Generalized Fock spaces and the Stirling numbers

The Bargmann-Fock-Segal space plays an important role in mathematical physics, and has been extended into a number of directions. In the present paper we imbed this space into a Gelfand triple. The spaces forming the Fr\'echet part (i.e. the space of test functions) of the triple are characterized both in a geometric way and in terms of the adjoint of multiplication by the complex variable, using the Stirling numbers of the second kind. The dual of the space of test functions has a topological algebra structure, of the kind introduced and studied by the first named author and G. Salomon.Comment: revised versio

A generalization of Cauchy-Bunyakovsky integral inequality via means with max and min values

In the paper, we give a brief survey of a method for constructing generalizations of Cauchy-Bunyakovsky integral inequality using abstract mean values. One special inequality of this type is considered in details in terms of min and max functions. Some direct proofs of this inequality are given and application to inequalities for special function

The Pathway Tools cellular overview diagram and Omics Viewer

The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic proteins. Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram. Furthermore, a software component called the Omics Viewer provides visual analysis of whole-organism datasets using the overview diagram as an organizing framework. For example, gene expression and metabolomics measurements, alone or in combination, can be painted onto the overview, as can computed whole-organism datasets, such as predicted reaction-flux values. The cellular overview and Omics Viewer provide a mechanism whereby biologists can apply the pattern-recognition capabilities of the human visual system to analyze large-scale datasets in a biologically meaningful context. SRI's BioCyc.org website provides overview diagrams for more than 200 organisms. This article describes enhancements to the overview made since a 1999 publication, including the automatic layout capability, expansion of the cellular machinery that it includes, new semantic zooming and poster-generating capabilities, and extension of the Omics Viewer to support painting of metabolites, animations and zooming to individual pathway diagrams

Improved Parallel Rabin-Karp Algorithm Using Compute Unified Device Architecture

String matching algorithms are among one of the most widely used algorithms in computer science. Traditional string matching algorithms efficiency of underlaying string matching algorithm will greatly increase the efficiency of any application. In recent years, Graphics processing units are emerged as highly parallel processor. They out perform best of the central processing units in scientific computation power. By combining recent advancement in graphics processing units with string matching algorithms will allows to speed up process of string matching. In this paper we proposed modified parallel version of Rabin-Karp algorithm using graphics processing unit. Based on that, result of CPU as well as parallel GPU implementations are compared for evaluating effect of varying number of threads, cores, file size as well as pattern size.Comment: Information and Communication Technology for Intelligent Systems (ICTIS 2017

Dictionary matching in a stream

We consider the problem of dictionary matching in a stream. Given a set of strings, known as a dictionary, and a stream of characters arriving one at a time, the task is to report each time some string in our dictionary occurs in the stream. We present a randomised algorithm which takes O(log log(k + m)) time per arriving character and uses O(k log m) words of space, where k is the number of strings in the dictionary and m is the length of the longest string in the dictionary

An advanced web query interface for biological databases

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs

A systematic study of genome context methods: calibration, normalization and combination

<p>Abstract</p> <p>Background</p> <p>Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use.</p> <p>Results</p> <p>We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the four methods. A thorough exploration of the parameter space for each method is performed and results across different target organisms are presented.</p> <p>We propose the use of normalization procedures as those used on microarray data for the genome context scores. We show that substantial gains can be achieved from the use of a simple normalization technique. In particular, the sensitivity of the phylogenetic profile method is improved by around 25% after normalization, resulting, to our knowledge, on the best-performing phylogenetic profile system in the literature.</p> <p>Finally, we show results from combining the various genome context methods into a single score. When using a cross-validation procedure to train the combiners, with both original and normalized scores as input, a decision tree combiner results in gains of up to 20% with respect to the gene neighbor method. Overall, this represents a gain of around 15% over what can be considered the state of the art in this area: the four original genome context methods combined using a procedure like that used in the STRING database. Unfortunately, we find that these gains disappear when the combiner is trained only with organisms that are phylogenetically distant from the target organism.</p> <p>Conclusions</p> <p>Our experiments indicate that gene neighbor is the best individual genome context method and that gains from the combination of individual methods are very sensitive to the training data used to obtain the combiner's parameters. If adequate training data is not available, using the gene neighbor score by itself instead of a combined score might be the best choice.</p

Machine learning methods for metabolic pathway prediction

<p>Abstract</p> <p>Background</p> <p>A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism.</p> <p>Results</p> <p>To quantitatively validate methods for pathway prediction, we developed a large "gold standard" dataset of 5,610 pathway instances known to be present or absent in curated metabolic pathway databases for six organisms. We defined a collection of 123 pathway features, whose information content we evaluated with respect to the gold standard. Feature data were used as input to an extensive collection of machine learning (ML) methods, including naïve Bayes, decision trees, and logistic regression, together with feature selection and ensemble methods. We compared the ML methods to the previous PathoLogic algorithm for pathway prediction using the gold standard dataset. We found that ML-based prediction methods can match the performance of the PathoLogic algorithm. PathoLogic achieved an accuracy of 91% and an F-measure of 0.786. The ML-based prediction methods achieved accuracy as high as 91.2% and F-measure as high as 0.787. The ML-based methods output a probability for each predicted pathway, whereas PathoLogic does not, which provides more information to the user and facilitates filtering of predicted pathways.</p> <p>Conclusions</p> <p>ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability. More advanced prediction methods and/or more sophisticated input features may improve the performance of ML methods. However, pathway prediction performance appears to be limited largely by the ability to correctly match enzymes to the reactions they catalyze based on genome annotations.</p

Aeronautical Ad Hoc Network for Civil Aviation

Aeronautical communication systems are constantly evolving in order to handle the always increasing flow of data generated by civil aviation. In this article we first present communication systems currently used for en-route aircraft. We then propose Aeronautical Ad hoc NETwork (AANET) as a complementary communication system and demonstrate its connectivity and assess the throughput by simulations based on real aircraft trajectories over the French sky and over the Atlantic ocean

Quantum symmetries and exceptional collections

We study the interplay between discrete quantum symmetries at certain points in the moduli space of Calabi-Yau compactifications, and the associated identities that the geometric realization of D-brane monodromies must satisfy. We show that in a wide class of examples, both local and compact, the monodromy identities in question always follow from a single mathematical statement. One of the simplest examples is the Z_5 symmetry at the Gepner point of the quintic, and the associated D-brane monodromy identity