Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors

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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

Incremental document map formation: multi-stage approach

The paper presents methodology for the incremental map formation in a multi-stage process of a search engine with the map based user interface1. The architecture of the experimental system allows for comparative evaluation of different constituent technologies for various stages of the process. The quality of the map generation process has been investigated based on a number of clustering and classification measures. Some conclusions concerning the impact of various technological solutions on map quality are presented

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

Multi-test Decision Tree and its Application to Microarray Data Classification

Objective: The desirable property of tools used to investigate biological data is easy to understand models and predictive decisions. Decision trees are particularly promising in this regard due to their comprehensible nature that resembles the hierarchical process of human decision making. However, existing algorithms for learning decision trees have tendency to underfit gene expression data. The main aim of this work is to improve the performance and stability of decision trees with only a small increase in their complexity. Methods: We propose a multi-test decision tree (MTDT); our main contribution is the application of several univariate tests in each non-terminal node of the decision tree. We also search for alternative, lower-ranked features in order to obtain more stable and reliable predictions. Results: Experimental validation was performed on several real-life gene expression datasets. Comparison results with eight classifiers show that MTDT has a statistically significantly higher accuracy than popular decision tree classifiers, and it was highly competitive with ensemble learning algorithms. The proposed solution managed to outperform its baseline algorithm on $14$ datasets by an average $6$ percent. A study performed on one of the datasets showed that the discovered genes used in the MTDT classification model are supported by biological evidence in the literature. Conclusion: This paper introduces a new type of decision tree which is more suitable for solving biological problems. MTDTs are relatively easy to analyze and much more powerful in modeling high dimensional microarray data than their popular counterparts

Influence of the selected pyrimidine compounds on the activity of thymidine phosphorylase from normal and tumor endometrial cells

loxymethylthymine was the strongest inhibitor of the TP activity in endometrium, and 1-N-allyloxymethyl-4-hydrokxy-5-nitro-6-oxopyrimidine in endometrial cancer, respectively. The most potent activators of TP in endometrial cancer was 5-bromodeoxyuridine and 1-N-allyloxymethyl-5-nitrouracil, which increased the TP activity about 100%. 5-fluorodeoxyuridine, 5-jododeoxyuridine and 2’-deoxyuridine activated the TP in statistically significant manner too, but stronger in case of endometrial cancer than in normal endometrium. The synthesized 5-bromo-6-acetyloaminouracil strongly inhibited the TP activity of endometrial cells and might be useful in reducing endometrial cancer angiogenesis. On the other hand 5-bromodeoxyuridine and the synthesized 1-N-allyloxymethyl-5-nitrouracil might increase the effect of antitumor therapy with the cytostatics. These conclusions ought to be confirmed by analyzing more tumor cases

Adaptive Document Maps

Abstract. As document map creation algorithms like WebSOM are computationally expensive, and hardly reconstructible even from the same set of documents, new methodology is urgently needed to allow to construct document maps to handle streams of new documents entering document collection. This challenge is dealt with within this paper. In a multi-stage process, incrementality of a document map is warranted. 1 . The architecture of the experimental system allows for comparative evaluation of different constituent technologies for various stages of the process. The quality of the map generation process has been investigated based on a number of clustering and classification measures. Some conclusions concerning the impact of incremental, topic-sensitive approach on map quality are presented

A feature selection method for classification within functional genomics experiments based on the proportional overlapping score

Background: Microarray technology, as well as other functional genomics experiments, allow simultaneous measurements of thousands of genes within each sample. Both the prediction accuracy and interpretability of a classifier could be enhanced by performing the classification based only on selected discriminative genes. We propose a statistical method for selecting genes based on overlapping analysis of expression data across classes. This method results in a novel measure, called proportional overlapping score (POS), of a feature's relevance to a classification task.Results: We apply POS, along-with four widely used gene selection methods, to several benchmark gene expression datasets. The experimental results of classification error rates computed using the Random Forest, k Nearest Neighbor and Support Vector Machine classifiers show that POS achieves a better performance.Conclusions: A novel gene selection method, POS, is proposed. POS analyzes the expressions overlap across classes taking into account the proportions of overlapping samples. It robustly defines a mask for each gene that allows it to minimize the effect of expression outliers. The constructed masks along-with a novel gene score are exploited to produce the selected subset of genes