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Generalized radial basis function networks for classification and novelty detection: self-organization of optimal Bayesian decision.

By adding reverse connections from the output layer to the central layer it is shown how a generalized radial basis functions (GRBF) network can self-organize to form a Bayesian classifier, which is also capable of novelty detection. For this purpose, three stochastic sequential learning rules are introduced from biological considerations which pertain to the centers, the shapes, and the widths of the receptive fields of the neurons and allow ajoint optimization of all network parameters. The rules are shown to generate maximum-likelihood estimates of the class-conditional probability density functions of labeled data in terms of multivariate normal mixtures. Upon combination with a hierarchy of deterministic annealing procedures, which implement a multiple-scale approach, the learning process can avoid the convergence problems hampering conventional expectation-maximization algorithms. Using an example from the field of speech recognition, the stages of the learning process and the capabilities of the self-organizing GRBF classifier are illustrated.

Artificial Intelligence↗

Solitary pulmonary nodules: determining the likelihood of malignancy with neural network analysis.

PURPOSE: To test a neural network in differentiation of benign from malignant solitary pulmonary nodules. MATERIALS AND METHODS: Neural networks were trained and tested on the characteristics of 318 nodules. Predictive accuracy of the network was judged for calibration and discrimination. Network results were compared with those with a simpler Bayesian method. RESULTS: The Brier score was 0.142 (calibration, 0.003; discrimination, 0.139) for the neural network and 0.133 for the Bayesian analysis (calibration, 0.012; discrimination, 0.121). Analysis of the calibration curve revealed no significant difference (P < .05) between the slope (b = 1.09) and the line of identity (b = 1) for the neural network or the Bayesian analysis. The area under the receiver operating characteristic curve was 0.871 for the neural network and 0.894 for the Bayesian analysis (P < .05). There were 23 and 21 false-positive predictions and 18 and six false-negative predictions for the neural network and Bayesian analysis, respectively. CONCLUSION: The Bayesian method was better than the neural network in prediction of probability of malignancy in solitary pulmonary nodules.

Adult↗

Integrating multi-attribute similarity networks for robust representation of the protein space.

MOTIVATION: A global view of the protein space is essential for functional and evolutionary analysis of proteins. In order to achieve this, a similarity network can be built using pairwise relationships among proteins. However, existing similarity networks employ a single similarity measure and therefore their utility depends highly on the quality of the selected measure. A more robust representation of the protein space can be realized if multiple sources of information are used. RESULTS: We propose a novel approach for analyzing multi-attribute similarity networks by combining random walks on graphs with Bayesian theory. A multi-attribute network is created by combining sequence and structure based similarity measures. For each attribute of the similarity network, one can compute a measure of affinity from a given protein to every other protein in the network using random walks. This process makes use of the implicit clustering information of the similarity network, and we show that it is superior to naive, local ranking methods. We then combine the computed affinities using a Bayesian framework. In particular, when we train a Bayesian model for automated classification of a novel protein, we achieve high classification accuracy and outperform single attribute networks. In addition, we demonstrate the effectiveness of our technique by comparison with a competing kernel-based information integration approach.

Algorithms↗

The application of an artificial neural network to Doppler ultrasound waveforms for the classification of arterial disease.

In this study we have investigated the application of an Artificial Neural Net classifier to the diagnosis of vascular disease using Doppler ultrasound blood-velocity/time waveforms. A multi-layer perceptron network was trained with waveforms from control subjects and from patients with arterial disease. The diseased cases were confirmed by angiography and allocated to three groups according to the location of the stenosis: proximal or distal to the site of measurement or multi-segmental. We compared network classification results with a Bayesian classifier following a Principal Component Analysis of the waveforms. Versions of both classifiers were trained to discriminate two classes (normal v. abnormal) and four classes. In both cases the neural networks gave superior discrimination to the Bayesian classifier. While the four-class network was unable to provide useful discrimination among the stenosis sites, discrimination between abnormal classes was obtained which is comparable to that achieved by a human expert observer.

Adult↗

Antipsychotic drugs and heart muscle disorder in international pharmacovigilance: data mining study.

