Diffusion map for clustering fMRI spatial maps extracted by independent component analysis

Functional magnetic resonance imaging (fMRI) produces data about activity inside the brain, from which spatial maps can be extracted by independent component analysis (ICA). In datasets, there are n spatial maps that contain p voxels. The number of voxels is very high compared to the number of analyzed spatial maps. Clustering of the spatial maps is usually based on correlation matrices. This usually works well, although such a similarity matrix inherently can explain only a certain amount of the total variance contained in the high-dimensional data where n is relatively small but p is large. For high-dimensional space, it is reasonable to perform dimensionality reduction before clustering. In this research, we used the recently developed diffusion map for dimensionality reduction in conjunction with spectral clustering. This research revealed that the diffusion map based clustering worked as well as the more traditional methods, and produced more compact clusters when needed.Comment: 6 pages. 8 figures. Copyright (c) 2013 IEEE. Published at 2013 IEEE International Workshop on Machine Learning for Signal Processin

The Hidden Convexity of Spectral Clustering

In recent years, spectral clustering has become a standard method for data analysis used in a broad range of applications. In this paper we propose a new class of algorithms for multiway spectral clustering based on optimization of a certain "contrast function" over the unit sphere. These algorithms, partly inspired by certain Independent Component Analysis techniques, are simple, easy to implement and efficient. Geometrically, the proposed algorithms can be interpreted as hidden basis recovery by means of function optimization. We give a complete characterization of the contrast functions admissible for provable basis recovery. We show how these conditions can be interpreted as a "hidden convexity" of our optimization problem on the sphere; interestingly, we use efficient convex maximization rather than the more common convex minimization. We also show encouraging experimental results on real and simulated data.Comment: 22 page

Clustering student skill set profiles in a unit hypercube using mixtures of multivariate betas

<br>This paper presents a finite mixture of multivariate betas as a new model-based clustering method tailored to applications where the feature space is constrained to the unit hypercube. The mixture component densities are taken to be conditionally independent, univariate unimodal beta densities (from the subclass of reparameterized beta densities given by Bagnato and Punzo 2013). The EM algorithm used to fit this mixture is discussed in detail, and results from both this beta mixture model and the more standard Gaussian model-based clustering are presented for simulated skill mastery data from a common cognitive diagnosis model and for real data from the Assistment System online mathematics tutor (Feng et al 2009). The multivariate beta mixture appears to outperform the standard Gaussian model-based clustering approach, as would be expected on the constrained space. Fewer components are selected (by BIC-ICL) in the beta mixture than in the Gaussian mixture, and the resulting clusters seem more reasonable and interpretable.</br> <br>This article is in technical report form, the final publication is available at http://www.springerlink.com/openurl.asp?genre=article &id=doi:10.1007/s11634-013-0149-z</br&gt

Clustering by non-negative matrix factorization with independent principal component initialization

Non negative matrix factorization (NMF) is a dimensionality reduction and clustering method, and has been applied to many areas such as bioinformatics, face images classification, and so on. Based on the traditional NMF, researchers recently have put forward several new algorithms on the initialization area to improve its performance. In this paper, we explore the clustering performance of the NMF algorithm, with emphasis on the initialization problem. We propose an initialization method based on independent principal component analysis (IPCA) for NMF. The experiments were carried out on the four real datasets and the results showed that the IPCA-based initialization of NMF gets better clustering of the datasets compared with both random and PCA-based initializations

Dimensionality Reduction for k-Means Clustering and Low Rank Approximation

We show how to approximate a data matrix $\mathbf{A}$ with a much smaller sketch $\mathbf{\tilde A}$ that can be used to solve a general class of constrained k-rank approximation problems to within $(1+\epsilon)$ error. Importantly, this class of problems includes $k$-means clustering and unconstrained low rank approximation (i.e. principal component analysis). By reducing data points to just $O(k)$ dimensions, our methods generically accelerate any exact, approximate, or heuristic algorithm for these ubiquitous problems. For $k$-means dimensionality reduction, we provide $(1+\epsilon)$ relative error results for many common sketching techniques, including random row projection, column selection, and approximate SVD. For approximate principal component analysis, we give a simple alternative to known algorithms that has applications in the streaming setting. Additionally, we extend recent work on column-based matrix reconstruction, giving column subsets that not only `cover' a good subspace for \bv{A}, but can be used directly to compute this subspace. Finally, for $k$-means clustering, we show how to achieve a $(9+\epsilon)$ approximation by Johnson-Lindenstrauss projecting data points to just $O(\log k/\epsilon^2)$ dimensions. This gives the first result that leverages the specific structure of $k$-means to achieve dimension independent of input size and sublinear in $k$

Least Dependent Component Analysis Based on Mutual Information

We propose to use precise estimators of mutual information (MI) to find least dependent components in a linearly mixed signal. On the one hand this seems to lead to better blind source separation than with any other presently available algorithm. On the other hand it has the advantage, compared to other implementations of `independent' component analysis (ICA) some of which are based on crude approximations for MI, that the numerical values of the MI can be used for: (i) estimating residual dependencies between the output components; (ii) estimating the reliability of the output, by comparing the pairwise MIs with those of re-mixed components; (iii) clustering the output according to the residual interdependencies. For the MI estimator we use a recently proposed k-nearest neighbor based algorithm. For time sequences we combine this with delay embedding, in order to take into account non-trivial time correlations. After several tests with artificial data, we apply the resulting MILCA (Mutual Information based Least dependent Component Analysis) algorithm to a real-world dataset, the ECG of a pregnant woman. The software implementation of the MILCA algorithm is freely available at http://www.fz-juelich.de/nic/cs/softwareComment: 18 pages, 20 figures, Phys. Rev. E (in press