10,454 research outputs found
Structured, sparse regression with application to HIV drug resistance
We introduce a new version of forward stepwise regression. Our modification
finds solutions to regression problems where the selected predictors appear in
a structured pattern, with respect to a predefined distance measure over the
candidate predictors. Our method is motivated by the problem of predicting
HIV-1 drug resistance from protein sequences. We find that our method improves
the interpretability of drug resistance while producing comparable predictive
accuracy to standard methods. We also demonstrate our method in a simulation
study and present some theoretical results and connections.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS428 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Accelerating delayed-acceptance Markov chain Monte Carlo algorithms
Delayed-acceptance Markov chain Monte Carlo (DA-MCMC) samples from a
probability distribution via a two-stages version of the Metropolis-Hastings
algorithm, by combining the target distribution with a "surrogate" (i.e. an
approximate and computationally cheaper version) of said distribution. DA-MCMC
accelerates MCMC sampling in complex applications, while still targeting the
exact distribution. We design a computationally faster, albeit approximate,
DA-MCMC algorithm. We consider parameter inference in a Bayesian setting where
a surrogate likelihood function is introduced in the delayed-acceptance scheme.
When the evaluation of the likelihood function is computationally intensive,
our scheme produces a 2-4 times speed-up, compared to standard DA-MCMC.
However, the acceleration is highly problem dependent. Inference results for
the standard delayed-acceptance algorithm and our approximated version are
similar, indicating that our algorithm can return reliable Bayesian inference.
As a computationally intensive case study, we introduce a novel stochastic
differential equation model for protein folding data.Comment: 40 pages, 21 figures, 10 table
Connectionist Theory Refinement: Genetically Searching the Space of Network Topologies
An algorithm that learns from a set of examples should ideally be able to
exploit the available resources of (a) abundant computing power and (b)
domain-specific knowledge to improve its ability to generalize. Connectionist
theory-refinement systems, which use background knowledge to select a neural
network's topology and initial weights, have proven to be effective at
exploiting domain-specific knowledge; however, most do not exploit available
computing power. This weakness occurs because they lack the ability to refine
the topology of the neural networks they produce, thereby limiting
generalization, especially when given impoverished domain theories. We present
the REGENT algorithm which uses (a) domain-specific knowledge to help create an
initial population of knowledge-based neural networks and (b) genetic operators
of crossover and mutation (specifically designed for knowledge-based networks)
to continually search for better network topologies. Experiments on three
real-world domains indicate that our new algorithm is able to significantly
increase generalization compared to a standard connectionist theory-refinement
system, as well as our previous algorithm for growing knowledge-based networks.Comment: See http://www.jair.org/ for any accompanying file
GFLIB: an Open Source Library for Genetic Folding Solving Optimization Problems
This paper aims at presenting GFLIB, a Genetic Folding MATLAB toolbox for supervised learning problems. In essence, the goal of GFLIB is to build a concise model of supervised learning, andĀ a free open source MATLAB toolbox for performing classification and regression. The GFLIB isĀ specifically designed for most of the traditionally used features,Ā to evolve in applications of mathematical models. The toolbox suits all kinds of users;Ā from the users who implemented GFLIB as āblack boxā, to advanced researchersĀ who want to generate and test new functionalities and parameters of GF algorithm. The toolbox and its documentation are freely available for download at: https://github.com/mohabedalgani/gflib.git
A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory
Despite great advances in discovering cancer molecular profiles, the proper application of microarray technology to routine clinical diagnostics is still a challenge. Current practices in the classification of microarrays' data show two main limitations: the reliability of the training data sets used to build the classifiers, and the classifiers' performances, especially when the sample to be classified does not belong to any of the available classes. In this case, state-of-the-art algorithms usually produce a high rate of false positives that, in real diagnostic applications, are unacceptable. To address this problem, this paper presents a new cDNA microarray data classification algorithm based on graph theory and is able to overcome most of the limitations of known classification methodologies. The classifier works by analyzing gene expression data organized in an innovative data structure based on graphs, where vertices correspond to genes and edges to gene expression relationships. To demonstrate the novelty of the proposed approach, the authors present an experimental performance comparison between the proposed classifier and several state-of-the-art classification algorithm
A Framework for Genetic Algorithms Based on Hadoop
Genetic Algorithms (GAs) are powerful metaheuristic techniques mostly used in
many real-world applications. The sequential execution of GAs requires
considerable computational power both in time and resources. Nevertheless, GAs
are naturally parallel and accessing a parallel platform such as Cloud is easy
and cheap. Apache Hadoop is one of the common services that can be used for
parallel applications. However, using Hadoop to develop a parallel version of
GAs is not simple without facing its inner workings. Even though some
sequential frameworks for GAs already exist, there is no framework supporting
the development of GA applications that can be executed in parallel. In this
paper is described a framework for parallel GAs on the Hadoop platform,
following the paradigm of MapReduce. The main purpose of this framework is to
allow the user to focus on the aspects of GA that are specific to the problem
to be addressed, being sure that this task is going to be correctly executed on
the Cloud with a good performance. The framework has been also exploited to
develop an application for Feature Subset Selection problem. A preliminary
analysis of the performance of the developed GA application has been performed
using three datasets and shown very promising performance
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