OBJECTIVES: To examine the relation between antipsychotic drugs and myocarditis and cardiomyopathy. DESIGN: Data mining using bayesian statistics implemented in a neural network architecture. SETTING: International database on adverse drug reactions run by the World Health Organization programme for international drug monitoring. MAIN OUTCOME MEASURES: Reports mentioning antipsychotic drugs, cardiomyopathy, or myocarditis. RESULTS: A strong signal existed for an association between clozapine and cardiomyopathy and myocarditis. An association was also seen with other antipsychotics as a group. The association was based on sufficient cases with adequate documentation and apparent lack of confounding to constitute a signal. Associations between myocarditis or cardiomyopathy and lithium, chlorpromazine, fluphenazine, haloperidol, and risperidone need further investigation. CONCLUSIONS: Some antipsychotic drugs seem to be linked to cardiomyopathy and myocarditis. The study shows the potential of bayesian neural networks in analysing data on drug safety.

Antipsychotic Agents↗

Computing with continuous attractors: stability and online aspects.

Two issues concerning the application of continuous attractors in neural systems are investigated: the computational robustness of continuous attractors with respect to input noises and the implementation of Bayesian online decoding. In a perfect mathematical model for continuous attractors, decoding results for stimuli are highly sensitive to input noises, and this sensitivity is the inevitable consequence of the system's neutral stability. To overcome this shortcoming, we modify the conventional network model by including extra dynamical interactions between neurons. These interactions vary according to the biologically plausible Hebbian learning rule and have the computational role of memorizing and propagating stimulus information accumulated with time. As a result, the new network model responds to the history of external inputs over a period of time, and hence becomes insensitive to short-term fluctuations. Also, since dynamical interactions provide a mechanism to convey the prior knowledge of stimulus, that is, the information of the stimulus presented previously, the network effectively implements online Bayesian inference. This study also reveals some interesting behavior in neural population coding, such as the trade-off between decoding stability and the speed of tracking time-varying stimuli, and the relationship between neural tuning width and the tracking speed.

Humans↗

The Bayesian evidence scheme for regularizing probability-density estimating neural networks.

Training probability-density estimating neural networks with the expectation-maximization (EM) algorithm aims to maximize the likelihood of the training set and therefore leads to overfitting for sparse data. In this article, a regularization method for mixture models with generalized linear kernel centers is proposed, which adopts the Bayesian evidence approach and optimizes the hyperparameters of the prior by type II maximum likelihood. This includes a marginalization over the parameters, which is done by Laplace approximation and requires the derivation of the Hessian of the log-likelihood function. The incorporation of this approach into the standard training scheme leads to a modified form of the EM algorithm, which includes a regularization term and adapts the hyperparameters on-line after each EM cycle. The article presents applications of this scheme to classification problems, the prediction of stochastic time series, and latent space models.

Acquired Immunodeficiency Syndrome↗

Modeling of cyclin-dependent kinase inhibition by 1H-pyrazolo[3,4-d]pyrimidine derivatives using artificial neural network ensembles.

Artificial neural network ensembles were used for modeling the cyclin-dependent kinase inhibition of 1H-pyrazolo[3,4-d]pyrimidine derivatives. The structural characteristics of these inhibitors were encoded in relevant 3D-spatial descriptors extracted by genetic algorithm feature selection. Bayesian-regularized multilayer neural networks, trained by the back-propagation algorithm, were developed using these variables as inputs. The predictive power of the model was tested by leave-one-out cross validation. In addition, for a more rigorous measure of the predictive capacity, multiple validation sets were randomly generated as members of neural network ensembles, which makes doing averaged predictions feasible. In this way, the predictive power was analyzed accounting for the averaged test set R values and test set mean-square errors. Otherwise, Kohonen self-organizing maps were used as an additional tool for the same modeling. The location of the inhibitors in a map facilitates the analysis of the connection between compounds and serves as a useful tool for qualitative predictions.

Algorithms↗

A new method for sleep apnea classification using wavelets and feedforward neural networks.

OBJECTIVES: This paper presents a novel approach for sleep apnea classification. The goal is to classify each apnea in one of three basic types: obstructive, central and mixed. MATERIALS AND METHODS: Three different supervised learning methods using a neural network were tested. The inputs of the neural network are the first level-5-detail coefficients obtained from a discrete wavelet transformation of the samples (previously detected as apnea) in the thoracic effort signal. In order to train and test the systems, 120 events from six different patients were used. The true error rate was estimated using a 10-fold cross validation. The results presented in this work were averaged over 100 different simulations and a multiple comparison procedure was used for model selection. RESULTS: The method finally selected is based on a feedforward neural network trained using the Bayesian framework and a cross-entropy error function. The mean classification accuracy, obtained over the test set was 83.78+/-1.90%. CONCLUSION: The proposed classifier surpasses, up to the author's knowledge, other previous results. Finally, a scheme to maintain and improve this system during its clinical use is also proposed.

Algorithms↗

A sequential injection electronic tongue employing the transient response from potentiometric sensors for anion multidetermination.

