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PubMed2004

A temporally adaptive classifier for multispectral imagery.

This paper presents a new temporally adaptive classification system for multispectral images. A spatial-temporal adaptation mechanism is devised to account for the changes in the feature space as a result of environmental variations. Classification based upon spatial features is performed using Bayesian framework or probabilistic neural networks (PNNs) while the temporal updating takes place using a spatial-temporal predictor. A simple iterative updating mechanism is also introduced for adjusting the parameters of these systems. The proposed methodology is used to develop a pixel-based cloud classification system. Experimental results on cloud classification from satellite imagery are provided to show the usefulness of this system.

Image Processing, Computer-Assisted↗
PubMed2005

Tandem machine learning for the identification of genes regulated by transcription factors.

BACKGROUND: The identification of promoter regions that are regulated by a given transcription factor has traditionally relied upon the identification and distributions of binding sites recognized by the factor. In this study, we have developed a tandem machine learning approach for the identification of regulatory target genes based on these parameters and on the corresponding binding site information contents that measure the affinities of the factor for these cognate elements. RESULTS: This method has been validated using models of DNA binding sites recognized by the xenobiotic-sensitive nuclear receptor, PXR/RXRalpha, for target genes within the human genome. An information theory-based weight matrix was first derived and refined from known PXR/RXRalpha binding sites. The promoter region of candidate genes was scanned with the weight matrix. A novel information density-based clustering algorithm was then used to identify clusters of information rich sites. Finally, transformed data representing metrics of location, strength and clustering of binding sites were used for classification of promoter regions using an ensemble approach involving neural networks, decision trees and Naïve Bayesian classification. The method was evaluated on a set of 24 known target genes and 288 genes known not to be regulated by PXR/RXRalpha. We report an average accuracy (proportion of correctly classified promoter regions) of 71%, sensitivity of 73%, and specificity of 70%, based on multiple cross-validation and the leave-one-out strategy. The performance on a test set of 13 genes showed that 10 were correctly classified. CONCLUSION: We have developed a machine learning approach for the successful detection of gene targets for transcription factors with high accuracy. The method has been validated for the transcription factor PXR/RXRalpha and has the potential to be extended to other transcription factors.

Algorithms↗
PubMedDate not supplied

Review of the development, validation, and application of predictive instruments in interventional cardiology.

Within the last few years, risk assessment has become an integral part of clinical practice, particularly for thoracic surgery and interventional procedures. Risk assessment statistical models are being used in medical decision making, quality improvement tools, and as aids to patient counseling. This literature review was conducted to evaluate the types of predictive models and outcomes measures that have been examined, and methods used in development, validation, and application of these models. A Medline search performed to identify articles (limited to human studies) published in English from 1980 to 1999 resulted in 89 articles, of which 71 were evaluable. Populations studied for model development included patients undergoing coronary artery bypass graft (CABG), percutaneous transluminal coronary revascularization (PTCR), cardiac catheterization, or stenting procedures and patients with angina or stroke. The models were equally developed from a single center versus multicenter and from retrospective databases versus prospective studies. In terms of model perspectives, only three of the models measured cost or cost-effectiveness as the outcome; the remainder considered only clinical outcomes. The most commonly reported types of predictive models were developed using logistic regression and Bayesian techniques, followed by neural networks, rule-based artificial intelligence, simultaneous equation system, and multiple linear regression. Factors to consider when developing or evaluating a predictive model include uniformity of definitions of outcomes, uniformity of definitions of variables, completeness of data, number and frequency of variables, timeliness and source of data, development population characteristics, development and testing (validation) cohorts, and calibration and discrimination. Application of these models to an individual patient can spur quality improvement efforts that can lead to dramatic, system-wide improvements in outcomes.

Cardiovascular Diseases↗
PubMed2025

Detecting Interspecific Positive Selection Using Convolutional Neural Networks.

Traditional statistical methods using maximum likelihood and Bayesian inference can detect positive selection from an interspecific phylogeny and a codon sequence alignment based on model assumptions, but they are prone to false positives due to alignment errors and can lack power. These problems are particularly pronounced when faced with high levels of indels and divergence. To address these issues, we trained and tested convolutional neural network models on simulated data and achieved higher accuracy in detecting selection across a specific range of phylogenetic scenarios and evolutionary modes. This advantage is particularly evident when performing inference on noisy data prone to misalignments. Our method shows some ability to account for these errors, where most statistical frameworks fail to do so in a tractable manner. We explore the generalizability of our convolutional neural network models to unseen evolutionary scenarios and identify future avenues to achieve broader utility. Once trained, our convolutional neural network model is faster at test time, making it a scalable alternative to traditional statistical methods for large-scale, multigene analyses. In addition to binary classification (inference of the presence or absence of positive selection during the evolution of the sequences), we use saliency maps to understand what the model learns and observe how this could be leveraged for sitewise inference of positive selection.

