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PubMed2006

Exact simulation of integrate-and-fire models with synaptic conductances.

Computational neuroscience relies heavily on the simulation of large networks of neuron models. There are essentially two simulation strategies: (1) using an approximation method (e.g., Runge-Kutta) with spike times binned to the time step and (2) calculating spike times exactly in an event-driven fashion. In large networks, the computation time of the best algorithm for either strategy scales linearly with the number of synapses, but each strategy has its own assets and constraints: approximation methods can be applied to any model but are inexact; exact simulation avoids numerical artifacts but is limited to simple models. Previous work has focused on improving the accuracy of approximation methods. In this article, we extend the range of models that can be simulated exactly to a more realistic model: an integrate-and-fire model with exponential synaptic conductances.

Action Potentials↗

PubMed1999

Using partial directed coherence to describe neuronal ensemble interactions.

This paper illustrates the use of the recently introduced method of partial directed coherence in approaching how interactions among neural structures change over short time spans that characterize well defined behavioral states. Central to the method is its use of multivariate time series modelling in conjunction with the concept of Granger causality. Simulated neural network models were used to illustrate the technique's power and limitations when dealing with neural spiking data. This was followed by the analysis of multi-unit activity data illustrating dynamical change in the interaction of thalamo-cortical structures in a behaving rat.

Action Potentials↗

PubMed1995

Neural network classification of corneal topography. Preliminary demonstration.

PURPOSE: Videokeratography is a powerful tool for the diagnosis of corneal shape abnormalities. However, interpretation of the topographic map is sometimes difficult, especially when pathologies with similar topographic patterns are suspected. The neural networks model, an artificial intelligence approach, was applied for automated pattern interpretation in corneal topography, and its usefulness was assessed. METHODS: One hundred eighty-three topographic maps were selected and classified by human experts into seven categories: normal, with-the-rule astigmatism, keratoconus (mild, moderate, advanced), postphotorefractive keratectomy, and postkeratoplasty. The maps were divided into a training set (108 maps) and a test set (75 maps). For each map, 11 topography-characterizing indices calculated from the data provided by the TMS-1 videokeratoscope, plus the corresponding diagnosis category, were used to train a neural network. RESULTS: The correct classification was achieved by a trained neural network for all 108 maps in the training set. In the test set, the neural network correctly classified 60 of 75 maps (80%). For every category, accuracy and specificity were greater than 90%, whereas sensitivity ranged from 44% to 100%. CONCLUSIONS: With further testing and refinement, the neural networks paradigm for computer-assisted interpretation or objective classification of videokeratography may become a useful tool to aid the clinician in the diagnosis of corneal topographic abnormalities.

Cornea↗

PubMed2004

An improved Maxnet.

In the proposed model, dynamic inhibitory weights are used to speed up the convergence rate, and a new convergence rule is applied to find all maxima. The hardware implementation of the proposed model is presented in the study, and simulation results indicate that the proposed model converges much faster than the other networks.

Algorithms↗

PubMed1998

Predicting nucleic acid torsion angle values using artificial neural networks.

By means of an error back-propagation artificial neural network, a new method to predict the torsion angles, chi, zeta and alpha from torsion angles delta, epsilon, beta and gamma for nucleic acid dinucleotides is introduced. To build a model, training sets and test sets of 163 and 81 dinucleotides, respectively, with known crystal structures, were assembled. With 7 hidden units in a three-layered network a model with good predictive ability is constructed. About 70 to 80% of the residuals for predicted torsion angles are smaller than 10 degrees. This means that such a model can be used to construct trial structures for conformational analysis that can be refined further. Moreover, when reasonable estimates for delta, epsilon, beta and gamma are extracted from COSY experiments, this procedure can easily be extended to predict torsion angles for structures in solution.

Base Sequence↗

PubMed1992

An artificial neural network for lesion detection on single-photon emission computed tomographic images.