Intelligent and automatic systems based on arrays of non-specific-response chemical sensors were recently developed in our laboratory. For multidetermination applications, the normal choice is an array of potentiometric sensors to generate the signal, and an artificial neural network (ANN) correctly trained to obtain the calibration model. As a great amount of information is required for the proper modelling, we proposed its automated generation by using the sequential injection analysis (SIA) technique. First signals used were steady-state: the equilibrium signal after a step-change in concentration. We have now adapted our procedures to record the transient response corresponding to a sample step. The novelty in this approach is therefore the use of the dynamic components of the signal in order to better discriminate or differentiate a sample. In the developed electronic tongue systems, detection is carried out by using a sensor array formed by five potentiometric sensors based on PVC membranes. For the developed application we employed two different chloride-selective sensors, two nitrate-selective sensors and one generic response sensor. As the amount of raw data (fivefold recordings corresponding to the five sensors) is excessive for an ANN, some feature extraction step prior to the modelling was needed. In order to attain substantial data reduction and noise filtering, the data obtained were fitted with orthonormal Legendre polynomials. In this case, a third-degree Legendre polynomial was shown to be sufficient to fit the data. The coefficients of these polynomials were the input information fed into the ANN used to model the concentrations of the determined species (Cl-, NO3- and HCO3-). Best results were obtained by using a backpropagation neural network trained with the Bayesian regularisation algorithm; the net had a single hidden layer containing three neurons with the tansig transfer function. The results obtained from the time-dependent response were compared with those obtained from steady-state conditions, showing the former superior performance. Finally, the method was applied for determining anions in synthetic samples and real water samples, where a satisfactory comparison was also achieved.

Algorithms↗

Data mining and computationally intensive methods: summary of Group 7 contributions to Genetic Analysis Workshop 13.

The Framingham Heart Study data, as well as a related simulated data set, were generously provided to the participants of the Genetic Analysis Workshop 13 in order that newly developed and emerging statistical methodologies could be tested on that well-characterized data set. The impetus driving the development of novel methods is to elucidate the contributions of genes, environment, and interactions between and among them, as well as to allow comparison between and validation of methods. The seven papers that comprise this group used data-mining methodologies (tree-based methods, neural networks, discriminant analysis, and Bayesian variable selection) in an attempt to identify the underlying genetics of cardiovascular disease and related traits in the presence of environmental and genetic covariates. Data-mining strategies are gaining popularity because they are extremely flexible and may have greater efficiency and potential in identifying the factors involved in complex disorders. While the methods grouped together here constitute a diverse collection, some papers asked similar questions with very different methods, while others used the same underlying methodology to ask very different questions. This paper briefly describes the data-mining methodologies applied to the Genetic Analysis Workshop 13 data sets and the results of those investigations.

Bayes Theorem↗

Comparison of data mining methodologies using Japanese spontaneous reports.

PURPOSE: Five data mining methodologies for detecting a possible signal from spontaneous reports on adverse drug reactions (ADRs) were compared. METHODS: The five methodologies, the Bayesian method using the Gamma Poissson Shrinker (GPS), the method employed in the UK Medicines Control Agency (MCA), the Bayesian Confidence Propagation Neural Network (BCPNN), the method using the 95% confidence interval (CI) for the reporting odds ratio (RORCI) and that using the 95% CI of the proportional reporting ratio (PRRCI) were compared using Japanese data obtained between 1998 and 2000. RESULTS: There were all in all 38,731 drug-ADR combinations. The count of drug-ADR pairs was equal to 1 or 2 for 31,230 combinations and none of them were identified as a possible signal with the MCA or BCPNN. Similarly, the GPS detected a possible signal in none of the combinations where the count was equal to 1 but in 7.5% of the combinations where the count was equal to 2. The RORCI and PRRCI detected a possible signal in more than half of the combinations where the count was equal to 1 or 2. When the pairwise agreement on whether or not a drug-ADR combination satisfied the criteria for a possible signal was assessed for the 38,731 combinations, the concordance measure kappa was greater than 0.9 between the MCA and BCPNN and between the RORCI and PRRCI. Kappa was around 0.6 between the GPS and MCA and between the GPS and BCPNN. Otherwise, kappa was smaller than 0.2. CONCLUSIONS: The drug-ADR combinations detected as a possible signal vary between different methodologies.

Adverse Drug Reaction Reporting Systems↗

Data-mining analyses of pharmacovigilance signals in relation to relevant comparison drugs.

