MOTIVATION Gene set analysis is the analysis of a set of genes that collectively contribute to a biological process. Most popular gene set analysis methods are based on empirical P-value that requires large number of permutations. Despite numerous gene set analysis methods developed in the past decade, the most popular methods still suffer from serious limitations. RESULTS We present a gene s...

RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed these prediction purposes, such molecular docking or scoring functions, are parametrized protein targets. The performance methods, when applied to RNA-ligand systems, insufficient. To overcome problems, we AnnapuRN...

We have developed a generic evolutionary method with an empirical scoring function for the protein-ligand docking, which is a problem of paramount importance in structure-based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein-ligand complexe...

Real world networks typically exhibit non uniform edge densities with there being a higher concentration of edges within modules or communities. Various scoring functions have been proposed to quantify the quality of such communities. In this paper, we argue that the popular scoring functions suffer from certain limitations. We identify the necessary features that a scoring function should inco...

This paper proposes a novel automatic pronunciation scoring framework using learning to rank. Human scores of the utterances are treated as ranks and are used as the ranking ground truths. Scores generated from various existing scoring methods are used as the features to train the learning to rank function. The output of the function is then segmented by the proposed DP-based method and hence b...