Optimizing amino acid groupings for GPCR classification

MOTIVATION: There is much interest in reducing the complexity inherent in the representation of the 20 standard amino acids within bioinformatics algorithms by developing a so-called reduced alphabet. Although there is no universally applicable residue grouping, there are numerous physiochemical criteria upon which one can base groupings. Local descriptors are a form of alignment-free analysis, the efficiency of which is dependent upon the correct selection of amino acid groupings. RESULTS: Within the context of G-protein coupled receptor (GPCR) classification, an optimization algorithm was developed, which was able to identify the most efficient grouping when used to generate local descriptors. The algorithm was inspired by the relatively new computational intelligence paradigm of artificial immune systems. A number of amino acid groupings produced by this algorithm were evaluated with respect to their ability to generate local descriptors capable of providing an accurate classification algorithm for GPCRs.

An Ontology- Content-based Filtering Method

Traditional content-based filtering methods usually utilize text extraction and classification techniques for building user profiles as well as for representations of contents, i.e. item profiles. These methods have some disadvantages e.g. mismatch between user profile terms and item profile terms, leading to low performance. Some of the disadvantages can be overcome by incorporating a common ontology which enables representing both the users' and the items' profiles with concepts taken from the same vocabulary. We propose a new content-based method for filtering and ranking the relevancy of items for users, which utilizes a hierarchical ontology. The method measures the similarity of the user's profile to the items' profiles, considering the existing of mutual concepts in the two profiles, as well as the existence of "related" concepts, according to their position in the ontology. The proposed filtering algorithm computes the similarity between the users' profiles and the items' profiles, and rank-orders the relevant items according to their relevancy to each user. The method is being implemented in ePaper, a personalized electronic newspaper project, utilizing a hierarchical ontology designed specifically for classification of News items. It can, however, be utilized in other domains and extended to other ontologies.

A Domain-Independent Otology-based Approach to Representation of Courseware Knowledge

This paper proposes an ontology-based approach to representation of courseware knowledge in different domains. The focus is on a three-level semantic graph, modeling respectively the course as a whole, its structure, and domain contents itself. The authors plan to use this representation for flexibie e- learning and generation of different study plans for the learners.

Hierarchical Logical Description and Neural Recognition of Complex Patterns

Authors suggested earlier hierarchical method for definition of class description at pattern recognition problems solution. In this paper development and use of such hierarchical descriptions for parallel representation of complex patterns on the base of multi-core computers or neural networks is proposed.

Symplectic Representation of a Braid Group on 3-Sheeted Covers of the Riemann Sphere

We define Picard cycles on each smooth three-sheeted Galois cover C of the Riemann sphere. The moduli space of all these algebraic curves is a nice Shimura surface, namely a symmetric quotient of the projective plane uniformized by the complex two-dimensional unit ball. We show that all Picard cycles on C form a simple orbit of the Picard modular group of Eisenstein numbers. The proof uses a special surface classification in connection with the uniformization of a classical Picard-Fuchs system. It yields an explicit symplectic representation of the braid groups (coloured or not) of four strings.

Ontological Approach to Domain Knowledge Representation for Information Retrieval in Multiagent Systems

An ontological representation of buyer interests’ knowledge in process of e-commerce is proposed to use. It makes it more efficient to make a search of the most appropriate sellers via multiagent systems. An algorithm of a comparison of buyer ontology with one of e-shops (the taxonomies) and an e-commerce multiagent system are realised using ontology of information retrieval in distributed environment.

A Mathematical Apparatus for Domain Ontology Simulation. Logical Relationship Systems

* This paper was made according to the program of fundamental scientific research of the Presidium of the Russian Academy of Sciences «Mathematical simulation and intellectual systems», the project "Theoretical foundation of the intellectual systems based on ontologies for intellectual support of scientific researches".

The Knowledge: Its Presentation and Role in Recognition Systems

The concept of knowledge is the central one used when solving the various problems of data mining and pattern recognition in finite spaces of Boolean or multi-valued attributes. A special form of knowledge representation, called implicative regularities, is proposed for applying in two powerful tools of modern logic: the inductive inference and the deductive inference. The first one is used for extracting the knowledge from the data. The second is applied when the knowledge is used for calculation of the goal attribute values. A set of efficient algorithms was developed for that, dealing with Boolean functions and finite predicates represented by logical vectors and matrices.

