Pablo Moscato

A Gentle Introduction to Memetic Algorithms

The generic denomination of ‘Memetic Algorithms’ (MAs) is used to encompass a broad class of metaheuristics (i.e. general purpose methods aimed to guide an underlying heuristic). The method is based on a population of agents and proved to be of practical success in a variety of problem domains and in particular for the approximate solution of NP Optimization problems. Unlike traditional Evolutionary Computation (EC) methods, MAs are intrinsically concerned with exploiting all available knowledge about the problem under study. The incorporation of problem domain knowledge is not an optional mechanism, but a fundamental feature that characterizes MAs. This functioning philosophy is perfectly illustrated by the term “memetic”. Coined by R. Dawkins [52], the word ‘meme’ denotes an analogous to the gene in the context of cultural evolution [154]. In Dawkins’ words:

Genome-wide analysis of long noncoding RNA stability

Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life < 2 h) intergenic, cis-antisense, and intronic lncRNAs, as well as lncRNAs showing extreme stability (half-life > 16 h). Analysis of lncRNA features revealed that intergenic and cis-antisense RNAs are more stable than those derived from introns, as are spliced lncRNAs compared to unspliced (single exon) transcripts. Subcellular localization of lncRNAs indicated widespread trafficking to different cellular locations, with nuclear-localized lncRNAs more likely to be unstable. Surprisingly, one of the least stable lncRNAs is the well-characterized paraspeckle RNA Neat1, suggesting Neat1 instability contributes to the dynamic nature of this subnuclear domain. We have created an online interactive resource (http://stability.matticklab.com) that allows easy navigation of lncRNA and mRNA stability profiles and provides a comprehensive annotation of ~7200 mouse lncRNAs.

Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci

To perform a 1‐stage meta‐analysis of genome‐wide association studies (GWAS) of multiple sclerosis (MS) susceptibility and to explore functional consequences of new susceptibility loci.

On the Rank of Extreme Matrices in Semidefinite Programs and the Multiplicity of Optimal Eigenvalues

We derive some basic results on the geometry of semidefinite programming (SDP) and eigenvalue-optimization, i.e., the minimization of the sum of the k largest eigenvalues of a smooth matrix-valued function. We provide upper bounds on the rank of extreme matrices in SDPs, and the first theoretically solid explanation of a phenomenon of intrinsic interest in eigenvalue-optimization. In the spectrum of an optimal matrix, the kth and (k + 1)st largest eigenvalues tend to be equal and frequently have multiplicity greater than two. This clustering is intuitively plausible and has been observed as early as 1975. When the matrix-valued function is affine, we prove that clustering must occur at extreme points of the set of optimal solutions, if the number of variables is sufficiently large. We also give a lower bound on the multiplicity of the critical eigenvalue. These results generalize to the case of a general matrix-valued function under appropriate conditions.

Handbook of Memetic Algorithms

Memetic Algorithms (MAs) are computational intelligence structures combining multiple and various operators in order to address optimization problems. The combination and interaction amongst operators evolves and promotes the diffusion of the most successful units and generates an algorithmic behavior which can handle complex objective functions and hard fitness landscapes. Handbook of Memetic Algorithms organizes, in a structured way, all the the most important results in the field of MAs since their earliest definition until now. A broad review including various algorithmic solutions as well as successful applications is included in this book. Each class of optimization problems, such as constrained optimization, multi-objective optimization, continuous vs combinatorial problems, uncertainties, are analysed separately and, for each problem, memetic recipes for tackling the difficulties are given with some successful examples. Although this book contains chapters written by multiple authors, a great attention has been given by the editors to make it a compact and smooth work which covers all the main areas of computational intelligence optimization. It is not only a necessary read for researchers working in the research area, but also a useful handbook for practitioners and engineers who need to address real-world optimization problems. In addition, the book structure makes it an interesting work also for graduate students and researchers is related fields of mathematics and computer science.

A memetic algorithm for the total tardiness single machine scheduling problem

Abstract In this paper, a new memetic algorithm (MA) for the total tardiness single machine scheduling (SMS) problem with due dates and sequence-dependent setup times is proposed. The main contributions with respect to the implementation of the hybrid population approach are a hierarchically structured population conceived as a ternary tree and the evaluation of three recombination operators. Concerning the local improvement procedure, several neighborhood reduction schemes are developed and proved to be effective when compared to the complete neighborhood. Results of computational experiments are reported for a set of randomly generated test problems. The memetic approach and a pure genetic algorithm (GA) version are compared with a multiple start algorithm that employs the all-pairs neighborhood as well as two constructive heuristics.