Neural Networks, Computer↗
PubMed1997

Comparison between conventional and neural network classifiers for rat sleep-wake stage discrimination.

This article describes an approach to selecting the most efficient classifier for rat sleep staging (waking, REM sleep and NREM sleep) discrimination. Three conventional (bayesian, linear, and euclidean) and two neural network (multilayer perceptrons integrating or not integrating contextual information) classifiers were compared. For each classifier, performances were presented in the form of a statistical concordance matrix comparing classifier results versus human expert results on 6 24-hour records (1 record per animal). Comparison between classifiers was based on the estimation and accuracy of global agreements. Interest was also focused on REM sleep state discrimination. The results show that neural network classifiers are appropriate tools to be integrated in an automatic rat sleep-wake stage system. The approach presented should help scientists in choosing a method of data classification.

Animals↗
PubMedDate not supplied

Evaluation of a neural network classifier for pancreatic masses based on CT findings.

We have investigated a neural network classifier based on CT findings extracted by a radiologist for the differential diagnosis between the pancreatic ductal adenocarcinoma and mass-forming pancreatitis, and compared its classification performance with that of Bayesian analysis, Hayashi's quantification method II, and radiologists. The three computerized classification methods were designed to classify categorized CT findings extracted by a radiologist, and were trained and tested on 71 cases. There was comparable performance between the neural the network, the Bayesian analysis, Hayashi's quantification method II, and the radiologists, in classifying pancreatic carcinoma and inflammatory mass.

Adult↗
PubMedDate not supplied

Optimisation of the predictive ability of artificial neural network (ANN) models: a comparison of three ANN programs and four classes of training algorithm.

The purpose of this study was to determine whether artificial neural network (ANN) programs implementing different backpropagation algorithms and default settings are capable of generating equivalent highly predictive models. Three ANN packages were used: INForm, CAD/Chem and MATLAB. Twenty variants of gradient descent, conjugate gradient, quasi-Newton and Bayesian regularization algorithms were used to train networks containing a single hidden layer of 3-12 nodes. All INForm and CAD/Chem models trained satisfactorily for tensile strength, disintegration time and percentage dissolution at 15, 30, 45 and 60 min. Similarly, acceptable training was obtained for MATLAB models using Bayesian regularization. Training of MATLAB models with other algorithms was erratic. This effect was attributed to a tendency for the MATLAB implementation of the algorithms to attenuate training in local minima of the error surface. Predictive models for tablet capping and friability could not be generated. The most predictive models from each ANN package varied with respect to the optimum network architecture and training algorithm. No significant differences were found in the predictive ability of these models. It is concluded that comparable models are obtainable from different ANN programs provided that both the network architecture and training algorithm are optimised. A broad strategy for optimisation of the predictive ability of an ANN model is proposed.

Algorithms↗
PubMed2006

FCMAC-BYY: fuzzy CMAC using Bayesian Ying-Yang learning.

As an associative memory neural network model, the cerebellar model articulation controller (CMAC) has attractive properties of fast learning and simple computation, but its rigid structure makes it difficult to approximate certain functions. This research attempts to construct a novel neural fuzzy CMAC, in which Bayesian Ying-Yang (BYY) learning is introduced to determine the optimal fuzzy sets, and a truth-value restriction inference scheme is subsequently employed to derive the truth values of the rule weights of implication rules. The BYY is motivated from the famous Chinese ancient Ying-Yang philosophy: everything in the universe can be viewed as a product of a constant conflict between opposites-Ying and Yang, a perfect status is reached when Ying and Yang achieve harmony. The proposed fuzzy CMAC (FCMAC)-BYY enjoys the following advantages. First, it has a higher generalization ability because the fuzzy rule sets are systematically optimized by BYY; second, it reduces the memory requirement of the network by a significant degree as compared to the original CMAC; and third, it provides an intuitive fuzzy logic reasoning and has clear semantic meanings. The experimental results on some benchmark datasets show that the proposed FCMAC-BYY outperforms the existing representative techniques in the research literature.

Algorithms↗
PubMed2025

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

MOTIVATION: Genome-wide association studies (GWAS) have identified genetic variants, usually single-nucleotide polymorphisms (SNPs), associated with human traits, including disease and disease risk. These variants (or causal variants in linkage disequilibrium with them) usually affect the regulation or function of a nearby gene. A GWAS locus can span many genes, however, and prioritizing which gene or genes in a locus are most likely to be causal remains a challenge. Better prioritization and prediction of causal genes could reveal disease mechanisms and suggest interventions. RESULTS: We describe a new Bayesian method, termed SigNet for significance networks, that combines information both within and across loci to identify the most likely causal gene at each locus. The SigNet method builds on existing methods that focus on individual loci with evidence from gene distance and expression quantitative trait loci (eQTL) by sharing information across loci using protein-protein and gene regulatory interaction network data. In an application to cardiac electrophysiology with 226 GWAS loci, only 46 (20%) have within-locus evidence from Mendelian genes, protein-coding changes, or colocalization with eQTL signals. At the remaining 180 loci lacking functional information, SigNet selects 56 genes other than the minimum distance gene, equal to 31% of the information-poor loci and 25% of the GWAS loci overall. Assessment by pathway enrichment demonstrates improved performance by SigNet. Review of individual loci shows literature evidence for genes selected by SigNet, including PMP22 as a novel causal gene candidate.