RATIONALE AND OBJECTIVES: An artificial neural network (ANN) has been developed to detect nonactive circular lesions on single-slice, single-photon emission computed tomographic (SPECT) images reconstructed using filtered back projection (FBP). METHODS: The neural network is a single-layer perception which learns to identify features on the SPECT image using supervised training with a modified delta rule. The network was trained on a set of SPECT images containing clinically realistic levels of noise. The trained network was applied to a set of 120 images, and the detection performance was evaluated at several decision thresholds using receiver operating characteristic (ROC) analysis. RESULTS: The trained neural network performed better than human observers for the same detection task with the same images as reflected by a significantly larger ROC curve area. CONCLUSIONS: ANN can be trained successfully to perform lesion detection on reconstructed SPECT images.

Equipment Design↗

PubMed1999

The diagnostic value of computer-assisted primary cervical smear screening: a longitudinal cohort study.

OBJECTIVES: To assess computer-assisted (neural network based) cervical smear screening as a primary tool for the early detection of cervical dysplasia. DESIGN: Longitudinal cohort study. SETTING: Cytology laboratory reviewing cervical smears taken by general practitioners in a mass screening program in the Netherlands. SUBJECTS: 846 women who developed (pre-)neoplasia of the cervix in the seven years after the baseline smear, and 5217 controls. INTERVENTIONS: Cervical smears were evaluated both by conventional light microscopy and with use of the PAPNET Testing System by the same cytotechnologists. MAIN OUTCOME MEASURES: Seven year histological and cytological follow-up results were obtained for all women from a nation-wide pathology database. RESULTS: Conventional screening diagnosed dysplasia or carcinoma in the baseline smears of 458 (54.1%) of the 846 women who were diagnosed with (pre-)neoplasia during follow-up, whereas computer-assisted PAPNET analysis detected such lesions in 462 (54.6%) of these women. In the control population of 5217 (86.0%) women, in whom follow-up revealed no cervical dysplasia, conventional screening gave false positive results in 210 (4.0%) and computer-assisted PAPNET analysis gave false positive results in 207 (4.0%) smears. The areas under the receiver operation curves (AUC) were 80% (95% confidence interval, 78 to 82%) and 79% (95% confidence interval, 77 to 81%) for conventional and PAPNET-assisted screening, respectively. CONCLUSIONS: The PAPNET Testing System has similar diagnostic value as the conventional screening of Pap smears when used for primary screening.

Female↗

PubMed2003

Coupled prediction of protein secondary and tertiary structure.

The strong coupling between secondary and tertiary structure formation in protein folding is neglected in most structure prediction methods. In this work we investigate the extent to which nonlocal interactions in predicted tertiary structures can be used to improve secondary structure prediction. The architecture of a neural network for secondary structure prediction that utilizes multiple sequence alignments was extended to accept low-resolution nonlocal tertiary structure information as an additional input. By using this modified network, together with tertiary structure information from native structures, the Q3-prediction accuracy is increased by 7-10% on average and by up to 35% in individual cases for independent test data. By using tertiary structure information from models generated with the ROSETTA de novo tertiary structure prediction method, the Q3-prediction accuracy is improved by 4-5% on average for small and medium-sized single-domain proteins. Analysis of proteins with particularly large improvements in secondary structure prediction using tertiary structure information provides insight into the feedback from tertiary to secondary structure.

Computer Simulation↗

PubMed2000

A semi-parametric hybrid neural model for nonlinear blind signal separation.

Nonlinear blind signal separation is an important but rather difficult problem. Any general nonlinear independent component analysis algorithm for such a problem should specify which solution it tries to find. Several recent neural networks for separating the post nonlinear blind mixtures are limited to the diagonal nonlinearity, where there is no cross-channel nonlinearity. In this paper, a new semi-parametric hybrid neural network is proposed to separate the post nonlinearly mixed blind signals where cross-channel disturbance is included. This hybrid network consists of two cascading modules, which are a neural nonlinear module for approximating the post nonlinearity and a linear module for separating the predicted linear blind mixtures. The nonlinear module is a semi-parametric expansion made up of two sub-networks, one of which is a linear model and the other of which is a three-layer perceptron. These two sub-networks together produce a "weak" nonlinear operator and can approach relatively strong nonlinearity by tuning parameters. A batch learning algorithm based on the entropy maximization and the gradient descent method is deduced. This model is successfully applied to a blind signal separation problem with two sources. Our simulation results indicate that this hybrid model can effectively approach the cross-channel post nonlinearity and achieve a good visual quality as well as a high signal-to-noise ratio in some cases.

