36,228 research outputs found
Efficient Parallel Statistical Model Checking of Biochemical Networks
We consider the problem of verifying stochastic models of biochemical
networks against behavioral properties expressed in temporal logic terms. Exact
probabilistic verification approaches such as, for example, CSL/PCTL model
checking, are undermined by a huge computational demand which rule them out for
most real case studies. Less demanding approaches, such as statistical model
checking, estimate the likelihood that a property is satisfied by sampling
executions out of the stochastic model. We propose a methodology for
efficiently estimating the likelihood that a LTL property P holds of a
stochastic model of a biochemical network. As with other statistical
verification techniques, the methodology we propose uses a stochastic
simulation algorithm for generating execution samples, however there are three
key aspects that improve the efficiency: first, the sample generation is driven
by on-the-fly verification of P which results in optimal overall simulation
time. Second, the confidence interval estimation for the probability of P to
hold is based on an efficient variant of the Wilson method which ensures a
faster convergence. Third, the whole methodology is designed according to a
parallel fashion and a prototype software tool has been implemented that
performs the sampling/verification process in parallel over an HPC
architecture
Parallel Cross-Entropy Optimization
The cross-entropy (CE) method is a modern and effective optimization method well suited to parallel implementations. There is a vast array of problems today, some of which are highly complex and can take weeks or even longer to solve using current optimization techniques. This paper presents a general method for designing parallel CE algorithms for multiple instruction multiple data (MIVID) distributed memory machines using the message passing interface (MPI) library routines. We provide examples of its performance for two well-known test-cases: the (discrete) Max-Cut problem and (continuous) Rosenbrock problem. Speedup factors and a comparison to sequential CE methods are reported
A numerically efficient implementation of the expectation maximization algorithm for state space models
Peer reviewedPostprin
Digging into acceptor splice site prediction : an iterative feature selection approach
Feature selection techniques are often used to reduce data dimensionality, increase classification performance, and gain insight into the processes that generated the data. In this paper, we describe an iterative procedure of feature selection and feature construction steps, improving the classification of acceptor splice sites, an important subtask of gene prediction.
We show that acceptor prediction can benefit from feature selection, and describe how feature selection techniques can be used to gain new insights in the classification of acceptor sites. This is illustrated by the identification of a new, biologically motivated feature: the AG-scanning feature.
The results described in this paper contribute both to the domain of gene prediction, and to research in feature selection techniques, describing a new wrapper based feature weighting method that aids in knowledge discovery when dealing with complex datasets
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
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