2,636 research outputs found
DeepSig: Deep learning improves signal peptide detection in proteins
Motivation:
The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization.
Results:
Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification.
Availability and implementation:
DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website
Spectral Sequence Motif Discovery
Sequence discovery tools play a central role in several fields of
computational biology. In the framework of Transcription Factor binding
studies, motif finding algorithms of increasingly high performance are required
to process the big datasets produced by new high-throughput sequencing
technologies. Most existing algorithms are computationally demanding and often
cannot support the large size of new experimental data. We present a new motif
discovery algorithm that is built on a recent machine learning technique,
referred to as Method of Moments. Based on spectral decompositions, this method
is robust under model misspecification and is not prone to locally optimal
solutions. We obtain an algorithm that is extremely fast and designed for the
analysis of big sequencing data. In a few minutes, we can process datasets of
hundreds of thousand sequences and extract motif profiles that match those
computed by various state-of-the-art algorithms.Comment: 20 pages, 3 figures, 1 tabl
Comparing Probabilistic Models for Melodic Sequences
Modelling the real world complexity of music is a challenge for machine
learning. We address the task of modeling melodic sequences from the same music
genre. We perform a comparative analysis of two probabilistic models; a
Dirichlet Variable Length Markov Model (Dirichlet-VMM) and a Time Convolutional
Restricted Boltzmann Machine (TC-RBM). We show that the TC-RBM learns
descriptive music features, such as underlying chords and typical melody
transitions and dynamics. We assess the models for future prediction and
compare their performance to a VMM, which is the current state of the art in
melody generation. We show that both models perform significantly better than
the VMM, with the Dirichlet-VMM marginally outperforming the TC-RBM. Finally,
we evaluate the short order statistics of the models, using the
Kullback-Leibler divergence between test sequences and model samples, and show
that our proposed methods match the statistics of the music genre significantly
better than the VMM.Comment: in Proceedings of the ECML-PKDD 2011. Lecture Notes in Computer
Science, vol. 6913, pp. 289-304. Springer (2011
Alignment, Clustering and Extraction of Structured Motifs in DNA Promoter Sequences
A simple motif is a short DNA sequence found in the promoter region and believed to act as a binding site for a transcription factor protein. A structured motif is a sequence of simple motifs (boxes) separated by short sequences (gaps). Biologists theorize that the presence of these motifs play a key role in gene expression regulation. Discovering these patterns is an important step towards understanding protein-gene and gene-gene interaction thus facilitates the building of accurate gene regulatory network models. DNA sequence motif extraction is an important problem in bioinformatics. Many studies have proposed algorithms to solve the problem instance of simple motif extraction. Only in the past decade has the more complex structured motif extraction problem been examined by researchers.
The problem is inherently challenging as structured motif patterns are segmented into several boxes separated by variable size gaps for each instance. These boxes may not be exact copies, but may have multiple mismatched positions. The challenge is extenuated by the lack of resources for real datasets covering a wide range of possible cases. Also, incomplete annotation of real data leads to the discovery of unknown motifs that may be regarded as false positives. Furthermore, current algorithms demand unreasonable amount of prior knowledge to successfully extract the target pattern.
The contributions of this research are four new algorithms. First, SMGenerate generates simulated datasets of implanted motifs that covers a wide range of biologically possible cases. Second, SMAlign aligns a pair of structured motifs optimally and efficiently given their gap constraints. Third, SMCluster produces multiple alignment of structured motifs through hierarchical clustering using SMAlign\u27s affinity score. Finally, SMExtract extracts structured motifs from a set of sequences by using SMCluster to construct the target pattern from the top reported two-box patterns (fragments), extracted using an existing algorithm (Exmotif) and a two-box template. The main advantage of SMExtract is its efficiency to extract longer degenerate patterns while requiring less prior knowledge, about the pattern to be extracted, than current algorithms
Kernel methods in genomics and computational biology
Support vector machines and kernel methods are increasingly popular in
genomics and computational biology, due to their good performance in real-world
applications and strong modularity that makes them suitable to a wide range of
problems, from the classification of tumors to the automatic annotation of
proteins. Their ability to work in high dimension, to process non-vectorial
data, and the natural framework they provide to integrate heterogeneous data
are particularly relevant to various problems arising in computational biology.
In this chapter we survey some of the most prominent applications published so
far, highlighting the particular developments in kernel methods triggered by
problems in biology, and mention a few promising research directions likely to
expand in the future
Rethinking Recurrent Latent Variable Model for Music Composition
We present a model for capturing musical features and creating novel
sequences of music, called the Convolutional Variational Recurrent Neural
Network. To generate sequential data, the model uses an encoder-decoder
architecture with latent probabilistic connections to capture the hidden
structure of music. Using the sequence-to-sequence model, our generative model
can exploit samples from a prior distribution and generate a longer sequence of
music. We compare the performance of our proposed model with other types of
Neural Networks using the criteria of Information Rate that is implemented by
Variable Markov Oracle, a method that allows statistical characterization of
musical information dynamics and detection of motifs in a song. Our results
suggest that the proposed model has a better statistical resemblance to the
musical structure of the training data, which improves the creation of new
sequences of music in the style of the originals.Comment: Published as a conference paper at IEEE MMSP 201
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