This paper proposes deep learning methods with signal alignment that facilitate the end-to-end classification of raw electrocardiogram (ECG) signals into heartbeat types, i.e., normal beat or different types of arrhythmias. Time-domain sample points are extracted from raw ECG signals, and consecutive vectors are extracted from a sliding time-window covering these sample points. Each of these vectors comprises the consecutive sample points of a complete heartbeat cycle, which includes not only the QRS complex but also the P and T waves. Unlike existing heartbeat classification methods in which medical doctors extract handcrafted features from raw ECG signals, the proposed end-to-end method leverages a deep neural network (DNN) for both feature extraction and classification based on aligned heartbeats. This strategy not only obviates the need to handcraft the features but also produces optimized ECG representation for heartbeat classification. Evaluations on the MIT-BIH arrhythmia database show that at the same specificity, the proposed patient-independent classifier can detect supraventricular- and ventricular-ectopic beats at a sensitivity that is at least 10% higher than current state-of-the-art methods. More importantly, there is a wide range of operating points in which both the sensitivity and specificity of the proposed classifier are higher than those achieved by state-of-the-art classifiers. The proposed classifier can also perform comparable to patient-specific classifiers, but at the same time enjoys the advantage of patient independency.

Background: Although 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. Results: This 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%). Conclusions: mGOASVM can efficiently predict the subcellular locations of multi-label proteins. The mGOASVM predictor is available online athttp://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html.

When training data are scarce, it is challenging to train a deep neural network without causing the overfitting problem. For overcoming this challenge, this article proposes a new data augmentation network--namely adversarial data augmentation network (ADAN)-- based on generative adversarial networks (GANs). The ADAN consists of a GAN, an autoencoder, and an auxiliary classifier. These networks are trained adversarially to synthesize class-dependent feature vectors in both the latent space and the original feature space, which can be augmented to the real training data for training classifiers. Instead of using the conventional cross-entropy loss for adversarial training, the Wasserstein divergence is used in an attempt to produce high-quality synthetic samples. The proposed networks were applied to speech emotion recognition using EmoDB and IEMOCAP as the evaluation data sets. It was found that by forcing the synthetic latent vectors and the real latent vectors to share a common representation, the gradient vanishing problem can be largely alleviated. Also, results show that the augmented data generated by the proposed networks are rich in emotion information. Thus, the resulting emotion classifiers are competitive with state-of-the-art speech emotion recognition systems.

Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

This paper proposes to incorporate full covariance matrices into the radial basis function (RBF) networks and to use the expectation-maximization (EM) algorithm to estimate the basis function parameters. The resulting networks, referred to as elliptical basis function (EBF) networks, are evaluated through a series of text-independent speaker verification experiments involving 258 speakers from a phonetically balanced, continuous speech corpus (TIMIT). We propose a verification procedure using RBF and EBF networks as speaker models and show that the networks are readily applicable to verifying speakers using LP-derived cepstral coefficients as features. Experimental results show that small EBF networks with basis function parameters estimated by the EM algorithm outperform the large RBF networks trained in the conventional approach. The results also show that the equal error rate achieved by the EBF networks is about two-third of that achieved by the vector quantization-based speaker models.