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

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

Image Retrieval Using Circular Hidden Markov Models with a Garbage State

Shape-based image and video retrieval is an active research topic in multimedia information retrieval. It is well known that there are significant variations in shapes of the same category extracted from images and videos. In this paper, we propose to use circular hidden Markov models for shape recognition and image retrieval. In our approach, we use a garbage state to explicitly deal with shape mismatch caused by shape deformation and occlusion. We will propose a modi¯ed circular hidden Markov model (HMM)for shape-based image retrieval and then use circular HMMs with a garbage state to further improve the performance. To evaluate the proposed algorithms, we have conducted experiments using the database of the MPEG-7 Core Experiments Shape-1, Part B. The experiments show that our approaches are robust to shape deformations such as shape variations and occlusion. The performance of our approaches is comparable to that of the state-of-the-art shape-based image retrieval systems in terms of accuracy and speed

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