Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties

Subunit vaccine discovery is an accepted clinical priority. The empirical approach is time- and labor-consuming and can often end in failure. Rational information-driven approaches can overcome these limitations in a fast and efficient manner. However, informatics solutions require reliable algorithms for antigen identification. All known algorithms use sequence similarity to identify antigens. However, antigenicity may be encoded subtly in a sequence and may not be directly identifiable by sequence alignment. We propose a new alignment-independent method for antigen recognition based on the principal chemical properties of protein amino acid sequences. The method is tested by cross-validation on a training set of bacterial antigens and external validation on a test set of known antigens. The prediction accuracy is 83% for the cross-validation and 80% for the external test set. Our approach is accurate and robust, and provides a potent tool for the in silico discovery of medically relevant subunit vaccines.

Enhanced information transmission with signal-dependent noise in an array of nonlinear elements

We have investigated information transmission in an array of threshold units that have signal-dependent noise and a common input signal. We demonstrate a phenomenon similar to stochastic resonance and suprathreshold stochastic resonance with additive noise and show that information transmission can be enhanced by a nonzero level of noise. By comparing system performance to one with additive noise we also demonstrate that the information transmission of weak signals is significantly better with signal-dependent noise. Indeed, information rates are not compromised even for arbitrary small input signals. Furthermore, by an appropriate selection of parameters, we observe that the information can be made to be (almost) independent of the level of the noise, thus providing a robust method of transmitting information in the presence of noise. These result could imply that the ability of hair cells to code and transmit sensory information in biological sensory systems is not limited by the level of signal-dependent noise. © 2007 The American Physical Society.

Incremental tensor biased discriminant analysis:a new color-based visual tracking method

Most existing color-based tracking algorithms utilize the statistical color information of the object as the tracking clues, without maintaining the spatial structure within a single chromatic image. Recently, the researches on the multilinear algebra provide the possibility to hold the spatial structural relationship in a representation of the image ensembles. In this paper, a third-order color tensor is constructed to represent the object to be tracked. Considering the influence of the environment changing on the tracking, the biased discriminant analysis (BDA) is extended to the tensor biased discriminant analysis (TBDA) for distinguishing the object from the background. At the same time, an incremental scheme for the TBDA is developed for the tensor biased discriminant subspace online learning, which can be used to adapt to the appearance variant of both the object and background. The experimental results show that the proposed method can track objects precisely undergoing large pose, scale and lighting changes, as well as partial occlusion. © 2009 Elsevier B.V.

Case-based Reasoning Method for Real-time Expert Diagnostics Systems

The method of case-based reasoning for a solution of problems of real-time diagnostics and forecasting in intelligent decision support systems (IDSS) is considered. Special attention is drawn to case library structure for real-time IDSS (RT IDSS) and algorithm of k-nearest neighbors type. This work was supported by RFBR.

Leontief Model Analysis with Fuzzy Parameters by Basic Matrixes Method

The basic matrixes method is suggested for the Leontief model analysis (LM) with some of its components indistinctly given. LM can be construed as a forecast task of product’s expenses-output on the basis of the known statistic information at indistinctly given several elements’ meanings of technological matrix, restriction vector and variables’ limits. Elements of technological matrix, right parts of restriction vector LM can occur as functions of some arguments. In this case the task’s dynamic analog occurs. LM essential complication lies in inclusion of variables restriction and criterion function in it.

Using the Agglomerative Method of Hierarchical Clustering as a Data Mining Tool in Capital Market

The purpose of this paper is to explain the notion of clustering and a concrete clustering method- agglomerative hierarchical clustering algorithm. It shows how a data mining method like clustering can be applied to the analysis of stocks, traded on the Bulgarian Stock Exchange in order to identify similar temporal behavior of the traded stocks. This problem is solved with the aid of a data mining tool that is called XLMiner™ for Microsoft Excel Office.

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 Method of Context-sensitive Help Generation Using a Task Project

The article presents a new method to automatic generation of help in software. Help generation is realized in the framework of the tool for development and automatic generation of user interfaces based on ontologies. The principal features of the approach are: support for context-sensitive help, automatic generation of help using a task project and an expandable system of help generation.

Investigating the Relations of Attacks, Methods and Objects in Regard to Information Security in Network TCP/IP Environment

Possibilities for investigations of 43 varieties of file formats (objects), joined in 10 groups; 89 information attacks, joined in 33 groups and 73 methods of compression, joined in 10 groups are described in the paper. Experimental, expert, possible and real relations between attacks’ groups, method’ groups and objects’ groups are determined by means of matrix transformations and the respective maximum and potential sets are defined. At the end assessments and conclusions for future investigation are proposed.

Development of the Combined Method for Designing Dataflow Systems

The methods of designing of information systems for large organizations are considered in the paper. The structural and object-oriented approaches are compared. For the practical realization of the automated dataflow systems the combined method for the system development and analysis is proposed.

An Effective Method for Constructing Data Structures Solving an Array Maintenance Problem

In this paper a constructive method of data structures solving an array maintenance problem is offered. These data structures are defined in terms of a family of digraphs which have previously been defined, representing solutions for this problem. We present as well a prototype of the method in Haskell.

A Method of Estimating Usability of a User Interface Based on its Model

The article presents a new method to estimating usability of a user interface based on its model. The principal features of the method are: creation of an expandable knowledge base of usability defects, detection defects based on the interface model, within the design phase, and information to the developer not only about existence of defects but also advice on their elimination.

The Inflation Index Prognosis Based on the Method of Decision-Marking “Tree”

The description of the support system for marking decision in terms of prognosing the inflation level based on the multifactor dependence represented by the decision – marking “tree” is given in the paper. The interrelation of factors affecting the inflation level – economic, financial, political, socio-demographic ones, is considered. The perspectives for developing the method of decision – marking “tree”, and pointing out the so- called “narrow” spaces and further analysis of possible scenarios for inflation level prognosing in particular, are defined.

Application of the Heterogeneous System Prediction Method to Pattern Recognition Problem

* This work was financially supported by RFBR-04-01-00858.

Analysis and Coordination of Expert Statements in the Problems of Intellectual Information Search

* This work was financially supported by RFBF-04-01-00858.