OBJECTIVE: The aim of this paper is to demonstrate the usefulness of the Bayesian Confidence Propagation Neural Network (BCPNN) in the detection of drug-specific and drug-group effects in the database of adverse drug reactions of the World Health Organization Programme for International Drug Monitoring. METHODS: Examples of drug-adverse reaction combinations highlighted by the BCPNN as quantitative associations were selected. The anatomical therapeutic chemical (ATC) group to which the drug belonged was then identified, and the information component (IC) was calculated for this ATC group and the adverse drug reaction (ADR). The IC of the ATC group with the ADR was then compared with the IC of the drug-ADR by plotting the change in IC and its 95% confidence limit over time for both. RESULTS: The chosen examples show that the BCPNN data-mining approach can identify drug-specific as well as group effects. In the known examples that served as test cases, beta-blocking agents other than practolol are not associated with sclerosing peritonitis, but all angiotensin-converting enzyme inhibitors are associated with coughing, as are antihistamines with heart-rhythm disorders and antipsychotics with myocarditis. The recently identified association between antipsychotics and myocarditis remains even after consideration of concomitant medication. CONCLUSION: The BCPNN can be used to improve the ability of a signal detection system to highlight group and drug-specific effects.

Adverse Drug Reaction Reporting Systems↗

QSAR models for predicting the activity of non-peptide luteinizing hormone-releasing hormone (LHRH) antagonists derived from erythromycin A using quantum chemical properties.

Multiple linear regression (MLR) combined with genetic algorithm (GA) and Bayesian-regularized Genetic Neural Networks (BRGNNs) were used to model the binding affinity (pK(I)) of 38 11,12-cyclic carbamate derivatives of 6-O-methylerythromycin A for the Human Luteinizing Hormone-Releasing Hormone (LHRH) receptor using quantum chemical descriptors. A multiparametric MLR equation with good statistical quality was obtained that describes the features relevant for antagonistic activity when the substituent at the position 3 of the erythronolide core was varied. In addition, four-descriptor linear and nonlinear models were established for the whole dataset. Such models showed high statistical quality. However, the BRGNN model was better than the linear model according to the external validation process. In general, our linear and nonlinear models reveal that the binding affinity of the compounds studied for the LHRH receptor is modulated by electron-related terms.

Animals↗

Simultaneous optimization by neuro-genetic approach of a multiresidue method for determination of pesticides in Passiflora alata infuses using headspace solid phase microextraction and gas chromatography.

A simultaneous optimization strategy based on neuro-genetic approach has been applied to a HS-SPME-GC-ECD (Headspace Solid Phase Microextraction coupled to Gas Chromatography with Electron Capture Detection) method for simultaneous determination of the pesticides chlorotalonil, methyl parathion, malathion, alpha-endosulfan and beta-endosulfan in herbal infusions of Passiflora alata (Dryander). Two types of extractive fibers were used: a home-made device coated by sol-gel process with polydimethylsiloxane-poly(vinyl alcohol) (PDMS/PVA) and a commercial PDMS. The effects of extraction parameters such as dilution of the infusion, extraction temperature and time, as well as sample ionic strength were evaluated through the Doehlert design. To find a model that could relate these extraction parameters with the extraction efficiency of all pesticide simultaneously, a Bayesian Regularized Artificial Neural Network (BRANN) approach was employed. Subsequently, Genetic Algorithm (GA) was applied to attain the optimum values from the model developed by the neural network. The use of the proposed approach allowed the determination of a single extraction condition that maximized the peak areas of all pesticides simultaneously, showing a promising and a suitable new procedure to the optimization process of complex analytical problems.

Algorithms↗

A comparison of renal-related adverse drug reactions between rofecoxib and celecoxib, based on the World Health Organization/Uppsala Monitoring Centre safety database.

