11,064 research outputs found
Application of Subspace Clustering in DNA Sequence Analysis
Identification and clustering of orthologous genes plays an important role in developing evolutionary models such as validating convergent and divergent phylogeny and predicting functional proteins in newly sequenced species of unverified nucleotide protein mappings. Here, we introduce an application of subspace clustering as applied to orthologous gene sequences and discuss the initial results. The working hypothesis is based upon the concept that genetic changes between nucleotide sequences coding for proteins among selected species and groups may lie within a union of subspaces for clusters of the orthologous groups. Estimates for the subspace dimensions were computed for a small population sample. A series of experiments was performed to cluster randomly selected sequences. The experimental design allows for both false positives and false negatives, and estimates for the statistical significance are provided. The clustering results are consistent with the main hypothesis. A simple random mutation binary tree model is used to simulate speciation events that show the interdependence of the subspace rank versus time and mutation rates. The simple mutation model is found to be largely consistent with the observed subspace clustering singular value results. Our study indicates that the subspace clustering method may be applied in orthology analysis
The discriminative functional mixture model for a comparative analysis of bike sharing systems
Bike sharing systems (BSSs) have become a means of sustainable intermodal
transport and are now proposed in many cities worldwide. Most BSSs also provide
open access to their data, particularly to real-time status reports on their
bike stations. The analysis of the mass of data generated by such systems is of
particular interest to BSS providers to update system structures and policies.
This work was motivated by interest in analyzing and comparing several European
BSSs to identify common operating patterns in BSSs and to propose practical
solutions to avoid potential issues. Our approach relies on the identification
of common patterns between and within systems. To this end, a model-based
clustering method, called FunFEM, for time series (or more generally functional
data) is developed. It is based on a functional mixture model that allows the
clustering of the data in a discriminative functional subspace. This model
presents the advantage in this context to be parsimonious and to allow the
visualization of the clustered systems. Numerical experiments confirm the good
behavior of FunFEM, particularly compared to state-of-the-art methods. The
application of FunFEM to BSS data from JCDecaux and the Transport for London
Initiative allows us to identify 10 general patterns, including pathological
ones, and to propose practical improvement strategies based on the system
comparison. The visualization of the clustered data within the discriminative
subspace turns out to be particularly informative regarding the system
efficiency. The proposed methodology is implemented in a package for the R
software, named funFEM, which is available on the CRAN. The package also
provides a subset of the data analyzed in this work.Comment: Published at http://dx.doi.org/10.1214/15-AOAS861 in the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Estimating Time-Varying Effective Connectivity in High-Dimensional fMRI Data Using Regime-Switching Factor Models
Recent studies on analyzing dynamic brain connectivity rely on sliding-window
analysis or time-varying coefficient models which are unable to capture both
smooth and abrupt changes simultaneously. Emerging evidence suggests
state-related changes in brain connectivity where dependence structure
alternates between a finite number of latent states or regimes. Another
challenge is inference of full-brain networks with large number of nodes. We
employ a Markov-switching dynamic factor model in which the state-driven
time-varying connectivity regimes of high-dimensional fMRI data are
characterized by lower-dimensional common latent factors, following a
regime-switching process. It enables a reliable, data-adaptive estimation of
change-points of connectivity regimes and the massive dependencies associated
with each regime. We consider the switching VAR to quantity the dynamic
effective connectivity. We propose a three-step estimation procedure: (1)
extracting the factors using principal component analysis (PCA) and (2)
identifying dynamic connectivity states using the factor-based switching vector
autoregressive (VAR) models in a state-space formulation using Kalman filter
and expectation-maximization (EM) algorithm, and (3) constructing the
high-dimensional connectivity metrics for each state based on subspace
estimates. Simulation results show that our proposed estimator outperforms the
K-means clustering of time-windowed coefficients, providing more accurate
estimation of regime dynamics and connectivity metrics in high-dimensional
settings. Applications to analyzing resting-state fMRI data identify dynamic
changes in brain states during rest, and reveal distinct directed connectivity
patterns and modular organization in resting-state networks across different
states.Comment: 21 page
Kernel discriminant analysis and clustering with parsimonious Gaussian process models
This work presents a family of parsimonious Gaussian process models which
allow to build, from a finite sample, a model-based classifier in an infinite
dimensional space. The proposed parsimonious models are obtained by
constraining the eigen-decomposition of the Gaussian processes modeling each
class. This allows in particular to use non-linear mapping functions which
project the observations into infinite dimensional spaces. It is also
demonstrated that the building of the classifier can be directly done from the
observation space through a kernel function. The proposed classification method
is thus able to classify data of various types such as categorical data,
functional data or networks. Furthermore, it is possible to classify mixed data
by combining different kernels. The methodology is as well extended to the
unsupervised classification case. Experimental results on various data sets
demonstrate the effectiveness of the proposed method
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