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Motivation: The still emerging combination of technologies that enable description and characterization of all expressed proteins in a biological system is known as proteomics. Although many separation and analysis technologies have been employed in proteomics, it remains a challenge to predict peptide behavior during separation processes. New informatics tools are needed to model the experimental analysis method that will allow scientists to predict peptide separation and assist with required data mining steps, such as protein identification., Results: We developed a software package to predict the separation of peptides in strong anion exchange (SAX) chromatography using artificial neural network based pattern classification techniques. A multi-layer perceptron is used as a pattern classifier and it is designed with feature vectors extracted from the peptides so that the classification error is minimized. A genetic algorithm is employed to train the neural network. The developed system was tested using 14 protein digests, and the sensitivity analysis was carried out to investigate the significance of each feature., Availability: The software and testing results can be downloaded from ftp://ftp.bbc.purdue.edu.

This paper is concerned with large scale associative memory design. A serious problem with neural associative memories is the quadratic growth of the number of interconnections with the problem size. An overlapping decomposition algorithm is proposed to attack this problem. Specifically, a pattern to be processed is decomposed into overlapping sub-patterns. Then, neural sub-networks are constructed that process the sub-patterns. An error correction algorithm operates on the outputs of each sub-network in order to correct the mismatches between sub-patterns that are obtained from the independent recall processes of individual sub-networks. The performance of the proposed large scale associative memory is illustrated using two-dimensional images. It is shown that the proposed method reduces the computing cost of the design of the associative memories compared with non-interconnected associative memories. [ABSTRACT FROM AUTHOR]