Manifold Learning in MR spectroscopy using nonlinear dimensionality reduction and unsupervised clustering

Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion The LE method is promising for unsupervised clustering to separate brain and tumor tissue with automated color-coding for visualization of 1H MRSI data after cluster analysis

Jitter and Shimmer measurements for speaker diarization

Jitter and shimmer voice quality features have been successfully used to characterize speaker voice traits and detect voice pathologies. Jitter and shimmer measure variations in the fundamental frequency and amplitude of speaker's voice, respectively. Due to their nature, they can be used to assess differences between speakers. In this paper, we investigate the usefulness of these voice quality features in the task of speaker diarization. The combination of voice quality features with the conventional spectral features, Mel-Frequency Cepstral Coefficients (MFCC), is addressed in the framework of Augmented Multiparty Interaction (AMI) corpus, a multi-party and spontaneous speech set of recordings. Both sets of features are independently modeled using mixture of Gaussians and fused together at the score likelihood level. The experiments carried out on the AMI corpus show that incorporating jitter and shimmer measurements to the baseline spectral features decreases the diarization error rate in most of the recordings.Peer ReviewedPostprint (published version

Fast redshift clustering with the Baire (ultra) metric

The Baire metric induces an ultrametric on a dataset and is of linear computational complexity, contrasted with the standard quadratic time agglomerative hierarchical clustering algorithm. We apply the Baire distance to spectrometric and photometric redshifts from the Sloan Digital Sky Survey using, in this work, about half a million astronomical objects. We want to know how well the (more cos\ tly to determine) spectrometric redshifts can predict the (more easily obtained) photometric redshifts, i.e. we seek to regress the spectrometric on the photometric redshifts, and we develop a clusterwise nearest neighbor regression procedure for this.Comment: 14 pages, 6 figure

Adaptive Evolutionary Clustering

In many practical applications of clustering, the objects to be clustered evolve over time, and a clustering result is desired at each time step. In such applications, evolutionary clustering typically outperforms traditional static clustering by producing clustering results that reflect long-term trends while being robust to short-term variations. Several evolutionary clustering algorithms have recently been proposed, often by adding a temporal smoothness penalty to the cost function of a static clustering method. In this paper, we introduce a different approach to evolutionary clustering by accurately tracking the time-varying proximities between objects followed by static clustering. We present an evolutionary clustering framework that adaptively estimates the optimal smoothing parameter using shrinkage estimation, a statistical approach that improves a naive estimate using additional information. The proposed framework can be used to extend a variety of static clustering algorithms, including hierarchical, k-means, and spectral clustering, into evolutionary clustering algorithms. Experiments on synthetic and real data sets indicate that the proposed framework outperforms static clustering and existing evolutionary clustering algorithms in many scenarios.Comment: To appear in Data Mining and Knowledge Discovery, MATLAB toolbox available at http://tbayes.eecs.umich.edu/xukevin/affec