A Factor Graph Approach to Automated GO Annotation

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.Fil: Spetale, Flavio Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Krsticevic, Flavia Jorgelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Roda, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Bulacio, Pilar Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentin

Fine-grained or coarse-grained? Strategies for implementing parallel genetic algorithms in a programmable neuromorphic platform

Genetic Algorithm (GA) is one of popular heuristic-based optimization methods that attracts engineers and scientists for many years. With the advancement of multi- and many-core technologies, GAs are transformed into more powerful tools by parallelising their core processes. This paper describes a feasibility study of implementing parallel GAs (pGAs) on a SpiNNaker. As a many-core neuromorphic platform, SpiNNaker offers a possibility to scale-up a parallelised algorithm, such as a pGA, whilst offering low power consumption on its processing and communication overhead. However, due to its small packets distribution mechanism and constrained processing resources, parallelising processes of a GA in SpiNNaker is challenging. In this paper we show how a pGA can be implemented on SpiNNaker and analyse its performance. Due to inherently numerous parameter and classification of pGAs, we evaluate only the most common aspects of a pGA and use some artificial benchmarking test functions. The experiments produced some promising results that may lead to further developments of massively parallel GAs on SpiNNaker

Exploring density functional subspaces with genetic algorithms

We use a genetic algorithm to explore the subspace of combination and parametrization patterns spanned by a set of popular exchange and correlation functional approximations. Using the well-balanced GMTKN30 benchmark database to guide the evolutionary process, we find that the genetic algorithm is able to recover variants of several popular generalized gradient approximation functionals and hybrid functionals. For the latter class, the algorithm is able to identify a reparametrized version of the three-parameter hybrid B3PW91, which shows significantly improved performance compared to conventional versions of B3PW91. Furthermore, the possible application of this algorithm to automatically construct so-called “niche”-functionals—specially tailored to specific applications—is demonstrated

Solving Partial Differential Equation Using FPGA Technology

This chapter introduces the method of using CNN technology on FPGA chips to solve differential equation with large space, with lager computing space, while limitation of resource chip on FPGA is needed, we have to find solution to separate differential space into several subspaces. Our solution will do: firstly, division of the computing space into smaller areas and combination of sequential and parallel computing; secondly, division and combination of boundary areas that are required to be continuous to avoid losing temporary data while processing (using buffer memory to store); and thirdly, real-time data exchange. The control unit controls the activities of the whole system set by the algorithm. We have configured the CNN chip for solving Navier-Stokes equation for the hydraulic fluid flow successfully on the Virtex 6 chip XCVL240T-1FFG1156 by Xilinx and giving acceptance results as well

An Overview of Self-Consistent Field Calculations Within Finite Basis Sets

A uniform derivation of the self-consistent field equations in a finite basis set is presented. Both restricted and unrestricted Hartree–Fock (HF) theory as well as various density functional approximations are considered. The unitary invariance of the HF and density functional models is discussed, paving the way for the use of localized molecular orbitals. The self-consistent field equations are derived in a non-orthogonal basis set, and their solution is discussed also in the presence of linear dependencies in the basis. It is argued why iterative diagonalization of the Kohn–Sham–Fock matrix leads to the minimization of the total energy. Alternative methods for the solution of the self-consistent field equations via direct minimization as well as stability analysis are briefly discussed. Explicit expressions are given for the contributions to the Kohn–Sham–Fock matrix up to meta-GGA functionals. Range-separated hybrids and non-local correlation functionals are summarily reviewed

Optimization of a Quantum Cascade Laser Operating in the Terahertz Frequency Range Using a Multiobjective Evolutionary Algorithm

A quantum cascade (QC) laser is a specific type of semiconductor laser that operates through principles of quantum mechanics. In less than a decade QC lasers are already able to outperform previously designed double heterostructure semiconductor lasers. Because there is a genuine lack of compact and coherent devices which can operate in the far-infrared region the motivation exists for designing a terahertz QC laser. A device operating at this frequency is expected to be more efficient and cost effective than currently existing devices. It has potential applications in the fields of spectroscopy, astronomy, medicine and free-space communication as well as applications to near-space radar and chemical/biological detection. The overarching goal of this research was to find QC laser parameter combinations which can be used to fabricate viable structures. To ensure operation in the THz region the device must conform to the extremely small energy level spacing range from ~10-15 meV. The time and expense of the design and production process is prohibitive, so an alternative to fabrication was necessary. To accomplish this goal a model of a QC laser, developed at Worchester Polytechnic Institute with sponsorship from the Air Force Research Laboratory Sensors Directorate, and the General Multiobjective Parallel Genetic Algorithm (GenMOP), developed at the Air Force Institute of Technology, were integrated to form a computer simulation which stochastically searches for feasible solutions

Coarse-grained parallel genetic algorithms: Three implementations and their analysis

Although solutions to many problems can be found using direct analytical methods such as those calculus provides, many problems simply are too large or too difficult to solve using traditional techniques. Genetic algorithms provide an indirect approach to solving those problems. A genetic algorithm applies biological genetic procedures and principles to a randomly generated collection of potential solutions. The result is the evolution of new and better solutions. Coarse-Grained Parallel Genetic Algorithms extend the basic genetic algorithm by introducing genetic isolation and distribution of the problem domain. This thesis compares the capabilities of a serial genetic algorithm and three coarse-grained parallel genetic algorithms (a standard parallel algorithm, a non-uniform parallel algorithm and an adaptive parallel algorithm). The evaluation is done using an instance of the traveling salesman problem. It is shown that while the standard course-grained parallel algorithm provides more consistent results than the serial genetic algorithm, the adaptive distributed algorithm out-performs them both. To facilitate this analysis, an extensible object-oriented library for genetic algorithms, encompassing both serial and coarse-grained parallel genetic algorithms, was developed. The Java programming language was used throughout