Algorithms↗

PubMed2006

A bidirectional heteroassociative memory for binary and grey-level patterns.

Typical bidirectional associative memories (BAM) use an offline, one-shot learning rule, have poor memory storage capacity, are sensitive to noise, and are subject to spurious steady states during recall. Recent work on BAM has improved network performance in relation to noisy recall and the number of spurious attractors, but at the cost of an increase in BAM complexity. In all cases, the networks can only recall bipolar stimuli and, thus, are of limited use for grey-level pattern recall. In this paper, we introduce a new bidirectional heteroassociative memory model that uses a simple self-convergent iterative learning rule and a new nonlinear output function. As a result, the model can learn online without being subject to overlearning. Our simulation results show that this new model causes fewer spurious attractors when compared to others popular BAM networks, for a comparable performance in terms of tolerance to noise and storage capacity. In addition, the novel output function enables it to learn and recall grey-level patterns in a bidirectional way.

Algorithms↗

PubMed1999

A neural network model approach to the study of human TAP transporter.

We used an artificial neural network (ANN) computer model to study peptide binding to the human transporter associated with antigen processing (TAP). After validation, an ANN model of TAP-peptide binding was used to mine a database of HLA-binding peptides to elucidate patterns of TAP binding. The affinity of HLA-binding peptides for TAP was found to differ according to the HLA supertype concerned: HLA-B27, -A3 or -A24 binding peptides had high, whereas HLA-A2, -B7 or -B8 binding peptides had low affinity for TAP. These results support the idea that TAP and particular HLA molecules may have co-evolved for efficient peptide processing and presentation. The strong similarity between the sets of peptides bound by TAP or HLA-B27 suggests functional co-evolution whereas the lack of a relationship between the sets of peptides bound by TAP or HLA-A2 is against these particular molecules having co-evolved. In support of these conclusions, the affinities of HLA-A2 and HLA-B7 binding peptides for TAP show similar distributions to that of randomly generated peptides. On the basis of these results we propose that HLA alleles 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). Computer modelling can be used to complement laboratory experiments and thereby speed up knowledge discovery in biology. In particular, we provide evidence that large-scale experiments can be avoided by combining initial experimental data with limited laboratory experiments sufficient to develop and validate appropriate computer models. These models can then be used to perform large-scale simulated experiments the results of which can then be validated by further small-scale laboratory experiments.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1998

Genomic regulation modeled as a network with basins of attraction.

Many natural processes consist of networks of interacting elements which affect each other's state over time, the dynamics depending on the pattern of connections and the updating rules for each element. Genomic regulatory networks are arguably networks of this sort. An attempt to understand genomic networks would benefit from the context of a general theory of discrete dynamical networks which is currently emerging. A key notion here is global dynamics, whereby state-space is organized into basins of attraction, objects that have only recently become accessible by computer simulation of idealized models, in particular "random Boolean networks". Cell types have been explained as attractors in genomic networks, where the network architecture is biased to achieve a balance between stability and adaptability in response to perturbation. Based on computer simulations using the software Discrete Dynamics Lab (DDLab), these ideas are described, as well as order-chaos measures on typical trajectories that further characterize network dynamics.

Algorithms↗

PubMedDate not supplied

A regenerating spiking neural network.

Due to their distributed architecture, artificial neural networks often show a graceful performance degradation to the loss of few units or connections. Living systems also display an additional source of fault-tolerance obtained through distributed processes of self-healing: defective components are actively regenerated. In this paper, we present results obtained with a model of development for spiking neural networks undergoing sustained levels of cell loss. To test their resistance to faults, networks are subjected to random faults during development and mutilated several times during operation. Results show that, evolved to control simulated Khepera robots in a simple navigation task, plastic and non-plastic networks develop fault-tolerant structures which can recover normal operation to various degrees.

Algorithms↗

PubMed1997

Computerized tumor boundary detection using a Hopfield neural network.

