rmcfs: An R Package for Monte Carlo Feature Selection and Interdependency Discovery

We describe the R package rmcfs that implements an algorithm for ranking features from high dimensional data according to their importance for a given supervised classification task. The ranking is performed prior to addressing the classification task per se. This R package is the new and extended version of the MCFS (Monte Carlo feature selection) algorithm where an early version was published in 2005. The package provides an easy R interface, a set of tools to review results and the new ID (interdependency discovery) component. The algorithm can be used on continuous and/or categorical features (e.g., gene expression and phenotypic data) to produce an objective ranking of features with a statistically well-defined cutoff between informative and non-informative ones. Moreover, the directed ID graph that presents interdependencies between informative features is provided

A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

Reverse transcriptase (RT) is a viral enzyme crucial for HIV-1 replication. Currently, 12 drugs are targeted against the RT. The low fidelity of the RT-mediated transcription leads to the quick accumulation of drug-resistance mutations. The sequence-resistance relationship remains only partially understood. Using publicly available data collected from over 15 years of HIV proteome research, we have created a general and predictive rule-based model of HIV-1 resistance to eight RT inhibitors. Our rough set-based model considers changes in the physicochemical properties of a mutated sequence as compared to the wild-type strain. Thanks to the application of the Monte Carlo feature selection method, the model takes into account only the properties that significantly contribute to the resistance phenomenon. The obtained results show that drug-resistance is determined in more complex way than believed. We confirmed the importance of many resistance-associated sites, found some sites to be less relevant than formerly postulated and—more importantly—identified several previously neglected sites as potentially relevant. By mapping some of the newly discovered sites on the 3D structure of the RT, we were able to suggest possible molecular-mechanisms of drug-resistance. Importantly, our model has the ability to generalize predictions to the previously unseen cases. The study is an example of how computational biology methods can increase our understanding of the HIV-1 resistome

Stochastic approximation. II. Optimization methods with constraints

.This is a critical review of recent results in stochastic approximation methods for optimization problems. Part II deals with constrained optimization; here, the stochastic variants of the penalty function method, the method of feasible directions and the method of Lagrange functions are discussed

Review: M. Csörgö, P. Révész; Strong approximations in probability and statistics

Artykuł nie zawiera streszczeniaThe article contains no abstrac

On the placement the applications of mathematics in the mathematical sciences

Coraz więcej sygnałów wskazuje, że zmienia się stosunek społeczności matematyków do wyżej wymienionej kwestii. Do niedawna stopnie naukowe i tytuł naukowy z nauk matematycznych miały być przyznawane jedynie za twórczy wkład w rozwój tej dziedziny. Ostatnio, przy okazji jednego z postępowań o nadanie tytułu naukowego, Rada Wydziału Matematyki i Mechaniki Uniwersytetu Warszawskiego stanęła implicite (poprzez wynik głosowania w tym postępowaniu) na stanowisku, iż owe stopnie i tytuł należą się także za mniej liczący się wkład w nauki matematyczne, ale za to istotny wkład w inne obszary nauki, uzyskany dzięki twórczemu i niebanalnemu zastosowaniu i/lub zmodyfikowaniu znanych metod z dziedziny nauk matematycznych.More and more signals indicates that the ratio of the community of mathematicians to the above mentioned issues. Until recently, the degrees and a degree in mathematical sciences were to be granted only for their creative contribution to the development of this field. Recently, on the occasion of one of the procedures for granting the academic title, the Council of the Faculty of Mathematics and Mechanics, University of Warsaw stood implicitly (by the outcome of the vote in the proceedings) the view that these steps and title are also less considerate contribution to the mathematical sciences, but as an important contribution to other areas of science, obtained by creatively and niebanalnemu use and / or modify the known methods of the mathematical sciences

S. N. Abdelhamid i D. Anbar „Określenie optymalnej funkcji obserwacji w jednowymiarowych procedurach aproksymacji stochastycznej"-Recenzja

Artykuł nie zawiera streszczeniaThe article contains no abstrac

Stochastic approximation. I. Optimization methods without constraints

.This is a critical review of recent results in stochastic approximation methods for optimization problems. Part I deals with unconstrained optimization, with special emphasis on the problem of choice of the direction and the length of iteration steps