Hidden Markov Models for Gene Sequence Classification: Classifying the VSG genes in the Trypanosoma brucei Genome

The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa causative agents of sleeping sickness and several diseases in domestic and wild animals. These parasites have a peculiar strategy to evade the host's immune system that consists in periodically changing their predominant cellular surface protein (VSG). The motivation for using patterns recognition methods to identify these genes, instead of traditional homology based ones, is that the levels of sequence identity (amino acid and DNA sequence) amongst these genes is often below of what is considered reliable in these methods. Among pattern recognition approaches, HMM are particularly suitable to tackle this problem because they can handle more naturally the determination of gene edges. We evaluate the performance of the model using different number of states in the Markov model, as well as several performance metrics. The model is applied using public genomic data. Our empirical results show that the VSG genes on T. brucei can be safely identified (high sensitivity and low rate of false positives) using HMM.Comment: Accepted article in July, 2015 in Pattern Analysis and Applications, Springer. The article contains 23 pages, 4 figures, 8 tables and 51 reference

Dialogue Act Recognition via CRF-Attentive Structured Network

Dialogue Act Recognition (DAR) is a challenging problem in dialogue interpretation, which aims to attach semantic labels to utterances and characterize the speaker's intention. Currently, many existing approaches formulate the DAR problem ranging from multi-classification to structured prediction, which suffer from handcrafted feature extensions and attentive contextual structural dependencies. In this paper, we consider the problem of DAR from the viewpoint of extending richer Conditional Random Field (CRF) structural dependencies without abandoning end-to-end training. We incorporate hierarchical semantic inference with memory mechanism on the utterance modeling. We then extend structured attention network to the linear-chain conditional random field layer which takes into account both contextual utterances and corresponding dialogue acts. The extensive experiments on two major benchmark datasets Switchboard Dialogue Act (SWDA) and Meeting Recorder Dialogue Act (MRDA) datasets show that our method achieves better performance than other state-of-the-art solutions to the problem. It is a remarkable fact that our method is nearly close to the human annotator's performance on SWDA within 2% gap.Comment: 10 pages, 4figure

An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes

Non-coding RNAs (ncRNA) are RNA molecules that function in the cells without being translated into proteins. In recent years, much evidence has been found that ncRNAs play a crucial role in various biological processes. As a result, there has been an increasing interest in the prediction of ncRNA genes. Due to the conserved secondary structure in ncRNAs, there exist pairwise dependencies between distant bases. These dependencies cannot be effectively modeled using traditional HMMs, and we need a more complex model such as the context-sensitive HMM (csHMM). In this paper, we overview the role of csHMMs in the RNA secondary structure analysis and the prediction of ncRNA genes. It is demonstrated that the context-sensitive HMMs can serve as an efficient framework for these purposes

Pop Music Highlighter: Marking the Emotion Keypoints

The goal of music highlight extraction is to get a short consecutive segment of a piece of music that provides an effective representation of the whole piece. In a previous work, we introduced an attention-based convolutional recurrent neural network that uses music emotion classification as a surrogate task for music highlight extraction, for Pop songs. The rationale behind that approach is that the highlight of a song is usually the most emotional part. This paper extends our previous work in the following two aspects. First, methodology-wise we experiment with a new architecture that does not need any recurrent layers, making the training process faster. Moreover, we compare a late-fusion variant and an early-fusion variant to study which one better exploits the attention mechanism. Second, we conduct and report an extensive set of experiments comparing the proposed attention-based methods against a heuristic energy-based method, a structural repetition-based method, and a few other simple feature-based methods for this task. Due to the lack of public-domain labeled data for highlight extraction, following our previous work we use the RWC POP 100-song data set to evaluate how the detected highlights overlap with any chorus sections of the songs. The experiments demonstrate the effectiveness of our methods over competing methods. For reproducibility, we open source the code and pre-trained model at https://github.com/remyhuang/pop-music-highlighter/.Comment: Transactions of the ISMIR vol. 1, no.

VGM-RNN: Recurrent Neural Networks for Video Game Music Generation

The recent explosion of interest in deep neural networks has affected and in some cases reinvigorated work in fields as diverse as natural language processing, image recognition, speech recognition and many more. For sequence learning tasks, recurrent neural networks and in particular LSTM-based networks have shown promising results. Recently there has been interest – for example in the research by Google’s Magenta team – in applying so-called “language modeling” recurrent neural networks to musical tasks, including for the automatic generation of original music. In this work we demonstrate our own LSTM-based music language modeling recurrent network. We show that it is able to learn musical features from a MIDI dataset and generate output that is musically interesting while demonstrating features of melody, harmony and rhythm. We source our dataset from VGMusic.com, a collection of user-submitted MIDI transcriptions of video game songs, and attempt to generate output which emulates this kind of music