In this paper, we present a new approach for detection of brain tumor boundaries in medical images using a Hopfield neural network. The boundary detection problem is formulated as an optimization process that seeks the boundary points to minimize an energy functional based on an active contour model. A modified Hopfield network is constructed to solve the optimization problem. Taking advantage of the collective computational ability and energy convergence capability of the Hopfield network, our method produces the results comparable to those of standard "snakes"-based algorithms, but it requires less computing time. With the parallel processing potential of the Hopfield network, the proposed boundary detection can be implemented for real time processing. Experiments on different magnetic resonance imaging (MRI) data sets show the effectiveness of our approach.

Algorithms↗

PubMedDate not supplied

Computational rules for chemotaxis in the nematode C. elegans.

We derive a linear neural network model of the chemotaxis control circuit in the nematode Caenorhabditis elegans and demonstrate that this model is capable of producing nematodelike chemotaxis. By expanding the analytic solution for the network output in time-derivatives of the network input, we extract simple computational rules that reveal how the model network controls chemotaxis. Based on these rules we find that optimized linear networks typically control chemotaxis by computing the first time-derivative of the chemical concentration and modulating the body turning rate in response to this derivative. We argue that this is consistent with behavioral studies and a plausible mechanism for at least one component of chemotaxis in real nematodes.

Animals↗

PubMed1995

Computer-aided diagnosis of breast cancer: artificial neural network approach for optimized merging of mammographic features.

RATIONALE AND OBJECTIVES: An artificial neural network (ANN) approach was developed for the computer-aided diagnosis of mammography using an optimally minimized number of input features. METHODS: A backpropagation ANN merged nine input features (age plus eight radiographic findings extracted by radiologists) to predict biopsy outcome as its output. The features were ranked, and more important ones were selected to produce an optimal subset of features. RESULTS: Given all nine features, the ANN performed with a receiver operator characteristic area under the curve (Az) of .95 +/- .01. Given only the four most important features, the ANN performed with an Az of .96 +/- .01. Although not significantly better than the ANN with all nine features, the ANN with the four optimized features was significantly better than expert radiologists' Az of .90 +/- .02 (p = .01). This four-feature ANN had a 95% sensitivity and an 81% specificity. For cases with calcifications, the radiologists' performance dropped to an Az of .85 +/- .04, whereas a specialized three-feature ANN performed significantly better with an Az of .95 +/- .02 (p = .02). CONCLUSION: Given only four input features, the ANN predicted biopsy outcome significantly better than did expert radiologists, who also had access to other radiographic and nonradiographic data. The reduced number of features would substantially decrease data entry efforts and potentially improve the ANN's general applicability.

Breast Neoplasms↗

PubMed1996

Manipulator adaptive control by neural networks in an orange picking robot.

The paper focuses on the use of neural networks for process identification in an orange-picking robot adaptive control system. The results that will be shown in the paper refer to a study carried out under the European Community ESPRIT project "CONNY", dealing with the application of neural networks to robotics. The aim of the research is to verify the possibility of integrating a neural identification module in a traditional system to control the movement of the manipulators of the robot. The paper illustrates integration of neural identification in the existing orange-picking robot control system, highlighting the improvement of performance obtainable. Although the proposal refers to a specific robot, it can be applied to any system with the same dynamic features.

Adaptation, Psychological↗

PubMed2000

Mapping and fuzzy classification of macromolecular images using self-organizing neural networks.

In this work the effectiveness of the fuzzy kohonen clustering network (FKCN) in the unsupervised classification of electron microscopic images of biological macromolecules is studied. The algorithm combines Kohonen's self-organizing feature maps (SOFM) and Fuzzy c-means (FCM) in order to obtain a powerful clustering technique with the best properties inherited from both. Exploratory data analysis using SOFM is also presented as a step previous to final clustering. Two different data sets obtained from the G40P helicase from B. Subtilis bacteriophage SPP1 have been used for testing the proposed method, one composed of 2458 rotational power spectra of individual images and the other composed by 338 images from the same macromolecule. Results of FKCN are compared with self-organizing feature maps (SOFM) and manual classification. Experimental results prove that this new technique is suitable for working with large, high-dimensional and noisy data sets and, thus, it is proposed to be used as a classification tool in electron microscopy.

Algorithms↗