Applications of the Sufficiency Principle in Acceleration of Neural Networks Trainig

One of the problems in AI tasks solving by neurocomputing methods is a considerable training time. This problem especially appears when it is needed to reach high quality in forecast reliability or pattern recognition. Some formalised ways for increasing of networks’ training speed without loosing of precision are proposed here. The offered approaches are based on the Sufficiency Principle, which is formal representation of the aim of a concrete task and conditions (limitations) of their solving [1]. This is development of the concept that includes the formal aims’ description to the context of such AI tasks as classification, pattern recognition, estimation etc.

Neural-Like Growing Networks in Intelligent System of Recognition of Images

The neural-like growing networks used in the intelligent system of recognition of images are under consideration in this paper. All operations made over the image on a pre-design stage and also classification and storage of the information about the images and their further identification are made extremely by mechanisms of neural-like networks without usage of complex algorithms requiring considerable volumes of calculus. At the conforming hardware support the neural network methods allow considerably to increase the effectiveness of the solution of the given class of problems, saving a high accuracy of result and high level of response, both in a mode of training, and in a mode of identification.

Cluster Analysis of Some Clases of Objects by Application of the Test Recognition Algorithms

The paper treats the task for cluster analysis of a given assembly of objects on the basis of the information contained in the description table of these objects. Various methods of cluster analysis are briefly considered. Heuristic method and rules for classification of the given assembly of objects are presented for the cases when their division into classes and the number of classes is not known. The algorithm is checked by a test example and two program products (PP) – learning systems and software for company management. Analysis of the results is presented.

Hierarchical Three-level Ontology for Text Processing

The principal feature of ontology, which is developed for a text processing, is wider knowledge representation of an external world due to introduction of three-level hierarchy. It allows to improve semantic interpretation of natural language texts.

Automatic ECG Analysis for Preliminary and Detailed Diagnostics Based on Scale-space Representation

A novel approach of automatic ECG analysis based on scale-scale signal representation is proposed. The approach uses curvature scale-space representation to locate main ECG waveform limits and peaks and may be used to correct results of other ECG analysis techniques or independently. Moreover dynamic matching of ECG CSS representations provides robust preliminary recognition of ECG abnormalities which has been proven by experimental results.

Linked knowledge sources for topic classification of microposts:a semantic graph-based approach

Short text messages a.k.a Microposts (e.g. Tweets) have proven to be an effective channel for revealing information about trends and events, ranging from those related to Disaster (e.g. hurricane Sandy) to those related to Violence (e.g. Egyptian revolution). Being informed about such events as they occur could be extremely important to authorities and emergency professionals by allowing such parties to immediately respond. In this work we study the problem of topic classification (TC) of Microposts, which aims to automatically classify short messages based on the subject(s) discussed in them. The accurate TC of Microposts however is a challenging task since the limited number of tokens in a post often implies a lack of sufficient contextual information. In order to provide contextual information to Microposts, we present and evaluate several graph structures surrounding concepts present in linked knowledge sources (KSs). Traditional TC techniques enrich the content of Microposts with features extracted only from the Microposts content. In contrast our approach relies on the generation of different weighted semantic meta-graphs extracted from linked KSs. We introduce a new semantic graph, called category meta-graph. This novel meta-graph provides a more fine grained categorisation of concepts providing a set of novel semantic features. Our findings show that such category meta-graph features effectively improve the performance of a topic classifier of Microposts. Furthermore our goal is also to understand which semantic feature contributes to the performance of a topic classifier. For this reason we propose an approach for automatic estimation of accuracy loss of a topic classifier on new, unseen Microposts. We introduce and evaluate novel topic similarity measures, which capture the similarity between the KS documents and Microposts at a conceptual level, considering the enriched representation of these documents. Extensive evaluation in the context of Emergency Response (ER) and Violence Detection (VD) revealed that our approach outperforms previous approaches using single KS without linked data and Twitter data only up to 31.4% in terms of F1 measure. Our main findings indicate that the new category graph contains useful information for TC and achieves comparable results to previously used semantic graphs. Furthermore our results also indicate that the accuracy of a topic classifier can be accurately predicted using the enhanced text representation, outperforming previous approaches considering content-based similarity measures. © 2014 Elsevier B.V. All rights reserved.

AstroWeb – A Graphical Representation of an Astronomical WFPDB Database Using a Web-Based Open Source Geographical Information System

ACM Computing Classification System (1998): H.5.2, H.2.8, J.2, H.5.3.