Fast search of sequences with complex symbol correlations using profile context-sensitive HMMS and pre-screening filters

Recently, profile context-sensitive HMMs (profile-csHMMs) have been proposed which are very effective in modeling the common patterns and motifs in related symbol sequences. Profile-csHMMs are capable of representing long-range correlations between distant symbols, even when these correlations are entangled in a complicated manner. This makes profile-csHMMs an useful tool in computational biology, especially in modeling noncoding RNAs (ncRNAs) and finding new ncRNA genes. However, a profile-csHMM based search is quite slow, hence not practical for searching a large database. In this paper, we propose a practical scheme for making the search speed significantly faster without any degradation in the prediction accuracy. The proposed method utilizes a pre-screening filter based on a profile-HMM, which filters out most sequences that will not be predicted as a match by the original profile-csHMM. Experimental results show that the proposed approach can make the search speed eighty times faster

Utilising Hidden Markov Modelling for the Assessment of Accommodation in Conversational Speech

The work presented here suggests a method for assessing speech accommodation in a holistic acoustic manner by utilising Hidden Markov Models (HMMs). The rationale for implementation of this method is presented along with an explanation of how HMMs work. Here, a heavily simplified HMM is used (single state; mixture of gaussians) in order to assess the applicability of more sophisticated HMMs. Results are presented from a small-scale study of six pairs of female Scottish-English speakers, showing measurement of significant trends and changes in holistic acoustic features of speakers during conversational interaction. Our findings suggest that methods integrating HMMs with current holistic acoustic measures of speech may be a useful tool in accounting for acoustic change due to speaker interaction

Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.

BackgroundOne of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to the sensitivity of the resulting profile. The inclusion of highly diverse sequences will presumably produce a more powerful profile, but distantly related sequences can be difficult to align accurately using only sequence information. Therefore, it would be expected that the use of protein structure alignments to improve the selection and alignment of diverse sequence homologs might yield improved profiles. However, the actual utility of such an approach has remained unclear.ResultsWe explored several iterative protocols for the generation of profile hidden Markov models. These protocols were tailored to allow the inclusion of protein structure alignments in the process, and were used for large-scale creation and benchmarking of structure alignment-enhanced models. We found that models using structure alignments did not provide an overall improvement over sequence-only models for superfamily-level structure predictions. However, the results also revealed that the structure alignment-enhanced models were complimentary to the sequence-only models, particularly at the edge of the "twilight zone". When the two sets of models were combined, they provided improved results over sequence-only models alone. In addition, we found that the beneficial effects of the structure alignment-enhanced models could not be realized if the structure-based alignments were replaced with sequence-based alignments. Our experiments with different iterative protocols for sequence-only models also suggested that simple protocol modifications were unable to yield equivalent improvements to those provided by the structure alignment-enhanced models. Finally, we found that models using structure alignments provided fold-level structure assignments that were superior to those produced by sequence-only models.ConclusionWhen attempting to predict the structure of remote homologs, we advocate a combined approach in which both traditional models and models incorporating structure alignments are used

Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results

Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs. Unfortunately, the annotation of ncRNA genes that give rise to functional RNA molecules has begun only recently, and it is far from being complete. Considering the huge amount of genome sequence data, we need efficient computational methods for finding ncRNA genes. One effective way of finding ncRNA genes is to look for regions that are similar to known ncRNA genes. As many ncRNAs have well-conserved secondary structures, we need statistical models that can represent such structures for this purpose. In this paper, we propose a new method for representing RNA sequence profiles and finding structural alignment of RNAs based on profile context-sensitive hidden Markov models (profile-csHMMs). Unlike existing models, the proposed approach can handle any kind of RNA secondary structures, including pseudoknots. We show that profile-csHMMs can provide an effective framework for the computational analysis of RNAs and the identification of ncRNA genes

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

Unsupervised Spoken Term Detection with Spoken Queries by Multi-level Acoustic Patterns with Varying Model Granularity

This paper presents a new approach for unsupervised Spoken Term Detection with spoken queries using multiple sets of acoustic patterns automatically discovered from the target corpus. The different pattern HMM configurations(number of states per model, number of distinct models, number of Gaussians per state)form a three-dimensional model granularity space. Different sets of acoustic patterns automatically discovered on different points properly distributed over this three-dimensional space are complementary to one another, thus can jointly capture the characteristics of the spoken terms. By representing the spoken content and spoken query as sequences of acoustic patterns, a series of approaches for matching the pattern index sequences while considering the signal variations are developed. In this way, not only the on-line computation load can be reduced, but the signal distributions caused by different speakers and acoustic conditions can be reasonably taken care of. The results indicate that this approach significantly outperformed the unsupervised feature-based DTW baseline by 16.16\% in mean average precision on the TIMIT corpus.Comment: Accepted by ICASSP 201