Training Bayesian networks for image segmentation

We are concerned with the problem of image segmentation in which each pixel is assigned to one of a predefined finite number of classes. In Bayesian image analysis, this requires fusing together local predictions for the class labels with a prior model of segmentations. Markov Random Fields (MRFs) have been used to incorporate some of this prior knowledge, but this not entirely satisfactory as inference in MRFs is NP-hard. The multiscale quadtree model of Bouman and Shapiro (1994) is an attractive alternative, as this is a tree-structured belief network in which inference can be carried out in linear time (Pearl 1988). It is an hierarchical model where the bottom-level nodes are pixels, and higher levels correspond to downsampled versions of the image. The conditional-probability tables (CPTs) in the belief network encode the knowledge of how the levels interact. In this paper we discuss two methods of learning the CPTs given training data, using (a) maximum likelihood and the EM algorithm and (b) emphconditional maximum likelihood (CML). Segmentations obtained using networks trained by CML show a statistically-significant improvement in performance on synthetic images. We also demonstrate the methods on a real-world outdoor-scene segmentation task.

Finding structures in information networks using the affinity network

This thesis proposes a novel graphical model for inference called the Affinity Network,which displays the closeness between pairs of variables and is an alternative to Bayesian Networks and Dependency Networks. The Affinity Network shares some similarities with Bayesian Networks and Dependency Networks but avoids their heuristic and stochastic graph construction algorithms by using a message passing scheme. A comparison with the above two instances of graphical models is given for sparse discrete and continuous medical data and data taken from the UCI machine learning repository. The experimental study reveals that the Affinity Network graphs tend to be more accurate on the basis of an exhaustive search with the small datasets. Moreover, the graph construction algorithm is faster than the other two methods with huge datasets. The Affinity Network is also applied to data produced by a synchronised system. A detailed analysis and numerical investigation into this dynamical system is provided and it is shown that the Affinity Network can be used to characterise its emergent behaviour even in the presence of noise.

Dynamic decision networks for decision-making in self-adaptive systems:a case study

Bayesian decision theory is increasingly applied to support decision-making processes under environmental variability and uncertainty. Researchers from application areas like psychology and biomedicine have applied these techniques successfully. However, in the area of software engineering and speci?cally in the area of self-adaptive systems (SASs), little progress has been made in the application of Bayesian decision theory. We believe that techniques based on Bayesian Networks (BNs) are useful for systems that dynamically adapt themselves at runtime to a changing environment, which is usually uncertain. In this paper, we discuss the case for the use of BNs, speci?cally Dynamic Decision Networks (DDNs), to support the decision-making of self-adaptive systems. We present how such a probabilistic model can be used to support the decision making in SASs and justify its applicability. We have applied our DDN-based approach to the case of an adaptive remote data mirroring system. We discuss results, implications and potential bene?ts of the DDN to enhance the development and operation of self-adaptive systems, by providing mechanisms to cope with uncertainty and automatically make the best decision.

Alpha helical trans-membrane proteins:enhanced prediction using a Bayesian approach

Membrane proteins, which constitute approximately 20% of most genomes, are poorly tractable targets for experimental structure determination, thus analysis by prediction and modelling makes an important contribution to their on-going study. Membrane proteins form two main classes: alpha helical and beta barrel trans-membrane proteins. By using a method based on Bayesian Networks, which provides a flexible and powerful framework for statistical inference, we addressed alpha-helical topology prediction. This method has accuracies of 77.4% for prokaryotic proteins and 61.4% for eukaryotic proteins. The method described here represents an important advance in the computational determination of membrane protein topology and offers a useful, and complementary, tool for the analysis of membrane proteins for a range of applications.

Beta barrel trans-membrane proteins:enhanced prediction using a Bayesian approach

Membrane proteins, which constitute approximately 20% of most genomes, form two main classes: alpha helical and beta barrel transmembrane proteins. Using methods based on Bayesian Networks, a powerful approach for statistical inference, we have sought to address beta-barrel topology prediction. The beta-barrel topology predictor reports individual strand accuracies of 88.6%. The method outlined here represents a potentially important advance in the computational determination of membrane protein topology.

