Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices

In the study of complex genetic diseases, the identification of subgroups of patients sharing similar genetic characteristics represents a challenging task, for example, to improve treatment decision. One type of genetic lesion, frequently investigated in such disorders, is the change of the DNA copy number (CN) at specific genomic traits. Non-negative Matrix Factorization (NMF) is a standard technique to reduce the dimensionality of a data set and to cluster data samples, while keeping its most relevant information in meaningful components. Thus, it can be used to discover subgroups of patients from CN profiles. It is however computationally impractical for very high dimensional data, such as CN microarray data. Deciding the most suitable number of subgroups is also a challenging problem. The aim of this work is to derive a procedure to compact high dimensional data, in order to improve NMF applicability without compromising the quality of the clustering. This is particularly important for analyzing high-resolution microarray data. Many commonly used quality measures, as well as our own measures, are employed to decide the number of subgroups and to assess the quality of the results. Our measures are based on the idea of identifying robust subgroups, inspired by biologically/clinically relevance instead of simply aiming at well-separated clusters. We evaluate our procedure using four real independent data sets. In these data sets, our method was able to find accurate subgroups with individual molecular and clinical features and outperformed the standard NMF in terms of accuracy in the factorization fitness function. Hence, it can be useful for the discovery of subgroups of patients with similar CN profiles in the study of heterogeneous diseases.

Quadratic Forms on Complex Random Matrices and Multiple-Antenna Systems

This research published in the foremost international journal in information theory and shows interplay between complex random matrix and multiantenna information theory. Dr T. Ratnarajah is leader in this area of research and his work has been contributed in the development of graduate curricula (course reader) in Massachusetts Institute of Technology (MIT), USA, By Professor Alan Edelman. The course name is "The Mathematics and Applications of Random Matrices", see http://web.mit.edu/18.338/www/projects.html

Robust Speaker Recognition in Noisy Conditions

This paper investigates the problem of speaker identi-fication and verification in noisy conditions, assuming that speechsignals are corrupted by environmental noise, but knowledgeabout the noise characteristics is not available. This research ismotivated in part by the potential application of speaker recog-nition technologies on handheld devices or the Internet. Whilethe technologies promise an additional biometric layer of securityto protect the user, the practical implementation of such systemsfaces many challenges. One of these is environmental noise. Due tothe mobile nature of such systems, the noise sources can be highlytime-varying and potentially unknown. This raises the require-ment for noise robustness in the absence of information about thenoise. This paper describes a method that combines multicondi-tion model training and missing-feature theory to model noisewith unknown temporal-spectral characteristics. Multiconditiontraining is conducted using simulated noisy data with limitednoise variation, providing a “coarse” compensation for the noise,and missing-feature theory is applied to refine the compensationby ignoring noise variation outside the given training conditions,thereby reducing the training and testing mismatch. This paperis focused on several issues relating to the implementation of thenew model for real-world applications. These include the gener-ation of multicondition training data to model noisy speech, thecombination of different training data to optimize the recognitionperformance, and the reduction of the model’s complexity. Thenew algorithm was tested using two databases with simulated andrealistic noisy speech data. The first database is a redevelopmentof the TIMIT database by rerecording the data in the presence ofvarious noise types, used to test the model for speaker identifica-tion with a focus on the varieties of noise. The second database isa handheld-device database collected in realistic noisy conditions,used to further validate the model for real-world speaker verifica-tion. The new model is compared to baseline systems and is foundto achieve lower error rates.