Particle Swarm Optimisation for learning Bayesian Networks

This paper discusses the potential of Particle Swarm Optimisation (PSO) for inducing Bayesian Networks (BNs). Specifically, we detail two methods which adopt the search and score approach to BN learning. The two algorithms are similar in that they both use PSO as the search algorithm, and the K2 metric to score the resulting network. The difference lies in the way networks are constructed. The CONstruct And Repair (CONAR) algorithm generates structures, validates, and repairs if required, and the REstricted STructure (REST) algorithm, only permits valid structures to be developed. Initial experiments indicate that these approaches produce promising results when compared to other BN learning strategies

The computational neurology of active vision

In this thesis, we appeal to recent developments in theoretical neurobiology – namely, active inference – to understand the active visual system and its disorders. Chapter 1 reviews the neurobiology of active vision. This introduces some of the key conceptual themes around attention and inference that recur through subsequent chapters. Chapter 2 provides a technical overview of active inference, and its interpretation in terms of message passing between populations of neurons. Chapter 3 applies the material in Chapter 2 to provide a computational characterisation of the oculomotor system. This deals with two key challenges in active vision: deciding where to look, and working out how to look there. The homology between this message passing and the brain networks solving these inference problems provide a basis for in silico lesion experiments, and an account of the aberrant neural computations that give rise to clinical oculomotor signs (including internuclear ophthalmoplegia). Chapter 4 picks up on the role of uncertainty resolution in deciding where to look, and examines the role of beliefs about the quality (or precision) of data in perceptual inference. We illustrate how abnormal prior beliefs influence inferences about uncertainty and give rise to neuromodulatory changes and visual hallucinatory phenomena (of the sort associated with synucleinopathies). We then demonstrate how synthetic pharmacological perturbations that alter these neuromodulatory systems give rise to the oculomotor changes associated with drugs acting upon these systems. Chapter 5 develops a model of visual neglect, using an oculomotor version of a line cancellation task. We then test a prediction of this model using magnetoencephalography and dynamic causal modelling. Chapter 6 concludes by situating the work in this thesis in the context of computational neurology. This illustrates how the variational principles used here to characterise the active visual system may be generalised to other sensorimotor systems and their disorders

Подходы к диагностике согласованности данных в байесовских сетях доверия

Bayesian belief networks provide the ability to combine different types of information, e.g. statistical or expert data, allow working with incomplete or inaccurate information; they have clarity and other useful properties. Due to this, Bayesian belief networks have become a popular and highly effective tool in many fields of research. However, in many research areas data provided by the experts can be incoherent, and so in some tasks one should use tools to verify their coherence. The paper discusses examples of application of the Bayesian belief networks in medicine and public health, ecology, economics and risk analysis, functional safety, sociology, and other research areas, and shows the need to develop methods to check the coherence of initial data. The purpose of this work is to systematize problems and examples that illustrate the use of Bayesian belief networks by reviewing and to assess their use of data coherence diagnosis and its importance.Байесовские сети доверия предоставляют возможность объединения нескольких видов информации, например полученной от экспертов или статистически, позволяют работать с неполной или неточной информацией, обладают наглядностью и другими полезными свойствами. Благодаря этому они стали популярным и весьма эффективным инструментом. Однако во многих областях исследования исходные используются полученные от экспертов данные, которые могут быть не согласованы, и поэтому в некоторых задачах следует использовать инструменты для проверки их согласованности. В работе рассмотрены примеры применения аппарата байесовских сетей доверия в медицине и здравоохранении, экологии, экономике и риск-анализе, функциональной безопасности, социологии и других предметных областях и показана необходимость разработки методов для проверки согласованности исходных данных. Цель работы – систематизировать с помощью обзора примеры и задачи, в которых применяются байесовские сети доверия, чтобы оценить, в какой степени в этих задачах учитывается диагностика согласованности исходных данных, и насколько важным является ее применение

Significant Gene Array Analysis and Cluster-Based Machine Learning for Disease Class Prediction

Gene expression analysis has been of major interest to biostatisticians for many decades. Such studies are necessary for the understanding of disease risk assessment and prediction, so that medical professionals and scientists alike may learn how to better create treatment plans to lessen symptoms and perhaps even find cures. In this study, we will investigate various gene expression analyses and machine learning techniques for disease class prediction, as well as assess predictive validity of these models and uncover differentially expressed (DE) genes for their relevant pathology datasets. Multiple gene expression datasets will be used to test model accuracies and will be obtained using the Affymetrix U133A platform (GPL96). Significant Analysis of Microarrays (SAM) had been used to identify potential disease biomarkers, followed by these predictive models: (a) random forest, (b) random forest with Gene eXpression Network Analysis (GXNA), (c) RF++, (d) LASSO, and (e) Bayesian Neural Networks. One of the intended goals for this study is to find clusters of co-expressed genes and identify the effect of clustering classification based on knowledge in gene expression data/microarray data. The other goal is to determine the usefulness of Automatic Relevancy Determination in Bayesian neural networks