Genome-Wide Association Study↗
PubMed2005

Comparison of recent methods for inference of variable influence in neural networks.

Neural networks (NNs) belong to 'black box' models and therefore 'suffer' from interpretation difficulties. Four recent methods inferring variable influence in NNs are compared in this paper. The methods assist the interpretation task during different phases of the modeling procedure. They belong to information theory (ITSS), the Bayesian framework (ARD), the analysis of the network's weights (GIM), and the sequential omission of the variables (SZW). The comparison is based upon artificial and real data sets of differing size, complexity and noise level. The influence of the neural network's size has also been considered. The results provide useful information about the agreement between the methods under different conditions. Generally, SZW and GIM differ from ARD regarding the variable influence, although applied to NNs with similar modeling accuracy, even when larger data sets sizes are used. ITSS produces similar results to SZW and GIM, although suffering more from the 'curse of dimensionality'.

Algorithms↗
PubMed2004

Bayesian inference for randomized clinical trials with treatment failures.

During the course of a clinical trial, subjects may experience treatment failure. For ethical reasons, it is necessary to administer emergency or rescue medications for such subjects. However, the rescue medications may bias the set of response measurements. This bias is of particular concern if a subject has been randomized to the control group, and the rescue medications improve the subject's condition. The standard approach to analysing data from a clinical trial is to perform an intent-to-treat (ITT) analysis, wherein the data are analysed according to treatment randomization. Supplementary analyses may be performed in addition to the ITT analysis to account for the effect of treatment failures and rescue medications. A Bayesian, counterfactual approach, which uses the data augmentation (DA) algorithm, is proposed for supplemental analysis. A simulation study is conducted to compare the operating characteristics of this procedure with a likelihood-based, counterfactual approach based on the EM algorithm. An example from the Asthma Clinical Research Network (ACRN) is used to illustrate the Bayesian procedure.

Algorithms↗
PubMed2005

Connectionist-based Dempster-Shafer evidential reasoning for data fusion.

Dempster-Shafer evidence theory (DSET) is a popular paradigm for dealing with uncertainty and imprecision. Its corresponding evidential reasoning framework is theoretically attractive. However, there are outstanding issues that hinder its use in real-life applications. Two prominent issues in this regard are 1) the issue of basic probability assignments (masses) and 2) the issue of dependence among information sources. This paper attempts to deal with these issues by utilizing neural networks in the context of pattern classification application. First, a multilayer perceptron neural network with the mean squared error as a cost function is implemented to calculate, for each information source, posteriori probabilities for all classes. Second, an evidence structure construction scheme is developed for transferring the estimated posteriori probabilities to a set of masses along with the corresponding focal elements, from a Bayesian decision point of view. Third, a network realization of the Dempster-Shafer evidential reasoning is designed and analyzed, and it is further extended to a DSET-based neural network, referred to as DSETNN, to manipulate the evidence structures. In order to tackle the issue of dependence between sources, DSETNN is tuned for optimal performance through a supervised learning process. To demonstrate the effectiveness of the proposed approach, we apply it to three benchmark pattern classification problems. Experiments reveal that the DSETNN out-performs DSET and provide encouraging results in terms of classification accuracy and the speed of learning convergence.

Algorithms↗
PubMed2001

Algebraic geometrical methods for hierarchical learning machines.

Hierarchical learning machines such as layered perceptrons, radial basis functions, Gaussian mixtures are non-identifiable learning machines, whose Fisher information matrices are not positive definite. This fact shows that conventional statistical asymptotic theory cannot be applied to neural network learning theory, for example either the Bayesian a posteriori probability distribution does not converge to the Gaussian distribution, or the generalization error is not in proportion to the number of parameters. The purpose of this paper is to overcome this problem and to clarify the relation between the learning curve of a hierarchical learning machine and the algebraic geometrical structure of the parameter space. We establish an algorithm to calculate the Bayesian stochastic complexity based on blowing-up technology in algebraic geometry and prove that the Bayesian generalization error of a hierarchical learning machine is smaller than that of a regular statistical model, even if the true distribution is not contained in the parametric model.

