10,790 research outputs found
Hierarchical Graphical Models for Multigroup Shape Analysis using Expectation Maximization with Sampling in Kendall's Shape Space
This paper proposes a novel framework for multi-group shape analysis relying
on a hierarchical graphical statistical model on shapes within a population.The
framework represents individual shapes as point setsmodulo translation,
rotation, and scale, following the notion in Kendall shape space.While
individual shapes are derived from their group shape model, each group shape
model is derived from a single population shape model. The hierarchical model
follows the natural organization of population data and the top level in the
hierarchy provides a common frame of reference for multigroup shape analysis,
e.g. classification and hypothesis testing. Unlike typical shape-modeling
approaches, the proposed model is a generative model that defines a joint
distribution of object-boundary data and the shape-model variables.
Furthermore, it naturally enforces optimal correspondences during the process
of model fitting and thereby subsumes the so-called correspondence problem. The
proposed inference scheme employs an expectation maximization (EM) algorithm
that treats the individual and group shape variables as hidden random variables
and integrates them out before estimating the parameters (population mean and
variance and the group variances). The underpinning of the EM algorithm is the
sampling of pointsets, in Kendall shape space, from their posterior
distribution, for which we exploit a highly-efficient scheme based on
Hamiltonian Monte Carlo simulation. Experiments in this paper use the fitted
hierarchical model to perform (1) hypothesis testing for comparison between
pairs of groups using permutation testing and (2) classification for image
retrieval. The paper validates the proposed framework on simulated data and
demonstrates results on real data.Comment: 9 pages, 7 figures, International Conference on Machine Learning 201
Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome
The central dogma of molecular biology states that the genetic information flows from DNA to RNA to protein. This dogma has exerted a substantial influence on our understanding of the genetic activities in the cells. Under this influence, the prevailing assumption until the recent past was that genes are basically repositories for protein coding information, and proteins are responsible for most of the important biological functions in all cells. In the meanwhile, the importance of RNAs has remained rather obscure, and RNA was mainly viewed as a passive intermediary that bridges the gap between DNA and protein. Except for classic examples such as tRNAs (transfer RNAs) and rRNAs (ribosomal RNAs), functional noncoding RNAs were considered to be rare.
However, this view has experienced a dramatic change during the last decade, as systematic screening of various genomes identified myriads of noncoding RNAs (ncRNAs), which are RNA molecules that function without being translated into proteins [11], [40]. It has been realized that many ncRNAs play important roles in various biological processes. As RNAs can interact with other RNAs and DNAs in a sequence-specific manner, they are especially useful in tasks that require highly specific nucleotide recognition [11]. Good examples are the miRNAs (microRNAs) that regulate gene expression by targeting mRNAs (messenger RNAs) [4], [20], and the siRNAs (small interfering RNAs) that take part in the RNAi (RNA interference) pathways for gene silencing [29], [30]. Recent developments show that ncRNAs are extensively involved in many gene regulatory mechanisms [14], [17].
The roles of ncRNAs known to this day are truly diverse. These include transcription and translation control, chromosome replication, RNA processing and modification, and protein degradation and translocation [40], just to name a few. These days, it is even claimed that ncRNAs dominate the genomic output of the higher organisms such as mammals, and it is being suggested that the greater portion of their genome (which does not encode proteins) is dedicated to the control and regulation of cell development [27]. As more and more evidence piles up, greater attention is paid to ncRNAs, which have been neglected for a long time. Researchers began to realize that the vast majority of the genome that was regarded as “junk,” mainly because it was not well understood, may indeed hold the key for the best kept secrets in life, such as the mechanism of alternative splicing, the control of epigenetic variations and so forth [27]. The complete range and extent of the role of ncRNAs are not so obvious at this point, but it is certain that a comprehensive understanding of cellular processes is not possible without understanding the functions of ncRNAs [47]
The EM Algorithm and the Rise of Computational Biology
In the past decade computational biology has grown from a cottage industry
with a handful of researchers to an attractive interdisciplinary field,
catching the attention and imagination of many quantitatively-minded
scientists. Of interest to us is the key role played by the EM algorithm during
this transformation. We survey the use of the EM algorithm in a few important
computational biology problems surrounding the "central dogma"; of molecular
biology: from DNA to RNA and then to proteins. Topics of this article include
sequence motif discovery, protein sequence alignment, population genetics,
evolutionary models and mRNA expression microarray data analysis.Comment: Published in at http://dx.doi.org/10.1214/09-STS312 the Statistical
Science (http://www.imstat.org/sts/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Multi-scale Discriminant Saliency with Wavelet-based Hidden Markov Tree Modelling
The bottom-up saliency, an early stage of humans' visual attention, can be
considered as a binary classification problem between centre and surround
classes. Discriminant power of features for the classification is measured as
mutual information between distributions of image features and corresponding
classes . As the estimated discrepancy very much depends on considered scale
level, multi-scale structure and discriminant power are integrated by employing
discrete wavelet features and Hidden Markov Tree (HMT). With wavelet
coefficients and Hidden Markov Tree parameters, quad-tree like label structures
are constructed and utilized in maximum a posterior probability (MAP) of hidden
class variables at corresponding dyadic sub-squares. Then, a saliency value for
each square block at each scale level is computed with discriminant power
principle. Finally, across multiple scales is integrated the final saliency map
by an information maximization rule. Both standard quantitative tools such as
NSS, LCC, AUC and qualitative assessments are used for evaluating the proposed
multi-scale discriminant saliency (MDIS) method against the well-know
information based approach AIM on its released image collection with
eye-tracking data. Simulation results are presented and analysed to verify the
validity of MDIS as well as point out its limitation for further research
direction.Comment: arXiv admin note: substantial text overlap with arXiv:1301.396
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