KL-Divergence Guided Two-Beam Viterbi Algorithm on Factorial HMMs

This thesis addresses the problem of the high computation complexity issue that arises when decoding hidden Markov models (HMMs) with a large number of states. A novel approach, the two-beam Viterbi, with an extra forward beam, for decoding HMMs is implemented on a system that uses factorial HMM to simultaneously recognize a pair of isolated digits on one audio channel. The two-beam Viterbi algorithm uses KL-divergence and hierarchical clustering to reduce the overall decoding complexity. This novel approach achieves 60% less computation compared to the baseline algorithm, the Viterbi beam search, while maintaining 82.5% recognition accuracy.Ope

A Short Survey on Data Clustering Algorithms

With rapidly increasing data, clustering algorithms are important tools for data analytics in modern research. They have been successfully applied to a wide range of domains; for instance, bioinformatics, speech recognition, and financial analysis. Formally speaking, given a set of data instances, a clustering algorithm is expected to divide the set of data instances into the subsets which maximize the intra-subset similarity and inter-subset dissimilarity, where a similarity measure is defined beforehand. In this work, the state-of-the-arts clustering algorithms are reviewed from design concept to methodology; Different clustering paradigms are discussed. Advanced clustering algorithms are also discussed. After that, the existing clustering evaluation metrics are reviewed. A summary with future insights is provided at the end

Parallel Reference Speaker Weighting for Kinematic-Independent Acoustic-to-Articulatory Inversion

Acoustic-to-articulatory inversion, the estimation of articulatory kinematics from an acoustic waveform, is a challenging but important problem. Accurate estimation of articulatory movements has the potential for significant impact on our understanding of speech production, on our capacity to assess and treat pathologies in a clinical setting, and on speech technologies such as computer aided pronunciation assessment and audio-video synthesis. However, because of the complex and speaker-specific relationship between articulation and acoustics, existing approaches for inversion do not generalize well across speakers. As acquiring speaker-specific kinematic data for training is not feasible in many practical applications, this remains an important and open problem. This paper proposes a novel approach to acoustic-to-articulatory inversion, Parallel Reference Speaker Weighting (PRSW), which requires no kinematic data for the target speaker and a small amount of acoustic adaptation data. PRSW hypothesizes that acoustic and kinematic similarities are correlated and uses speaker-adapted articulatory models derived from acoustically derived weights. The system was assessed using a 20-speaker data set of synchronous acoustic and Electromagnetic Articulography (EMA) kinematic data. Results demonstrate that by restricting the reference group to a subset consisting of speakers with strong individual speaker-dependent inversion performance, the PRSW method is able to attain kinematic-independent acoustic-to-articulatory inversion performance nearly matching that of the speaker-dependent model, with an average correlation of 0.62 versus 0.63. This indicates that given a sufficiently complete and appropriately selected reference speaker set for adaptation, it is possible to create effective articulatory models without kinematic training data

Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome

The central dogma of molecular biology states that the genetic information flows from DNA to RNA to protein. This dogma has exerted a substantial influence on our understanding of the genetic activities in the cells. Under this influence, the prevailing assumption until the recent past was that genes are basically repositories for protein coding information, and proteins are responsible for most of the important biological functions in all cells. In the meanwhile, the importance of RNAs has remained rather obscure, and RNA was mainly viewed as a passive intermediary that bridges the gap between DNA and protein. Except for classic examples such as tRNAs (transfer RNAs) and rRNAs (ribosomal RNAs), functional noncoding RNAs were considered to be rare. However, this view has experienced a dramatic change during the last decade, as systematic screening of various genomes identified myriads of noncoding RNAs (ncRNAs), which are RNA molecules that function without being translated into proteins [11], [40]. It has been realized that many ncRNAs play important roles in various biological processes. As RNAs can interact with other RNAs and DNAs in a sequence-specific manner, they are especially useful in tasks that require highly specific nucleotide recognition [11]. Good examples are the miRNAs (microRNAs) that regulate gene expression by targeting mRNAs (messenger RNAs) [4], [20], and the siRNAs (small interfering RNAs) that take part in the RNAi (RNA interference) pathways for gene silencing [29], [30]. Recent developments show that ncRNAs are extensively involved in many gene regulatory mechanisms [14], [17]. The roles of ncRNAs known to this day are truly diverse. These include transcription and translation control, chromosome replication, RNA processing and modification, and protein degradation and translocation [40], just to name a few. These days, it is even claimed that ncRNAs dominate the genomic output of the higher organisms such as mammals, and it is being suggested that the greater portion of their genome (which does not encode proteins) is dedicated to the control and regulation of cell development [27]. As more and more evidence piles up, greater attention is paid to ncRNAs, which have been neglected for a long time. Researchers began to realize that the vast majority of the genome that was regarded as “junk,” mainly because it was not well understood, may indeed hold the key for the best kept secrets in life, such as the mechanism of alternative splicing, the control of epigenetic variations and so forth [27]. The complete range and extent of the role of ncRNAs are not so obvious at this point, but it is certain that a comprehensive understanding of cellular processes is not possible without understanding the functions of ncRNAs [47]