Transcription factors are proteins that are able to bind to certain segments of DNA to control gene expression. We present an improvement upon supervised learning approaches used for finding transcription factor binding sites. We look at binding sites of the same length for a single transcription factor and use the Berg and von Hippel scoring method. Pairwise information content of positional d...

Poor performance of scoring functions is a well-known bottleneck in structure-based virtual screening (VS), which is most frequently manifested in the scoring functions' inability to discriminate between true ligands vs known nonbinders (therefore designated as binding decoys). This deficiency leads to a large number of false positive hits resulting from VS. We have hypothesized that filtering ...

It has been reported recently that consensus scoring, which combines multiple scoring functions in binding affinity estimation, leads to higher hit-rates in virtual library screening studies. This method seems quite independent to the target receptor, the docking program, or even the scoring functions under investigation. Here we present an idealized computer experiment to explore how consensus...

In this paper we report on a method of evaluating spoken language translation systems that builds upon a task-based evaluation method developed by CMU, but rather than relying on a predefined database of Interchange Format representations of spoken utterances, instead relies on a set of explicitly defined conventions for creating these interlingual representations. Our method also departs from ...

In this paper, we propose a new, effective, and unified scoring method for local feature-based image retrieval. The proposed scoring method is derived by solving the large-scale image retrieval problem as a classification problem with a large number of classes. The resulting proposed score is based on the ratio of the probability density function of an object model to that of a background model...

This paper introduces a discriminative decision function scoring method for speaker recognition with the Joint Factor Analysis (JFA) system. In the scoring module of the JFA system, an approximate form of the decision function is proposed. Based on the approximation, we present a discriminative decision function by reestimating the contribution of each speech sound unit to the decision function...

Many open domain question answering systems answer questions by first harvesting a large number of candidate answers, and then picking the most promising one from the list. One criterion for this answer selection is type checking: deciding whether the candidate answer is of the semantic type expected by the question. We define a general strategy for building redundancy-based type checkers, buil...

We describe a new method for identifying the sequences that signal the start of translation, and the boundaries between exons and introns (donor and acceptor sites) in human mRNA. According to the mandatory keyword, ORGANISM, and feature key, CDS, a large set of standard data for each signal site was extracted from the ASCII flat file, gbpri.seq, in the GenBank release 108.0. This was used to g...