Quantum-inspired feature and parameter optimization of evolving spiking neural networks with a case study from ecological modelling

The paper introduces a framework and implementation of an integrated connectionist system, where the features and the parameters of an evolving spiking neural network are optimised together using a quantum representation of the features and a quantum inspired evolutionary algorithm for optimisation. The proposed model is applied on ecological data modeling problem demonstrating a significantly better classification accuracy than traditional neural network approaches and a more appropriate feature subset selected from a larger initial number of features. Results are compared to a naive Bayesian classifier

AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations

BACKGROUND: In response to the rapid growth of available genome sequences, efforts have been made to develop automatic inference methods to functionally characterize them. Pipelines that infer functional annotation are now routinely used to produce new annotations at a genome scale and for a broad variety of species. These pipelines differ widely in their inference algorithms, confidence thresholds and data sources for reasoning. This heterogeneity makes a comparison of the relative merits of each approach extremely complex. The evaluation of the quality of the resultant annotations is also challenging given there is often no existing gold-standard against which to evaluate precision and recall. RESULTS: In this paper, we present a pragmatic approach to the study of functional annotations. An ensemble of 12 metrics, describing various aspects of functional annotations, is defined and implemented in a unified framework, which facilitates their systematic analysis and inter-comparison. The use of this framework is demonstrated on three illustrative examples: analysing the outputs of state-of-the-art inference pipelines, comparing electronic versus manual annotation methods, and monitoring the evolution of publicly available functional annotations. The framework is part of the AIGO library (http://code.google.com/p/aigo) for the Analysis and the Inter-comparison of the products of Gene Ontology (GO) annotation pipelines. The AIGO library also provides functionalities to easily load, analyse, manipulate and compare functional annotations and also to plot and export the results of the analysis in various formats. CONCLUSIONS: This work is a step toward developing a unified framework for the systematic study of GO functional annotations. This framework has been designed so that new metrics on GO functional annotations can be added in a very straightforward way

Generalized ocean color inversion model for retrieving marine inherent optical properties

Ocean color measured from satellites provides daily, global estimates of marine inherent optical properties (IOPs). Semi-analytical algorithms (SAAs) provide one mechanism for inverting the color of the water observed by the satellite into IOPs. While numerous SAAs exist, most are similarly constructed and few are appropriately parameterized for all water masses for all seasons. To initiate community-wide discussion of these limitations, NASA organized two workshops that deconstructed SAAs to identify similarities and uniqueness and to progress toward consensus on a unified SAA. This effort resulted in the development of the generalized IOP (GIOP) model software that allows for the construction of different SAAs at runtime by selection from an assortment of model parameterizations. As such, GIOP permits isolation and evaluation of specific modeling assumptions, construction of SAAs, development of regionally tuned SAAs, and execution of ensembe inversion modeling. Working groups associated with the workshops proposed a preliminary default configuration for GIOP (GIOP-DC), with alternative model parameterizations and features defined for subsequent evaluation. In this paper, we: (1) describe the theoretical basis of GIOP; (2) present GIOP-DC and verify its comparable performance to other popular SAAs using both in situ and synthetic data sets; and, (3) quantify the sensitivities of their output to their parameterization. We use the latter to develop a hierarchical sensitivity of SAAs to various model parameterizations, to identify components of SAAs that merit focus in future research, and to provide material for discussion on algorithm uncertainties and future ensemble applications

Developing integrated crop knowledge networks to advance candidate gene discovery

AbstractThe chances of raising crop productivity to enhance global food security would be greatly improved if we had a complete understanding of all the biological mechanisms that underpinned traits such as crop yield, disease resistance or nutrient and water use efficiency. With more crop genomes emerging all the time, we are nearer having the basic information, at the gene-level, to begin assembling crop gene catalogues and using data from other plant species to understand how the genes function and how their interactions govern crop development and physiology. Unfortunately, the task of creating such a complete knowledge base of gene functions, interaction networks and trait biology is technically challenging because the relevant data are dispersed in myriad databases in a variety of data formats with variable quality and coverage. In this paper we present a general approach for building genome-scale knowledge networks that provide a unified representation of heterogeneous but interconnected datasets to enable effective knowledge mining and gene discovery. We describe the datasets and outline the methods, workflows and tools that we have developed for creating and visualising these networks for the major crop species, wheat and barley. We present the global characteristics of such knowledge networks and with an example linking a seed size phenotype to a barley WRKY transcription factor orthologous to TTG2 from Arabidopsis, we illustrate the value of integrated data in biological knowledge discovery. The software we have developed (www.ondex.org) and the knowledge resources (http://knetminer.rothamsted.ac.uk) we have created are all open-source and provide a first step towards systematic and evidence-based gene discovery in order to facilitate crop improvement