The application of methods of uncertain reasoning to the biological classification of river water quality

This thesis presents an investigation into the application of methods of uncertain reasoning to the biological classification of river water quality. Existing biological methods for reporting river water quality are critically evaluated, and the adoption of a discrete biological classification scheme advocated. Reasoning methods for managing uncertainty are explained, in which the Bayesian and Dempster-Shafer calculi are cited as primary numerical schemes. Elicitation of qualitative knowledge on benthic invertebrates is described. The specificity of benthic response to changes in water quality leads to the adoption of a sensor model of data interpretation, in which a reference set of taxa provide probabilistic support for the biological classes. The significance of sensor states, including that of absence, is shown. Novel techniques of directly eliciting the required uncertainty measures are presented. Bayesian and Dempster-Shafer calculi were used to combine the evidence provided by the sensors. The performance of these automatic classifiers was compared with the expert's own discrete classification of sampled sites. Variations of sensor data weighting, combination order and belief representation were examined for their effect on classification performance. The behaviour of the calculi under evidential conflict and alternative combination rules was investigated. Small variations in evidential weight and the inclusion of evidence from sensors absent from a sample improved classification performance of Bayesian belief and support for singleton hypotheses. For simple support, inclusion of absent evidence decreased classification rate. The performance of Dempster-Shafer classification using consonant belief functions was comparable to Bayesian and singleton belief. Recommendations are made for further work in biological classification using uncertain reasoning methods, including the combination of multiple-expert opinion, the use of Bayesian networks, and the integration of classification software within a decision support system for water quality assessment.

Toward bacterial protein sub-cellular location prediction:single-class discrimminant models for all gram- and gram+ compartments

Based on Bayesian Networks, methods were created that address protein sequence-based bacterial subcellular location prediction. Distinct predictive algorithms for the eight bacterial subcellular locations were created. Several variant methods were explored. These variations included differences in the number of residues considered within the query sequence - which ranged from the N-terminal 10 residues to the whole sequence - and residue representation - which took the form of amino acid composition, percentage amino acid composition, or normalised amino acid composition. The accuracies of the best performing networks were then compared to PSORTB. All individual location methods outperform PSORTB except for the Gram+ cytoplasmic protein predictor, for which accuracies were essentially equal, and for outer membrane protein prediction, where PSORTB outperforms the binary predictor. The method described here is an important new approach to method development for subcellular location prediction. It is also a new, potentially valuable tool for candidate subunit vaccine selection.

A predictor of membrane class:discriminating α-helical and β-barrel membrane proteins from non-membranous proteins

Accurate protein structure prediction remains an active objective of research in bioinformatics. Membrane proteins comprise approximately 20% of most genomes. They are, however, poorly tractable targets of experimental structure determination. Their analysis using bioinformatics thus makes an important contribution to their on-going study. Using a method based on Bayesian Networks, which provides a flexible and powerful framework for statistical inference, we have addressed the alignment-free discrimination of membrane from non-membrane proteins. The method successfully identifies prokaryotic and eukaryotic α-helical membrane proteins at 94.4% accuracy, β-barrel proteins at 72.4% accuracy, and distinguishes assorted non-membranous proteins with 85.9% accuracy. The method here is an important potential advance in the computational analysis of membrane protein structure. It represents a useful tool for the characterisation of membrane proteins with a wide variety of potential applications.

Combining algorithms to predict bacterial protein sub-cellular location:parallel versus concurrent implementations

We describe a novel and potentially important tool for candidate subunit vaccine selection through in silico reverse-vaccinology. A set of Bayesian networks able to make individual predictions for specific subcellular locations is implemented in three pipelines with different architectures: a parallel implementation with a confidence level-based decision engine and two serial implementations with a hierarchical decision structure, one initially rooted by prediction between membrane types and another rooted by soluble versus membrane prediction. The parallel pipeline outperformed the serial pipeline, but took twice as long to execute. The soluble-rooted serial pipeline outperformed the membrane-rooted predictor. Assessment using genomic test sets was more equivocal, as many more predictions are made by the parallel pipeline, yet the serial pipeline identifies 22 more of the 74 proteins of known location.

