BackgroundAlthough many computational methods have been developed to predict protein subcellular localization, most of the methods are limited to the prediction of single-location proteins. Multi-location proteins are either not considered or assumed not existing. However, proteins with multiple locations are particularly interesting because they may have special biological functions, which are essential to both basic research and drug discovery.ResultsThis paper proposes an efficient multi-label predictor, namely mGOASVM, for predicting the subcellular localization of multi-location proteins. Given a protein, the accession numbers of its homologs are obtained via BLAST search. Then, the original accession number and the homologous accession numbers of the protein are used as keys to search against the Gene Ontology (GO) annotation database to obtain a set of GO terms. Given a set of training proteins, a set of T relevant GO terms is obtained by finding all of the GO terms in the GO annotation database that are relevant to the training proteins. These relevant GO terms then form the basis of a T-dimensional Euclidean space on which the GO vectors lie. A support vector machine (SVM) classifier with a new decision scheme is proposed to classify the multi-label GO vectors. The mGOASVM predictor has the following advantages: (1) it uses the frequency of occurrences of GO terms for feature representation; (2) it selects the relevant GO subspace which can substantially speed up the prediction without compromising performance; and (3) it adopts an efficient multi-label SVM classifier which significantly outperforms other predictors. Briefly, on two recently published virus and plant datasets, mGOASVM achieves an actual accuracy of 88.9% and 87.4%, respectively, which are significantly higher than those achieved by the state-of-the-art predictors such as iLoc-Virus (74.8%) and iLoc-Plant (68.1%).ConclusionsmGOASVM can efficiently predict the subcellular locations of multi-label proteins. The mGOASVM predictor is available online at http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html.

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Since 2008, interview-style speech has become an important part of the NIST Speaker Recognition Evaluations (SREs). Unlike telephone speech, interview speech has lower signal-to-noise ratio, which necessitates robust voice activity detectors (VADs). This paper highlights the characteristics of interview speech files in NIST SREs and discusses the difficulties in performing speech/non-speech segmentation in these files. To overcome these difficulties, this paper proposes using speech enhancement techniques as a preprocessing step for enhancing the reliability of energy-based and statisticalmodel-based VADs. A decision strategy is also proposed to overcome the undesirable effects caused by impulsive signals and sinusoidal background signals. The proposed VAD is compared with the ASR transcripts provided by NIST, VAD in the ETSI-AMR Option 2 coder, satistical-model (SM) based VAD, and Gaussian mixture model (GMM) based VAD. Experimental results based on the NIST 2010 SRE dataset suggest that the proposed VAD outperforms these conventional ones whenever interview-style speech is involved. This study also demonstrates that (1) noise reduction is vital for energy-based VAD under low SNR; (2) the ASR transcripts and ETSI-AMR speech coder do not produce accurate speech and non-speech segmentations; and (3) spectral subtraction makes better use of background spectra than the likelihood-ratio tests in the SM-based VAD. The segmentation files produced by the proposed VAD can be found in http://bioinfo.eie.polyu.edu.hk/ssvad.

Prediction of protein subcellular localization is an important yet challenging problem. Recently, several computational methods based on Gene Ontology (GO) have been proposed to tackle this problem and have demonstrated superiority over methods based on other features. Existing GO-based methods, however, do not fully use the GO information. This paper proposes an efficient GO method called GOASVM that exploits the information from the GO term frequencies and distant homologs to represent a protein in the general form of Chou's pseudo amino acid composition. The method first selects a subset of relevant GO terms to form a GO vector space. Then for each protein, the method uses the accession number (AC) of the protein or the ACs of its homologs to find the number of occurrences of the selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct GO vectors for support vector machines (SVMs) classification. With the advantages of GO term frequencies and a new strategy to incorporate useful homologous information, GOASVM can achieve a prediction accuracy of 72.2% on a new independent test set comprising novel proteins that were added to Swiss-Prot six years later than the creation date of the training set. GOASVM and Supplementary Materials are available online at

The performance of telephone-based speaker verification systems can be severely degraded by the acoustic mismatch caused by telephone handsets. This paper proposes to combine a handset selector with stochastic feature transformation to reduce the mismatch. Specifically, a GMM-based handset selector is trained to identify the most likely handset used by the claimants, and then handset-specific stochastic feature transformations are applied to the distorted feature vectors. To overcome the non-linear distortion introduced by telephone handsets, a 2nd-order stochastic feature transformation is proposed. Estimation algorithms based on the stochastic matching technique and the EM algorithm are derived. Experimental results based on 150 speakers of the HTIMIT corpus show that the handset selector is able to identify the handsets accurately (98.3%), and that both linear and non-linear transformation reduce the error rate significantly (from 12.37% to 5.49%).