Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

Segmenting the market of West Australian senior tourists using an artificial neural network

Measuring perceptions of customers can be a major problem for marketers of tourism and travel services. Much of the problem is to determine which attributes carry most weight in the purchasing decision. Older travellers weigh many travel features before making their travel decisions. This paper presents a descriptive analysis of neural network methodology and provides a research technique that assesses the weighting of different attributes and uses an unsupervised neural network model to describe a consumer-product relationship. The development of this rich class of models was inspired by the neural architecture of the human brain. These models mathematically emulate the neurophysical structure and decision making of the human brain, and, from a statistical perspective, are closely related to generalised linear models. Artificial neural networks or neural networks are, however, nonlinear and do not require the same restrictive assumptions about the relationship between the independent variables and dependent variables. Using neural networks is one way to determine what trade-offs older travellers make as they decide their travel plans. The sample of this study is from a syndicated data source of 200 valid cases from Western Australia. From senior groups, active learner, relaxed family body, careful participants and elementary vacation were identified and discussed. (C) 2003 Published by Elsevier Science Ltd.

Structure and dynamics of a gene network model incorporating small RNAs

As advances in molecular biology continue to reveal additional layers of complexity in gene regulation, computational models need to incorporate additional features to explore the implications of new theories and hypotheses. It has recently been suggested that eukaryotic organisms owe their phenotypic complexity and diversity to the exploitation of small RNAs as signalling molecules. Previous models of genetic systems are, for several reasons, inadequate to investigate this theory. In this study, we present an artificial genome model of genetic regulatory networks based upon previous work by Torsten Reil, and demonstrate how this model generates networks with biologically plausible structural and dynamic properties. We also extend the model to explore the implications of incorporating regulation by small RNA molecules in a gene network. We demonstrate how, using these signals, highly connected networks can display dynamics that are more stable than expected given their level of connectivity.

Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Typing mineral deposits using their grades and tonnages in an artificial neural network

A test of the ability of a probabilistic neural network to classify deposits into types on the basis of deposit tonnage and average Cu, Mo, Ag, Au, Zn, and Pb grades is conducted. The purpose is to examine whether this type of system might serve as a basis for integrating geoscience information available in large mineral databases to classify sites by deposit type. Benefits of proper classification of many sites in large regions are relatively rapid identification of terranes permissive for deposit types and recognition of specific sites perhaps worthy of exploring further. Total tonnages and average grades of 1,137 well-explored deposits identified in published grade and tonnage models representing 13 deposit types were used to train and test the network. Tonnages were transformed by logarithms and grades by square roots to reduce effects of skewness. All values were scaled by subtracting the variable's mean and dividing by its standard deviation. Half of the deposits were selected randomly to be used in training the probabilistic neural network and the other half were used for independent testing. Tests were performed with a probabilistic neural network employing a Gaussian kernel and separate sigma weights for each class (type) and each variable (grade or tonnage). Deposit types were selected to challenge the neural network. For many types, tonnages or average grades are significantly different from other types, but individual deposits may plot in the grade and tonnage space of more than one type. Porphyry Cu, porphyry Cu-Au, and porphyry Cu-Mo types have similar tonnages and relatively small differences in grades. Redbed Cu deposits typically have tonnages that could be confused with porphyry Cu deposits, also contain Cu and, in some situations, Ag. Cyprus and kuroko massive sulfide types have about the same tonnages. Cu, Zn, Ag, and Au grades. Polymetallic vein, sedimentary exhalative Zn-Pb, and Zn-Pb skarn types contain many of the same metals. Sediment-hosted Au, Comstock Au-Ag, and low-sulfide Au-quartz vein types are principally Au deposits with differing amounts of Ag. Given the intent to test the neural network under the most difficult conditions, an overall 75% agreement between the experts and the neural network is considered excellent. Among the largestclassification errors are skarn Zn-Pb and Cyprus massive sulfide deposits classed by the neuralnetwork as kuroko massive sulfides—24 and 63% error respectively. Other large errors are the classification of 92% of porphyry Cu-Mo as porphyry Cu deposits. Most of the larger classification errors involve 25 or fewer training deposits, suggesting that some errors might be the result of small sample size. About 91% of the gold deposit types were classed properly and 98% of porphyry Cu deposits were classes as some type of porphyry Cu deposit. An experienced economic geologist would not make many of the classification errors that were made by the neural network because the geologic settings of deposits would be used to reduce errors. In a separate test, the probabilistic neural network correctly classed 93% of 336 deposits in eight deposit types when trained with presence or absence of 58 minerals and six generalized rock types. The overall success rate of the probabilistic neural network when trained on tonnage and average grades would probably be more than 90% with additional information on the presence of a few rock types.

