Derivation of Context-free Stochastic L-Grammar Rules for Promoter Sequence Modeling Using Support Vector Machine

Formal grammars can used for describing complex repeatable structures such as DNA sequences. In this paper, we describe the structural composition of DNA sequences using a context-free stochastic L-grammar. L-grammars are a special class of parallel grammars that can model the growth of living organisms, e.g. plant development, and model the morphology of a variety of organisms. We believe that parallel grammars also can be used for modeling genetic mechanisms and sequences such as promoters. Promoters are short regulatory DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for successful gene prediction. Promoters can be recognized by certain patterns that are conserved within a species, but there are many exceptions which makes the promoter recognition a complex problem. We replace the problem of promoter recognition by induction of context-free stochastic L-grammar rules, which are later used for the structural analysis of promoter sequences. L-grammar rules are derived automatically from the drosophila and vertebrate promoter datasets using a genetic programming technique and their fitness is evaluated using a Support Vector Machine (SVM) classifier. The artificial promoter sequences generated using the derived L- grammar rules are analyzed and compared with natural promoter sequences.

On Minimizing ||S−(AX−XB)||Pp

In this paper, we minimize the map Fp (X)= ||S−(AX−XB)||Pp , where the pair (A, B) has the property (F P )Cp , S ∈ Cp , X varies such that AX − XB ∈ Cp and Cp denotes the von Neumann-Schatten class.

Branching Processes with Immigration and Integer-valued Time Series

In this paper, we indicate how integer-valued autoregressive time series Ginar(d) of ordre d, d ≥ 1, are simple functionals of multitype branching processes with immigration. This allows the derivation of a simple criteria for the existence of a stationary distribution of the time series, thus proving and extending some results by Al-Osh and Alzaid [1], Du and Li [9] and Gauthier and Latour [11]. One can then transfer results on estimation in subcritical multitype branching processes to stationary Ginar(d) and get consistency and asymptotic normality for the corresponding estimators. The technique covers autoregressive moving average time series as well.

Operating Model of Knowledge Quantum Engineering for Decision-Making in Conditions of Indeterminacy

The operating model of knowledge quantum engineering for identification and prognostic decision- making in conditions of α-indeterminacy is suggested in the article. The synthesized operating model solves three basic tasks: Аt-task to formalize tk-knowledge; Вt-task to recognize (identify) objects according to observed results; Сt-task to extrapolate (prognosticate) the observed results. Operating derivation of identification and prognostic decisions using authentic different-level algorithmic knowledge quantum (using tRAKZ-method) assumes synthesis of authentic knowledge quantum database (BtkZ) using induction operator as a system of implicative laws, and then using deduction operator according to the observed tk-knowledge and BtkZ a derivation of identification or prognostic decisions in a form of new tk-knowledge.

Applications of Nonclassical Logic Methods for Purposes of Knowledge Discovery and Data Mining

* The work is partially supported by Grant no. NIP917 of the Ministry of Science and Education – Republic of Bulgaria.

Representing Autoepistemic Logic in Modal Logic

The nonmonotonic logic called Autoepistemic Logic is shown to be representable in a monotonic Modal Quantificational Logic whose modal laws are stronger than S5. Specifically, it is proven that a set of sentences of First Order Logic is a fixed-point of the fixed-point equation of Autoepistemic Logic with an initial set of axioms if and only if the meaning or rather disquotation of that set of sentences is logically equivalent to a particular modal functor of the meaning of that initial set of sentences. This result is important because the modal representation allows the use of powerful automatic deduction systems for Modal Logic and unlike the original Autoepistemic Logic, it is easily generalized to the case where quantified variables may be shared across the scope of modal expressions thus allowing the derivation of quantified consequences. Furthermore, this generalization properly treats such quantifiers since both the Barcan formula and its converse hold.

Evaluation of Pareto/D/1/k Queue by Simulation

The finding that Pareto distributions are adequate to model Internet packet interarrival times has motivated the proposal of methods to evaluate steady-state performance measures of Pareto/D/1/k queues. Some limited analytical derivation for queue models has been proposed in the literature, but their solutions are often of a great mathematical challenge. To overcome such limitations, simulation tools that can deal with general queueing system must be developed. Despite certain limitations, simulation algorithms provide a mechanism to obtain insight and good numerical approximation to parameters of queues. In this work, we give an overview of some of these methods and compare them with our simulation approach, which are suited to solve queues with Generalized-Pareto interarrival time distributions. The paper discusses the properties and use of the Pareto distribution. We propose a real time trace simulation model for estimating the steady-state probability showing the tail-raising effect, loss probability, delay of the Pareto/D/1/k queue and make a comparison with M/D/1/k. The background on Internet traffic will help to do the evaluation correctly. This model can be used to study the long- tailed queueing systems. We close the paper with some general comments and offer thoughts about future work.

Adaptive SOA Infrastructure Based on Variability Management

In order to exploit the adaptability of a SOA infrastructure, it becomes necessary to provide platform mechanisms that support a mapping of the variability in the applications to the variability provided by the infrastructure. The approach focuses on the configuration of the needed infrastructure mechanisms including support for the derivation of the infrastructure variability model.

Hamilton’s Principle with Variable Order Fractional Derivatives

MSC 2010: 26A33, 70H25, 46F12, 34K37 Dedicated to 80-th birthday of Prof. Rudolf Gorenflo

A Note on Elementary Derivations

2000 Mathematics Subject Classification: Primary: 14R10. Secondary: 14R20, 13N15.

On the Range and the Kernel of Derivations

2000 Mathematics Subject Classification: Primary 47B47, 47B10; Secondary 47A30.

On Supra-Bayesian Weighted Combination of Available Data Determined by Kerridge Inaccuracy and Entropy

2010 Mathematics Subject Classification: 94A17.

Generalized D-Symmetric Operators I

2000 Mathematics Subject Classification: Primary: 47B47, 47B10; secondary 47A30.

Generalized Derivations and Norm Equality in Normed Ideals

2000 Mathematics Subject Classification: 47A10, 47A12, 47A30, 47B10, 47B20, 47B37, 47B47, 47D50.