Simple SVM based whole-genome segmentation

We present a support vector machine (SVM) based framework for DNA segmentation into binary classes. Two applications are explored: transcription start site prediction and transcription factor binding prediction. Experiments demonstrate our approach has significantly better performance than other methods on both tasks

The Recurrent Temporal Discriminative Restricted Boltzmann Machines

Classification of sequence data is the topic of interest for dynamic Bayesian models and Recurrent Neural Networks (RNNs). While the former can explicitly model the temporal dependencies between class variables, the latter have a capability of learning representations. Several attempts have been made to improve performance by combining these two approaches or increasing the processing capability of the hidden units in RNNs. This often results in complex models with a large number of learning parameters. In this paper, a compact model is proposed which offers both representation learning and temporal inference of class variables by rolling Restricted Boltzmann Machines (RBMs) and class variables over time. We address the key issue of intractability in this variant of RBMs by optimising a conditional distribution, instead of a joint distribution. Experiments reported in the paper on melody modelling and optical character recognition show that the proposed model can outperform the state-of-the-art. Also, the experimental results on optical character recognition, part-of-speech tagging and text chunking demonstrate that our model is comparable to recurrent neural networks with complex memory gates while requiring far fewer parameters

Sequence Classification Restricted Boltzmann Machines With Gated Units

For the classification of sequential data, dynamic Bayesian networks and recurrent neural networks (RNNs) are the preferred models. While the former can explicitly model the temporal dependences between the variables, and the latter have the capability of learning representations. The recurrent temporal restricted Boltzmann machine (RTRBM) is a model that combines these two features. However, learning and inference in RTRBMs can be difficult because of the exponential nature of its gradient computations when maximizing log likelihoods. In this article, first, we address this intractability by optimizing a conditional rather than a joint probability distribution when performing sequence classification. This results in the ``sequence classification restricted Boltzmann machine'' (SCRBM). Second, we introduce gated SCRBMs (gSCRBMs), which use an information processing gate, as an integration of SCRBMs with long short-term memory (LSTM) models. In the experiments reported in this article, we evaluate the proposed models on optical character recognition, chunking, and multiresident activity recognition in smart homes. The experimental results show that gSCRBMs achieve the performance comparable to that of the state of the art in all three tasks. gSCRBMs require far fewer parameters in comparison with other recurrent networks with memory gates, in particular, LSTMs and gated recurrent units (GRUs)