BACKGROUND: Two isoforms of cyclooxygenase (COX) have been identified, both of them inhibited by traditional nonsteroidal anti-inflammatory drugs (NSAIDs). Inhibition of COX-2 has been associated with the therapeutic effects of NSAIDs, whereas inhibition of COX-1 is believed to be the cause of the adverse gastrointestinal effects associated with NSAID therapy. When administered at therapeutic doses, new COX-2-specific inhibitors inhibit only the COX-2 isoform. OBJECTIVE: This study sought to compare renal safety signals between the COX-2-specific inhibitors rofecoxib and celecoxib, based on spontaneous reports of adverse drug reactions (ADRs) in the World Health Organization/Uppsala Monitoring Centre (WHO/UMC) safety database through the end of the second quarter 2000. METHODS: Disproportionality in the association between a particular drug and renal-related ADR was evaluated using a bayesian confidence propagation neural network method in which a statistical parameter, the information component (IC) value, was calculated for each drug-ADR combination. In this method, an IC value significantly greater than 0 implies that the association of a drug-ADR pair is stronger than background; the higher the IC value, the more the combination stands out from the background. The ratio of actual to expected numbers of ADRs was also used to assess disproportionality. RESULTS: As with traditional NSAIDs, both COX-2-specific inhibitors were associated with renal-related ADRs. However, the adverse renal impact of rofecoxib was significantly greater than that of celecoxib. IC values were significantly different for the following comparisons: water retention (1.97 rofecoxib vs 1.18 celecoxib; P < 0.01); abnormal renal function (2.38 vs 0.70; P < 0.01); renal failure (2.22 vs 1.09; P < 0.01); cardiac failure (2.39 vs 0.48; P < 0.01); and hypertension (2.15 vs 1.33; P < 0.01). In an additional analysis, celecoxib was shown to have a similar renal safety profile to that of diclofenac and ibuprofen. CONCLUSIONS: Based on spontaneous ADR reports in the WHO/UMC safety database at the end of the second quarter 2000, this analysis indicates that rofecoxib has significantly greater renal toxicity than celecoxib or traditional NSAIDs. This negative renal impact may have the potential to increase the risk for serious cardiac and/or cerebrovascular events.

Acute Kidney Injury↗

Standardized structure and modular design of a pharmacokinetic database.

BACKGROUND: The accumulated knowledge on drugs can be used for an individual drug dosage adjustment if it is placed at our disposal in an informatically structured form. THEORY AND METHODS: We have started building up a pharmacokinetic database aimed at adjusting drug dosages, in exemplary form, to patients with renal impairment. Parameters needed for the three dosage adjustment rules (Dettli, Kunin, Holford) and the most general concept of pharmacokinetics constituted the theoretical basis. TWO PROCESSES PERTAIN TO ALL DRUGS: Distribution and elimination. Total drug clearance and at least two parameters representing distribution and elimination processes are closely interdependent in mathematical terms (clearance = volume of distribution*rate of elimination). This relation yields the unifying concept that serves as a prerequisite for a structured recording of 30 assigned pharmacokinetic and pharmacodynamic parameters within an informatic database. SOLUTIONS AND RESULTS: The information is retrieved and referenced from 2383 original publications by means of a standardized input module. The complete database at present contains 15,397 records for 1573 drugs. A programmed meta-analytic algorithm is used to calculate the statistical measures for the central value and variance--as available--from the pooled values of primary records. The statistically standardized parameters are extracted for 6601 pharmacokinetic parameters, and placed at the users disposal with the output module. PRACTICAL UTILITY: Following meta-analysis, published pharmacokinetics can be used as statistical estimates of population parameters. The statistical estimates with variances permit an individual drug dosage adjustment by applying the Bayesian approach or neural networks.

Algorithms↗

Fine-needle aspiration biopsy of the thyroid.

The routine use of thyroid FNAB caused profound changes in the management of thyroid nodules. FNAB allows a prompt identification and treatment of thyroid malignancies and avoids unnecessary surgery in patients with benign lesions, improving quality of life in patients with thyroid nodules. Furthermore, FNAB provides guidance for the type of surgery and reduces costs of care. On average, standard FNAB is nondiagnostic in 25% to 40% of cases, which include inadequate specimens and indeterminate (suspicious) diagnoses. In addition, a small percentage of false-negative diagnoses occur, which are unavoidable and raise concern of a late diagnosis of cancer. To minimize the limitations of FNAB, every center should reach and maintain a high standard of expertise in all of the steps of smear preparation and interpretation. Alternative modes of sampling or sample preparation may result in a reduction of nondiagnostic samples and better accuracy. Every center should set up clinical guidelines tailored to their own FNAB results and including the evaluation of clinical data. More work is needed to increase the accuracy of FNAB in suspicious cases. Toward this goal a variety of molecular markers have been evaluated; although none of them are ideal, some are promising. More studies need to be carried out in larger series to further evaluate the accuracy of these markers in identifying specific cancer histotypes within the group of suspicious lesions. It is hoped that, in the near future, the routine use of a combination of these markers will cost-effectively improve the diagnosis of malignant nodules classified as suspicious on traditional cytology. Statistical methods such as bayesian analysis or neural networks can be advantageously used to integrate different relevant information derived from family and personal history, clinical data, cytologic results, and evaluation of molecular markers.

Biopsy, Needle↗