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Combining multiple evidence-types from different information sources has the potential to reveal new relationships in biological systems. The integrated information can be represented as a relationship network, and clustering the network can suggest possible functional modules. The value of such modules for gaining insight into the underlying biological processes depends on their functional coherence. The challenges that we wish to address are to define and quantify the functional coherence of modules in relationship networks, so that they can be used to infer function of as yet unannotated proteins, to discover previously unknown roles of proteins in diseases as well as for better understanding of the regulation and interrelationship between different elements of complex biological systems.</p> <p>Results</p> <p>We have defined the functional coherence of modules with respect to the Gene Ontology (GO) by considering two complementary aspects: (i) the fragmentation of the GO functional categories into the different modules and (ii) the most representative functions of the modules. We have proposed a set of metrics to evaluate these two aspects and demonstrated their utility in <it>Arabidopsis thaliana</it>. We selected 2355 proteins for which experimentally established protein-protein interaction (PPI) data were available. From these we have constructed five relationship networks, four based on single types of data: PPI, co-expression, co-occurrence of protein names in scientific literature abstracts and sequence similarity and a fifth one combining these four evidence types. The ability of these networks to suggest biologically meaningful grouping of proteins was explored by applying Markov clustering and then by measuring the functional coherence of the clusters.</p> <p>Conclusions</p> <p>Relationship networks integrating multiple evidence-types are biologically informative and allow more proteins to be assigned to a putative functional module. Using additional evidence types concentrates the functional annotations in a smaller number of modules without unduly compromising their consistency. These results indicate that integration of more data sources improves the ability to uncover functional association between proteins, both by allowing more proteins to be linked and producing a network where modular structure more closely reflects the hierarchy in the gene ontology.</p

Systems responses to progressive water stress in durum wheat

Durum wheat is susceptible to terminal drought which can greatly decrease grain yield. Breeding to improve crop yield is hampered by inadequate knowledge of how the physiological and metabolic changes caused by drought are related to gene expression. To gain better insight into mechanisms defining resistance to water stress we studied the physiological and transcriptome responses of three durum breeding lines varying for yield stability under drought. Parents of a mapping population (Lahn x Cham1) and a recombinant inbred line (RIL2219) showed lowered flag leaf relative water content, water potential and photosynthesis when subjected to controlled water stress time transient experiments over a six-day period. RIL2219 lost less water and showed constitutively higher stomatal conductance, photosynthesis, transpiration, abscisic acid content and enhanced osmotic adjustment at equivalent leaf water compared to parents, thus defining a physiological strategy for high yield stability under water stress. Parallel analysis of the flag leaf transcriptome under stress uncovered global trends of early changes in regulatory pathways, reconfiguration of primary and secondary metabolism and lowered expression of transcripts in photosynthesis in all three lines. Differences in the number of genes, magnitude and profile of their expression response were also established amongst the lines with a high number belonging to regulatory pathways. In addition, we documented a large number of genes showing constitutive differences in leaf transcript expression between the genotypes at control non-stress conditions. Principal Coordinates Analysis uncovered a high level of structure in the transcriptome response to water stress in each wheat line suggesting genome-wide co-ordination of transcription. Utilising a systems-based approach of analysing the integrated wheat's response to water stress, in terms of biological robustness theory, the findings suggest that each durum line transcriptome responded to water stress in a genome-specific manner which contributes to an overall different strategy of resistance to water stress

Homologie en Programmation Génétique<br />Application à la résolution d'un problème inverse

Evolutionary Algorithms (EA) are search methods working iteratively on a population of potential solutions that are randomly selected and modified. Genetic Programming (GP) is an EA that allows automatic search for programs, usually represented as syntax trees (TGP) or linear sequences (LGP). Two mechanisms perform the random variations needed to obtain new programs : the mutation operator (local variation) and the crossover operator (programs recombination). The crossover operator blindly exchanges parts of programs without taking the context into account, this is a "brutal" operation that may be responsible of the uncontrolled growth of programs during evolution. Mainly inspired by the homologous recombinaison of DNA strands, we introduce the Maximum Homologous Crossover for LGP. The MHC ensures, thanks to a measure of similarity, that recombinaison of programs is respectful. We show on classical GP benchmarks, e.g. the symbolic regression problem, that when using MHC the search process is less brutal and that an accurate control of programs size is also possible. These results are used to address a real world problem : the inversion of atmospheric components. We show that, with a constant computational effort, it is also possible to find teams of inversion predictors that outperform standard models.Les Algorithmes Évolutionnaires (AE) sont des méthodes de recherche par itération de sélections et de variations aléatoires sur une population de solutions potentielles. La Programmation Génétique (PG) est un AE qui permet la recherche automatique de programmes et qui manipule des représentations complexes : arbres (PGA) ou listes de longueur variables (PGL). Les variations aléatoires permettant de créer de nouveaux programmes peuvent être des modifications locales (mutations) ou des recombinaisons de programmes (croisements). L'opérateur de croisement recombine aléatoirement des sous-parties de programmes sans tenir compte du contexte : c'est une opération «brutale» qui est une des causes supposées de la croissance incontrôlée de la taille des programmes. Inspirés par la recombinaison homologue de l'ADN, nous définissons, le Croisement par Maximum d'Homologie (CMH) pour la PGL. A partir d'une mesure de similarité entre les expressions à recombiner, le CMH favorise les échanges qui respectent les structures communes préexistantes. La capacité du CMH à effectuer une recherche moins brutale et à permettre un contrôle précis de la taille des programmes est mise en évidence sur des problèmes classiques de PG comme l'approximation de fonctions par régression symbolique. En partant des différents résultats obtenus, nous appliquons notre méthode à la résolution d'un problème réel : l'inversion des composantes atmosphériques. De plus, nous montrons comment, à coût constant, il est possible de rechercher des combinaisons de modèles inverses dont les performances sont supérieures aux modèles standards