Advanced sequential Monte Carlo methods and their applications to sparse sensor network for detection and estimation

The general state space models present a flexible framework for modeling dynamic systems and therefore have vast applications in many disciplines such as engineering, economics, biology, etc. However, optimal estimation problems of non-linear non-Gaussian state space models are analytically intractable in general. Sequential Monte Carlo (SMC) methods become a very popular class of simulation-based methods for the solution of optimal estimation problems. The advantages of SMC methods in comparison with classical filtering methods such as Kalman Filter and Extended Kalman Filter are that they are able to handle non-linear non-Gaussian scenarios without relying on any local linearization techniques. In this thesis, we present an advanced SMC method and the study of its asymptotic behavior. We apply the proposed SMC method in a target tracking problem using different observation models. Specifically, a distributed SMC algorithm is developed for a wireless sensor network (WSN) that incorporates with an informative-sensor detection technique. The novel SMC algorithm is designed to surmount the degeneracy problem by employing a multilevel Markov chain Monte Carlo (MCMC) procedure constructed by engaging drift homotopy and likelihood bridging techniques. The observations are gathered only from the informative sensors, which are sensing useful observations of the nearby moving targets. The detection of those informative sensors, which are typically a small portion of the WSN, is taking place by using a sparsity-aware matrix decomposition technique. Simulation results showcase that our algorithm outperforms current popular tracking algorithms such as bootstrap filter and auxiliary particle filter in many scenarios

Multi-objective genetic programming with partial sampling and its extension to many-objective

This paper describes a technique on an optimization of tree-structure data by of multi-objective evolutionary algorithm, or multi-objective genetic programming. GP induces bloat of the tree structure as one of the major problem. The cause of bloat is that the tree structure obtained by the crossover operator grows bigger and bigger but its evaluation does not improve. To avoid the risk of bloat, a partial sampling operator is proposed as a mating operator. The size of the tree and a structural distance are introduced into the measure of the tree-structure data as the objective functions in addition to the index of the goodness of tree structure. GP is defined as a three-objective optimization problem. SD is also applied for the ranking of parent individuals instead to the crowding distance of the conventional NSGA-II. When the index of the goodness of tree-structure data is two or more, the number of objective functions in the above problem becomes four or more. We also propose an effective many-objective EA applicable to such the many-objective GP. We focus on NSGA-II based on Pareto partial dominance (NSGA-II-PPD). NSGA-II-PPD requires beforehand a combination list of the number of objective functions to be used for Pareto partial dominance (PPD). The contents of the combination list greatly influence the optimization result. We propose to schedule a parameter r meaning the subset size of objective functions for PPD and to eliminate individuals created by the mating having the same contents as the individual of the archive set

Evolutionary Multiobjective Optimization including Practically Desirable Solutions

In many practical situations the decision-maker has to pay special attention to decision space to determine the constructability of a potential solution, in addition to its optimality in objective space. Practically desirable solutions are those around preferred values in decision space and within a distance from optimality. This work investigates two methods to find simultaneously optimal and practically desirable solutions. The methods expand the objective space by adding fitness functions that favor preferred values for some variables. In addition, the methods incorporate a ranking mechanism that takes into account Pareto dominance in objective space and desirability in decision space. One method searches with one population in the expanded space, whereas the other one uses two populations to search concurrently in the original and expanded space. Our experimental results on benchmark and real world problems show that the proposed method can effectively find optimal and practically desirable solutions

Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis

<p>Abstract</p> <p>Background</p> <p>Sessile bivalves of the genus <it>Mytilus </it>are suspension feeders relatively tolerant to a wide range of environmental changes, used as sentinels in ecotoxicological investigations and marketed worldwide as seafood. Mortality events caused by infective agents and parasites apparently occur less in mussels than in other bivalves but the molecular basis of such evidence is unknown. The arrangement of Mytibase, interactive catalogue of 7,112 transcripts of <it>M. galloprovincialis</it>, offered us the opportunity to look for gene sequences relevant to the host defences, in particular the innate immunity related genes.</p> <p>Results</p> <p>We have explored and described the Mytibase sequence clusters and singletons having a putative role in recognition, intracellular signalling, and neutralization of potential pathogens in <it>M. galloprovincialis</it>. Automatically assisted searches of protein signatures and manually cured sequence analysis confirmed the molecular diversity of recognition/effector molecules such as the antimicrobial peptides and many carbohydrate binding proteins. Molecular motifs identifying complement C1q, C-type lectins and fibrinogen-like transcripts emerged as the most abundant in the Mytibase collection whereas, conversely, sequence motifs denoting the regulatory cytokine MIF and cytokine-related transcripts represent singular and unexpected findings. Using a cross-search strategy, 1,820 putatively immune-related sequences were selected to design oligonucleotide probes and define a species-specific Immunochip (DNA microarray). The Immunochip performance was tested with hemolymph RNAs from mussels injected with <it>Vibrio splendidus </it>at 3 and 48 hours post-treatment. A total of 143 and 262 differentially expressed genes exemplify the early and late hemocyte response of the <it>Vibrio</it>-challenged mussels, respectively, with AMP trends confirmed by qPCR and clear modulation of interrelated signalling pathways.</p> <p>Conclusions</p> <p>The Mytibase collection is rich in gene transcripts modulated in response to antigenic stimuli and represents an interesting window for looking at the mussel immunome (transcriptomes mediating the mussel response to non-self or abnormal antigens). On this basis, we have defined a new microarray platform, a mussel Immunochip, as a flexible tool for the experimental validation of immune-candidate sequences, and tested its performance on <it>Vibrio</it>-activated mussel hemocytes. The microarray platform and related expression data can be regarded as a step forward in the study of the adaptive response of the <it>Mytilus </it>species to an evolving microbial world.</p

Preventing premature convergence and proving the optimality in evolutionary algorithms

http://ea2013.inria.fr//proceedings.pdfInternational audienceEvolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution. Interval-based techniques, on the other hand, yield a numerical proof of optimality of the solution. However, they may fail to converge within a reasonable time due to their inability to quickly compute a good approximation of the global minimum and their exponential complexity. The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques. It prevents premature convergence toward local optima and outperforms both deterministic and stochastic existing approaches. We demonstrate its efficiency on a benchmark of highly multimodal problems, for which we provide previously unknown global minima and certification of optimality

Deciphering the historical recombination landscape of a migratory songbird, the Eurasian blackcap

Meiotic recombination involves the exchange of genetic information between parental chromosomes generating new combinations of alleles in the offspring. Recombination is a crucial determinant for reproductive success, proper chromosomal segregation, genetic variability, adaptation rates, and influencing the efficacy of selection. The historical recombination landscape comprises all recombination events captured in DNA sequences among individuals over many generations. Recombination involves different molecular mechanisms and recombining events are not spread randomly across the genome. The placement of recombination events in most mammals is defined by the protein PRDM9, a key player in the initiation of recombination dynamics. However, some organismal groups, such as birds, have lost this protein enabling them with unique recombining properties and conferring an apparent stasis in the positioning of recombination events. However, recent studies in species lacking PRDM9 demonstrated that recombination rates differ widely across the genome and between species. The variation in recombination rates, its causes, and its impact on evolutionary and behavioural processes remain poorly understood, particularly in natural bird populations. This thesis evaluates the variation of the historical recombination landscape in the Eurasian blackcap, Sylvia atricapilla, and the interplay of recombination rate variation with specific genomic and epigenetic features at different scales: across the genome, at inter- and intraspecific levels

Multi-and many-objective optimization: present and future in de novo drug design

de novo Drug Design (dnDD) aims to create new molecules that satisfy multiple conflicting objectives. Since several desired properties can be considered in the optimization process, dnDD is naturally categorized as a many-objective optimization problem (ManyOOP), where more than three objectives must be simultaneously optimized. However, a large number of objectives typically pose several challenges that affect the choice and the design of optimization methodologies. Herein, we cover the application of multi- and many-objective optimization methods, particularly those based on Evolutionary Computation and Machine Learning techniques, to enlighten their potential application in dnDD. Additionally, we comprehensively analyze how molecular properties used in the optimization process are applied as either objectives or constraints to the problem. Finally, we discuss future research in many-objective optimization for dnDD, highlighting two important possible impacts: i) its integration with the development of multi-target approaches to accelerate the discovery of innovative and more efficacious drug therapies and ii) its role as a catalyst for new developments in more fundamental and general methodological frameworks in the field