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.

A bayesian artificial neural network method to characterise laminar defects using dynamic measurements

This paper reports on the development of an artificial neural network (ANN) method to detect laminar defects following the pattern matching approach utilizing dynamic measurement. Although structural health monitoring (SHM) using ANN has attracted much attention in the last decade, the problem of how to select the optimal class of ANN models has not been investigated in great depth. It turns out that the lack of a rigorous ANN design methodology is one of the main reasons for the delay in the successful application of the promising technique in SHM. In this paper, a Bayesian method is applied in the selection of the optimal class of ANN models for a given set of input/target training data. The ANN design method is demonstrated for the case of the detection and characterisation of laminar defects in carbon fibre-reinforced beams using flexural vibration data for beams with and without non-symmetric delamination damage.

Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Development and evaluation of neural network freeway incident detection models using field data

This paper discusses a multi-layer feedforward (MLF) neural network incident detection model that was developed and evaluated using field data. In contrast to published neural network incident detection models which relied on simulated or limited field data for model development and testing, the model described in this paper was trained and tested on a real-world data set of 100 incidents. The model uses speed, flow and occupancy data measured at dual stations, averaged across all lanes and only from time interval t. The off-line performance of the model is reported under both incident and non-incident conditions. The incident detection performance of the model is reported based on a validation-test data set of 40 incidents that were independent of the 60 incidents used for training. The false alarm rates of the model are evaluated based on non-incident data that were collected from a freeway section which was video-taped for a period of 33 days. A comparative evaluation between the neural network model and the incident detection model in operation on Melbourne's freeways is also presented. The results of the comparative performance evaluation clearly demonstrate the substantial improvement in incident detection performance obtained by the neural network model. The paper also presents additional results that demonstrate how improvements in model performance can be achieved using variable decision thresholds. Finally, the model's fault-tolerance under conditions of corrupt or missing data is investigated and the impact of loop detector failure/malfunction on the performance of the trained model is evaluated and discussed. The results presented in this paper provide a comprehensive evaluation of the developed model and confirm that neural network models can provide fast and reliable incident detection on freeways. (C) 1997 Elsevier Science Ltd. All rights reserved.

Capillary network models for transport in packed beds: Considerations of pore aspect ratio

The conventional analysis for the estimation of the tortuosity factor for transport in porous media is modified here to account for the effect of pore aspect ratio. Structural models of the porous medium are also constructed for calculating the aspect ratio as a function of porosity. Comparison of the model predictions with the extensive data of Currie (1960) for the effective diffusivity of hydrogen in packed beds shows good agreement with a network model of randomly oriented intersecting pores for porosities upto about 50 percent, which is the region of practical interest. The predictions based on this network model are also found to be in better agreement with the data of Currie than earlier expressions developed for unconsolidated and grainy media.

Computational binding assays of antigenic peptides

Computer models can be combined with laboratory experiments for the efficient determination of (i) peptides that bind MHC molecules and (ii) T-cell epitopes. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures. This requires the definition of standards and experimental protocols for model application. We describe the requirements for validation and assessment of computer models. The utility of combining accurate predictions with a limited number of laboratory experiments is illustrated by practical examples. These include the identification of T-cell epitopes from IDDM-, melanoma- and malaria-related antigens by combining computational and conventional laboratory assays. The success rate in determining antigenic peptides, each in the context of a specific HLA molecule, ranged from 27 to 71%, while the natural prevalence of MHC-binding peptides is 0.1-5%.