Protein classification based on text document classification techniques.

The need for accurate, automated protein classification methods continues to increase as advances in biotechnology uncover new proteins. G-protein coupled receptors (GPCRs) are a particularly difficult superfamily of proteins to classify due to extreme diversity among its members. Previous comparisons of BLAST, k-nearest neighbor (k-NN), hidden markov model (HMM) and support vector machine (SVM) using alignment-based features have suggested that classifiers at the complexity of SVM are needed to attain high accuracy.

The optimal fraction of hydrophobic residues required to ensure protein collapse.

The hydrophobic interaction is the main driving force for protein folding. Here, we address the question of what is the optimal fraction, f of hydrophobic (H) residues required to ensure protein collapse. For very small f (say f<0.

Comparison of probabilistic combination methods for protein secondary structure prediction.

Motivation: Protein secondary structure prediction is an important step towards understanding how proteins fold in three dimensions. Recent analysis by information theory indicates that the correlation between neighboring secondary structures are much stronger than that of neighboring amino acids. In this article, we focus on the combination problem for sequences, i.

Automatic parsing of parental verbal input.

To evaluate theoretical proposals regarding the course of child language acquisition, researchers often need to rely on the processing of large numbers of syntactically parsed utterances, both from children and from their parents. Because it is so difficult to do this by hand, there are currently no parsed corpora of child language input data. To automate this process, we developed a system that combined the MOR tagger, a rule-based parser, and statistical disambiguation techniques.

Variational approach to moiré pattern synthesis.

Moiré phenomena occur when two or more images are nonlinearly combined to create a new superposition image. Moiré patterns are patterns that do not exist in any of the original images but appear in the superposition image, for example as the result of a multiplicative superposition rule. The topic of moiré pattern synthesis deals with creating images that when superimposed will reveal certain desired moiré patterns.