Predictive cognition in dementia: the case of music

The clinical complexity and pathological diversity of neurodegenerative diseases impose immense challenges for diagnosis and the design of rational interventions. To address these challenges, there is a need to identify new paradigms and biomarkers that capture shared pathophysiological processes and can be applied across a range of diseases. One core paradigm of brain function is predictive coding: the processes by which the brain establishes predictions and uses them to minimise prediction errors represented as the difference between predictions and actual sensory inputs. The processes involved in processing unexpected events and responding appropriately are vulnerable in common dementias but difficult to characterise. In my PhD work, I have exploited key properties of music – its universality, ecological relevance and structural regularity – to model and assess predictive cognition in patients representing major syndromes of frontotemporal dementia – non-fluent variant PPA (nfvPPA), semantic-variant PPA (svPPA) and behavioural-variant FTD (bvFTD) - and Alzheimer’s disease relative to healthy older individuals. In my first experiment, I presented patients with well-known melodies containing no deviants or one of three types of deviant - acoustic (white-noise burst), syntactic (key-violating pitch change) or semantic (key-preserving pitch change). I assessed accuracy detecting melodic deviants and simultaneously-recorded pupillary responses to these deviants. I used voxel-based morphometry to define neuroanatomical substrates for the behavioural and autonomic processing of these different types of deviants, and identified a posterior temporo-parietal network for detection of basic acoustic deviants and a more anterior fronto-temporo-striatal network for detection of syntactic pitch deviants. In my second chapter, I investigated the ability of patients to track the statistical structure of the same musical stimuli, using a computational model of the information dynamics of music to calculate the information-content of deviants (unexpectedness) and entropy of melodies (uncertainty). I related these information-theoretic metrics to performance for detection of deviants and to ‘evoked’ and ‘integrative’ pupil reactivity to deviants and melodies respectively and found neuroanatomical correlates in bilateral dorsal and ventral striatum, hippocampus, superior temporal gyri, right temporal pole and left inferior frontal gyrus. Together, chapters 3 and 4 revealed new hypotheses about the way FTD and AD pathologies disrupt the integration of predictive errors with predictions: a retained ability of AD patients to detect deviants at all levels of the hierarchy with a preserved autonomic sensitivity to information-theoretic properties of musical stimuli; a generalized impairment of surprise detection and statistical tracking of musical information at both a cognitive and autonomic levels for svPPA patients underlying a diminished precision of predictions; the exact mirror profile of svPPA patients in nfvPPA patients with an abnormally high rate of false-alarms with up-regulated pupillary reactivity to deviants, interpreted as over-precise or inflexible predictions accompanied with normal cognitive and autonomic probabilistic tracking of information; an impaired behavioural and autonomic reactivity to unexpected events with a retained reactivity to environmental uncertainty in bvFTD patients. Chapters 5 and 6 assessed the status of reward prediction error processing and updating via actions in bvFTD. I created pleasant and aversive musical stimuli by manipulating chord progressions and used a classic reinforcement-learning paradigm which asked participants to choose the visual cue with the highest probability of obtaining a musical ‘reward’. bvFTD patients showed reduced sensitivity to the consequence of an action and lower learning rate in response to aversive stimuli compared to reward. These results correlated with neuroanatomical substrates in ventral and dorsal attention networks, dorsal striatum, parahippocampal gyrus and temporo-parietal junction. Deficits were governed by the level of environmental uncertainty with normal learning dynamics in a structured and binarized environment but exacerbated deficits in noisier environments. Impaired choice accuracy in noisy environments correlated with measures of ritualistic and compulsive behavioural changes and abnormally reduced learning dynamics correlated with behavioural changes related to empathy and theory-of-mind. Together, these experiments represent the most comprehensive attempt to date to define the way neurodegenerative pathologies disrupts the perceptual, behavioural and physiological encoding of unexpected events in predictive coding terms

Network Modeling Sex Differences in Brain Integrity and Metabolic Health

Hypothesis-driven studies have demonstrated that sex moderates many of the relationships between brain health and cardiometabolic disease, which impacts risk for later-life cognitive decline. In the present study, we sought to further our understanding of the associations between multiple markers of brain integrity and cardiovascular risk in a midlife sample of 266 individuals by using network analysis, a technique specifically designed to examine complex associations among multiple systems at once. Separate network models were constructed for male and female participants to investigate sex differences in the biomarkers of interest, selected based on evidence linking them with risk for late-life cognitive decline: all components of metabolic syndrome (obesity, hypertension, dyslipidemia, and hyperglycemia); neuroimaging-derived brain-predicted age minus chronological age; ratio of white matter hyperintensities to whole brain volume; seed-based resting state functional connectivity in the Default Mode Network, and ratios of N-acetyl aspartate, glutamate and myo-inositol to creatine, measured through proton magnetic resonance spectroscopy. Males had a sparse network (87.2% edges = 0) relative to females (69.2% edges = 0), indicating fewer relationships between measures of cardiometabolic risk and brain integrity. The edges in the female network provide meaningful information about potential mechanisms between brain integrity and cardiometabolic health. Additionally, Apolipoprotein ϵ4 (ApoE ϵ4) status and waist circumference emerged as central nodes in the female model. Our study demonstrates that network analysis is a promising technique for examining relationships between risk factors for cognitive decline in a midlife population and that investigating sex differences may help optimize risk prediction and tailor individualized treatments in the future