors [Park2007].

A row vector of the basis matrix (W) indicates contributions of a feature to the r (i.e. columns of W) latent components. It might be informative to investigate features that have strong component-specific membership values to the latent components.

Return array with feature scores. Feature scores are real-valued from interval [0,1]. Higher value indicates greater feature specificity.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In standard NMF model or nonsmooth NMF model idx is always None.

select_features(idx=None)

Compute the most basis-specific features for each basis vector [Park2007].

[Park2007] scoring schema and feature selection method is used. The features are first scored using the score_features(). Then only the features that fulfill both the following criteria are retained:

1. score greater than u + 3s, where u and s are the median and the median absolute deviation (MAD) of the scores, resp.,
2. the maximum contribution to a basis component (i.e the maximal value in the corresponding row of the basis matrix (W)) is larger than the median of all contributions (i.e. of all elements of basis matrix (W)).

Return a boolean array indicating whether features were selected.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In standard NMF model or nonsmooth NMF model idx is always None.

sparseness(idx=None)

Compute sparseness of matrix (basis vectors matrix, mixture coefficients) [Hoyer2004].

Sparseness of a vector quantifies how much energy is packed into its components. The sparseness of a vector is a real number in [0, 1], where sparser vector has value closer to 1. Sparseness is 1 iff the vector contains a single nonzero component and is equal to 0 iff all components of the vector are equal.

Sparseness of a matrix is mean sparseness of its column vectors.

Return tuple that contains sparseness of the basis and mixture coefficients matrices.

Parameters:idx (None or str with values ‘coef’ or ‘coef1’ (int value of 0 or 1, respectively)) – Used in the multiple NMF model. In standard NMF model or nonsmooth NMF model idx is always None.

target(idx=None)

Return the target matrix. See NMF specific model.