Algorithms↗
PubMed2006

Determining hierarchical functional networks from auditory stimuli fMRI.

We determined connectivity of the human brain using functional magnetic resonance imaging (fMRI) while subjects experienced auditory stimuli in a 2-by-2 factorial design. The two factors in this study were "speaker" (same or different speaker) and "sentence" (same or different sentences). Connectivity studies allow us to ask how spatially remote brain regions are neurophysiologically related given these stimuli. In the context of this study, we examined how the "speaker" effect and "sentence" effect influenced these relationships. We applied a Bayesian connectivity method that determines hierarchical functional networks of functionally connected brain regions. Hierarchy in these functional networks is determined by conditional probabilities of elevated activity. For example, a brain region that becomes active a superset of the time of another region is considered ascendant to that brain region in the hierarchical network. For each factor level, we found a baseline functional network connecting the primary auditory cortex (Brodmann's Area [BA] 41) with the BA 42 and BA 22 of the superior temporal gyrus (STG). We also found a baseline functional network that includes Wernicke's Area (BA 22 posterior), STG, and BA 44 for each factor level. However, we additionally observed a strong ascendant connection from BA 41 to the posterior cingulate (BA 30) and Broca's Area and a stronger connection from Wernicke's Area to STG and the posterior cingulate while passively listening to different sentences rather than the same sentence repeatedly. Finally, our results revealed no significant "speaker" effect or interaction between "speaker" and "sentence."

Acoustic Stimulation↗
PubMed2006

Estimating the parameters of a model for protein-protein interaction graphs.

We find accurate approximations for the expected number of three-cycles and unchorded four-cycles under a stochastic distribution for graphs that has been proposed for modelling yeast two-hybrid protein-protein interaction networks. We show that unchorded four-cycles are characteristic motifs under this model and that the count of unchorded four-cycles in the graph is a reliable statistic on which to base parameter estimation. Finally, we test our model against a range of experimental data, obtain parameter estimates from these data and investigate possible improvements in the model. Characterization of this model lays the foundation for its use as a prior distribution in a Bayesian analysis of yeast two-hybrid networks that can potentially aid in identifying false-positive and false-negative results.

Algorithms↗
PubMed2006

Exploring candidate genes for human brain diseases from a brain-specific gene network.

It is believed that large numbers of genes are involved in common human brain diseases. Here, we propose a novel computational strategy for simultaneously identifying multiple candidate genes for genetic human brain diseases from a brain-specific gene network-level perspective. By integrating diverse genomic and proteomic datasets based on Bayesian statistical model, we built a large-scale human brain-specific gene network. Based on this network and minor prior knowledge of a specific brain disease, we can effectively identify multiple candidate genes for this disease. When four known Alzheimer's disease genes were used as the prior knowledge, among the top 46 high-scoring genes that we have found, 37 were previously reported to be associated with Alzheimer's disease. And the higher score a gene has, the more likely this gene is a disease-related one. The results suggest that the proposed method is effective, convenient, and applicable in the future genetic studies.

Alzheimer Disease↗
PubMedDate not supplied

Bayesian multisensory integration and cross-modal spatial links.

Our perception of the word is the result of combining information between several senses, such as vision, audition and proprioception. These sensory modalities use widely different frames of reference to represent the properties and locations of object. Moreover, multisensory cues come with different degrees of reliability, and the reliability of a given cue can change in different contexts. The Bayesian framework--which we describe in this review--provides an optimal solution to deal with this issue of combining cues that are not equally reliable. However, this approach does not address the issue of frames of references. We show that this problem can be solved by creating cross-modal spatial links in basis function networks. Finally, we show how the basis function approach can be combined with the Bayesian framework to yield networks that can perform optimal multisensory combination. On the basis of this theory, we argue that multisensory integration is a dialogue between sensory modalities rather that the convergence of all sensory information onto a supra-modal area.

Animals↗
PubMed2004

Bayesian computation in recurrent neural circuits.

A large number of human psychophysical results have been successfully explained in recent years using Bayesian models. However, the neural implementation of such models remains largely unclear. In this article, we show that a network architecture commonly used to model the cerebral cortex can implement Bayesian inference for an arbitrary hidden Markov model. We illustrate the approach using an orientation discrimination task and a visual motion detection task. In the case of orientation discrimination, we show that the model network can infer the posterior distribution over orientations and correctly estimate stimulus orientation in the presence of significant noise. In the case of motion detection, we show that the resulting model network exhibits direction selectivity and correctly computes the posterior probabilities over motion direction and position. When used to solve the well-known random dots motion discrimination task, the model generates responses that mimic the activities of evidence-accumulating neurons in cortical areas LIP and FEF. The framework we introduce posits a new interpretation of cortical activities in terms of log posterior probabilities of stimuli occurring in the natural world.

Action Potentials↗