DARPA neural network study final report /

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Generalization by symbolic abstraction in cascaded recurrent networks

Generalization performance in recurrent neural networks is enhanced by cascading several networks. By discretizing abstractions induced in one network, other networks can operate on a coarse symbolic level with increased performance on sparse and structural prediction tasks. The level of systematicity exhibited by the cascade of recurrent networks is assessed on the basis of three language domains. (C) 2004 Elsevier B.V. All rights reserved.

Genetic algorithms with applications in wireless communications

Genetic algorithms (GAs) are known to locate the global optimal solution provided sufficient population and/or generation is used. Practically, a near-optimal satisfactory result can be found by Gas with a limited number of generations. In wireless communications, the exhaustive searching approach is widely applied to many techniques, such as maximum likelihood decoding (MLD) and distance spectrum (DS) techniques. The complexity of the exhaustive searching approach in the MLD or the DS technique is exponential in the number of transmit antennas and the size of the signal constellation for the multiple-input multiple-output (MIMO) communication systems. If a large number of antennas and a large size of signal constellations, e.g. PSK and QAM, are employed in the MIMO systems, the exhaustive searching approach becomes impractical and time consuming. In this paper, the GAs are applied to the MLD and DS techniques to provide a near-optimal performance with a reduced computational complexity for the MIMO systems. Two different GA-based efficient searching approaches are proposed for the MLD and DS techniques, respectively. The first proposed approach is based on a GA with sharing function method, which is employed to locate the multiple solutions of the distance spectrum for the Space-time Trellis Coded Orthogonal Frequency Division Multiplexing (STTC-OFDM) systems. The second approach is the GA-based MLD that attempts to find the closest point to the transmitted signal. The proposed approach can return a satisfactory result with a good initial signal vector provided to the GA. Through simulation results, it is shown that the proposed GA-based efficient searching approaches can achieve near-optimal performance, but with a lower searching complexity comparing with the original MLD and DS techniques for the MIMO systems.

Predictive vaccinology: Optimisation of predictions using support vector machine classifiers

Promiscuous human leukocyte antigen (HLA) binding peptides are ideal targets for vaccine development. Existing computational models for prediction of promiscuous peptides used hidden Markov models and artificial neural networks as prediction algorithms. We report a system based on support vector machines that outperforms previously published methods. Preliminary testing showed that it can predict peptides binding to HLA-A2 and -A3 super-type molecules with excellent accuracy, even for molecules where no binding data are currently available.

Artificial neural network modeling of phytoestrogen binding to estrogen receptors

Differential pathophysiological roles of estrogen receptors alpha (ERα) and beta (ERβ) are of particular interest for phytochemical screening. A QSAR incorporating theoretical descriptors was developed in the present study utilizing sequential multiple-output artificial neural networks. Significant steric, constitutional, topological and electronic descriptors were identified enabling ER affinity differentiation.

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E-coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms. (c) 2005 Elsevier Ltd. All rights reserved.

Extreme learning machine for predicting HLA-peptide binding

Machine learning techniques have been recognized as powerful tools for learning from data. One of the most popular learning techniques, the Back-Propagation (BP) Artificial Neural Networks, can be used as a computer model to predict peptides binding to the Human Leukocyte Antigens (HLA). The major advantage of computational screening is that it reduces the number of wet-lab experiments that need to be performed, significantly reducing the cost and time. A recently developed method, Extreme Learning Machine (ELM), which has superior properties over BP has been investigated to accomplish such tasks. In our work, we found that the ELM is as good as, if not better than, the BP in term of time complexity, accuracy deviations across experiments, and most importantly - prevention from over-fitting for prediction of peptide binding to HLA.

Statistical racing techniques for improved empirical evaluation of evolutionary algorithms

In empirical studies of Evolutionary Algorithms, it is usually desirable to evaluate and compare algorithms using as many different parameter settings and test problems as possible, in border to have a clear and detailed picture of their performance. Unfortunately, the total number of experiments required may be very large, which often makes such research work computationally prohibitive. In this paper, the application of a statistical method called racing is proposed as a general-purpose tool to reduce the computational requirements of large-scale experimental studies in evolutionary algorithms. Experimental results are presented that show that racing typically requires only a small fraction of the cost of an exhaustive experimental study.

Real-Time Gene-Expression Extraction with Fast Classification (FC) Networks

Fast Classification (FC) networks were inspired by a biologically plausible mechanism for short term memory where learning occurs instantaneously. Both weights and the topology for an FC network are mapped directly from the training samples by using a prescriptive training scheme. Only two presentations of the training data are required to train an FC network. Compared with iterative learning algorithms such as Back-propagation (which may require many hundreds of presentations of the training data), the training of FC networks is extremely fast and learning convergence is always guaranteed. Thus FC networks may be suitable for applications where real-time classification is needed. In this paper, the FC networks are applied for the real-time extraction of gene expressions for Chlamydia microarray data. Both the classification performance and learning time of the FC networks are compared with the Multi-Layer Proceptron (MLP) networks and support-vector-machines (SVM) in the same classification task. The FC networks are shown to have extremely fast learning time and comparable classification accuracy.

An empirical study of Hoelfding Racing for model selction in K-nearest neighbor classification

Racing algorithms have recently been proposed as a general-purpose method for performing model selection in machine teaming algorithms. In this paper, we present an empirical study of the Hoeffding racing algorithm for selecting the k parameter in a simple k-nearest neighbor classifier. Fifteen widely-used classification datasets from UCI are used and experiments conducted across different confidence levels for racing. The results reveal a significant amount of sensitivity of the k-nn classifier to its model parameter value. The Hoeffding racing algorithm also varies widely in its performance, in terms of the computational savings gained over an exhaustive evaluation. While in some cases the savings gained are quite small, the racing algorithm proved to be highly robust to the possibility of erroneously eliminating the optimal models. All results were strongly dependent on the datasets used.

A neural network based technique for automatic classification of road cracks

This paper presents a neural network based technique for the classification of segments of road images into cracks and normal images. The density and histogram features are extracted. The features are passed to a neural network for the classification of images into images with and without cracks. Once images are classified into cracks and non-cracks, they are passed to another neural network for the classification of a crack type after segmentation. Some experiments were conducted and promising results were obtained. The selected results and a comparative analysis are included in this paper.