LIPPRED:a web server for accurate prediction of lipoprotein signal sequences and cleavage sites

Bacterial lipoproteins have many important functions and represent a class of possible vaccine candidates. The prediction of lipoproteins from sequence is thus an important task for computational vaccinology. Naïve-Bayesian networks were trained to identify SpaseII cleavage sites and their preceding signal sequences using a set of 199 distinct lipoprotein sequences. A comprehensive range of sequence models was used to identify the best model for lipoprotein signal sequences. The best performing sequence model was found to be 10-residues in length, including the conserved cysteine lipid attachment site and the nine residues prior to it. The sensitivity of prediction for LipPred was 0.979, while the specificity was 0.742. Here, we describe LipPred, a web server for lipoprotein prediction; available at the URL: http://www.jenner.ac.uk/LipPred/. LipPred is the most accurate method available for the detection of SpaseIIcleaved lipoprotein signal sequences and the prediction of their cleavage sites.

Handling high level of censoring for endovascular aortic repair risk prediction

Feature selection is important in medical field for many reasons. However, selecting important variables is a difficult task with the presence of censoring that is a unique feature in survival data analysis. This paper proposed an approach to deal with the censoring problem in endovascular aortic repair survival data through Bayesian networks. It was merged and embedded with a hybrid feature selection process that combines cox's univariate analysis with machine learning approaches such as ensemble artificial neural networks to select the most relevant predictive variables. The proposed algorithm was compared with common survival variable selection approaches such as; least absolute shrinkage and selection operator LASSO, and Akaike information criterion AIC methods. The results showed that it was capable of dealing with high censoring in the datasets. Moreover, ensemble classifiers increased the area under the roc curves of the two datasets collected from two centers located in United Kingdom separately. Furthermore, ensembles constructed with center 1 enhanced the concordance index of center 2 prediction compared to the model built with a single network. Although the size of the final reduced model using the neural networks and its ensembles is greater than other methods, the model outperformed the others in both concordance index and sensitivity for center 2 prediction. This indicates the reduced model is more powerful for cross center prediction.

Classification of oximetry signals using Bayesian neural networks to assist in the detection of obstructive sleep apnoea syndrome

In the present study, multilayer perceptron (MLP) neural networks were applied to help in the diagnosis of obstructive sleep apnoea syndrome (OSAS). Oxygen saturation (SaO2) recordings from nocturnal pulse oximetry were used for this purpose. We performed time and spectral analysis of these signals to extract 14 features related to OSAS. The performance of two different MLP classifiers was compared: maximum likelihood (ML) and Bayesian (BY) MLP networks. A total of 187 subjects suspected of suffering from OSAS took part in the study. Their SaO2 signals were divided into a training set with 74 recordings and a test set with 113 recordings. BY-MLP networks achieved the best performance on the test set with 85.58% accuracy (87.76% sensitivity and 82.39% specificity). These results were substantially better than those provided by ML-MLP networks, which were affected by overfitting and achieved an accuracy of 76.81% (86.42% sensitivity and 62.83% specificity). Our results suggest that the Bayesian framework is preferred to implement our MLP classifiers. The proposed BY-MLP networks could be used for early OSAS detection. They could contribute to overcome the difficulties of nocturnal polysomnography (PSG) and thus reduce the demand for these studies.

Bayesian training of mixture density networks

Mixture Density Networks (MDNs) are a well-established method for modelling the conditional probability density which is useful for complex multi-valued functions where regression methods (such as MLPs) fail. In this paper we extend earlier research of a regularisation method for a special case of MDNs to the general case using evidence based regularisation and we show how the Hessian of the MDN error function can be evaluated using R-propagation. The method is tested on two data sets and compared with early stopping.

Bayesian methods for neural networks

Bayesian techniques have been developed over many years in a range of different fields, but have only recently been applied to the problem of learning in neural networks. As well as providing a consistent framework for statistical pattern recognition, the Bayesian approach offers a number of practical advantages including a potential solution to the problem of over-fitting. This chapter aims to provide an introductory overview of the application of Bayesian methods to neural networks. It assumes the reader is familiar with standard feed-forward network models and how to train them using conventional techniques.

Bayesian methods for neural networks

Bayesian techniques have been developed over many years in a range of different fields, but have only recently been applied to the problem of learning in neural networks. As well as providing a consistent framework for statistical pattern recognition, the Bayesian approach offers a number of practical advantages including a potential solution to the problem of over-fitting. This chapter aims to provide an introductory overview of the application of Bayesian methods to neural networks. It assumes the reader is familiar with standard feed-forward network models and how to train them using conventional techniques.