94,212 research outputs found
Evaluation of clustering algorithms for gene expression data
BACKGROUND: Cluster analysis is an integral part of high dimensional data analysis. In the context of large scale gene expression data, a filtered set of genes are grouped together according to their expression profiles using one of numerous clustering algorithms that exist in the statistics and machine learning literature. A closely related problem is that of selecting a clustering algorithm that is "optimal" in some sense from a rather impressive list of clustering algorithms that currently exist. RESULTS: In this paper, we propose two validation measures each with two parts: one measuring the statistical consistency (stability) of the clusters produced and the other representing their biological functional congruence. Smaller values of these indices indicate better performance for a clustering algorithm. We illustrate this approach using two case studies with publicly available gene expression data sets: one involving a SAGE data of breast cancer patients and the other involving a time course cDNA microarray data on yeast. Six well known clustering algorithms UPGMA, K-Means, Diana, Fanny, Model-Based and SOM were evaluated. CONCLUSION: No single clustering algorithm may be best suited for clustering genes into functional groups via expression profiles for all data sets. The validation measures introduced in this paper can aid in the selection of an optimal algorithm, for a given data set, from a collection of available clustering algorithms
Consensus clustering and functional interpretation of gene-expression data
Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas
A data driven equivariant approach to constrained Gaussian mixture modeling
Maximum likelihood estimation of Gaussian mixture models with different
class-specific covariance matrices is known to be problematic. This is due to
the unboundedness of the likelihood, together with the presence of spurious
maximizers. Existing methods to bypass this obstacle are based on the fact that
unboundedness is avoided if the eigenvalues of the covariance matrices are
bounded away from zero. This can be done imposing some constraints on the
covariance matrices, i.e. by incorporating a priori information on the
covariance structure of the mixture components. The present work introduces a
constrained equivariant approach, where the class conditional covariance
matrices are shrunk towards a pre-specified matrix Psi. Data-driven choices of
the matrix Psi, when a priori information is not available, and the optimal
amount of shrinkage are investigated. The effectiveness of the proposal is
evaluated on the basis of a simulation study and an empirical example
Toeplitz Inverse Covariance-Based Clustering of Multivariate Time Series Data
Subsequence clustering of multivariate time series is a useful tool for
discovering repeated patterns in temporal data. Once these patterns have been
discovered, seemingly complicated datasets can be interpreted as a temporal
sequence of only a small number of states, or clusters. For example, raw sensor
data from a fitness-tracking application can be expressed as a timeline of a
select few actions (i.e., walking, sitting, running). However, discovering
these patterns is challenging because it requires simultaneous segmentation and
clustering of the time series. Furthermore, interpreting the resulting clusters
is difficult, especially when the data is high-dimensional. Here we propose a
new method of model-based clustering, which we call Toeplitz Inverse
Covariance-based Clustering (TICC). Each cluster in the TICC method is defined
by a correlation network, or Markov random field (MRF), characterizing the
interdependencies between different observations in a typical subsequence of
that cluster. Based on this graphical representation, TICC simultaneously
segments and clusters the time series data. We solve the TICC problem through
alternating minimization, using a variation of the expectation maximization
(EM) algorithm. We derive closed-form solutions to efficiently solve the two
resulting subproblems in a scalable way, through dynamic programming and the
alternating direction method of multipliers (ADMM), respectively. We validate
our approach by comparing TICC to several state-of-the-art baselines in a
series of synthetic experiments, and we then demonstrate on an automobile
sensor dataset how TICC can be used to learn interpretable clusters in
real-world scenarios.Comment: This revised version fixes two small typos in the published versio
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