Evolutionary algorithms for scheduling a flowshop manufacturing cell with sequence dependent family setups

This paper considers the problem of scheduling part families and jobs within each part family in a flowshop manufacturing cell with sequence dependent family setups times where it is desired to minimize the makespan while processing parts (jobs) in each family together. Two evolutionary algorithms-a Genetic Algorithm and a Memetic Algorithm with local search-are proposed and empirically evaluated as to their effectiveness in finding optimal permutation schedules. The proposed algorithms use a compact representation for the solution and a hierarchically structured population where the number of possible neighborhoods is limited by dividing the population into clusters. In comparison to a Multi-Start procedure, solutions obtained by the proposed evolutionary algorithms were very close to the lower bounds for all problem instances. Moreover, the comparison against the previous best algorithm, a heuristic named CMD, indicated a considerable performance improvement.

Common variants at 6p21.1 are associated with large artery atherosclerotic stroke

Genome-wide association studies (GWAS) have not consistently detected replicable genetic risk factors for ischemic stroke, potentially due to etiological heterogeneity of this trait. We performed GWAS of ischemic stroke and a major ischemic stroke subtype (large artery atherosclerosis, LAA) using 1,162 ischemic stroke cases (including 421 LAA cases) and 1,244 population controls from Australia. Evidence for a genetic influence on ischemic stroke risk was detected, but this influence was higher and more significant for the LAA subtype. We identified a new LAA susceptibility locus on chromosome 6p21.1 (rs556621: odds ratio (OR) = 1.62, P = 3.9 × 10−8) and replicated this association in 1,715 LAA cases and 52,695 population controls from 10 independent population cohorts (meta-analysis replication OR = 1.15, P = 3.9 × 10−4; discovery and replication combined OR = 1.21, P = 4.7 × 10−8). This study identifies a genetic risk locus for LAA and shows how analyzing etiological subtypes may better identify genetic risk alleles for ischemic stroke.

Uncovering molecular biomarkers that correlate cognitive decline with the changes of hippocampus' gene expression profiles in Alzheimer's disease.

Background Alzheimers disease (AD) is characterized by a neurodegenerative progression that alters cognition. On a phenotypical level, cognition is evaluated by means of the MiniMental State Examination (MMSE) and the post-morten examination of Neurofibrillary Tangle count (NFT) helps to confirm an AD diagnostic. The MMSE evaluates different aspects of cognition including orientation, short-term memory (retention and recall), attention and language. As there is a normal cognitive decline with aging, and death is the final state on which NFT can be counted, the identification of brain gene expression biomarkers from these phenotypical measures has been elusive. Methodology/Principal Findings We have reanalysed a microarray dataset contributed in 2004 by Blalock et al. of 31 samples corresponding to hippocampus gene expression from 22 AD subjects of varying degree of severity and 9 controls. Instead of only relying on correlations of gene expression with the associated MMSE and NFT measures, and by using modern bioinformatics methods based on information theory and combinatorial optimization, we uncovered a 1,372-probe gene expression signature that presents a high-consensus with established markers of progression in AD. The signature reveals alterations in calcium, insulin, phosphatidylinositol and wnt-signalling. Among the most correlated gene probes with AD severity we found those linked to synaptic function, neurofilament bundle assembly and neuronal plasticity. Conclusions/Significance A transcription factors analysis of 1,372-probe signature reveals significant associations with the EGR/KROX family of proteins, MAZ, and E2F1. The gene homologous of EGR1, zif268, Egr-1 or Zenk, together with other members of the EGR family, are consolidating a key role in the neuronal plasticity in the brain. These results indicate a degree of commonality between putative genes involved in AD and prion-induced neurodegenerative processes that warrants further investigation.

A New Memetic Algorithm for the Asymmetric Traveling Salesman Problem

This paper introduces a new memetic algorithm specialized for the asymmetric instances of the traveling salesman problem (ATSP). The method incorporates a new local search engine and many other features that contribute to its effectiveness, such as: (i) the topological organization of the population as a complete ternary tree with thirteen nodes; (ii) the hierarchical organization of the population in overlapping clusters leading to the special selection scheme; (iii) efficient data structures. Computational experiments are conducted on all ATSP instances available in the TSPLIB, and on a set of larger asymmetric instances with known optimal solutions. The comparisons show that the results obtained by our method compare favorably with those obtained by several other algorithms recently proposed for the ATSP.