19,324 research outputs found
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 â for example in the research by Googleâs Magenta team â in applying so-called âlanguage modelingâ 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
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