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At least 199 records · Page 11Linked to original sources
PubMed2006

A Bayesian belief network for quality assessment: application to employment officer support.

BACKGROUND: 'Supported' employment stipulates that disabled people should have real jobs for real pay. This paper models kinds of supported employment, assesses how the support and placement features affect its outcomes and its quality from the perspective of the employees, and provides a dynamic model to help explore what types of interventions might promote greater social inclusion for people with learning and other disabilities. METHOD: Bayesian belief networks (BBNs) provide the general framework for modelling the relationships between the variables and features of interest. The structure, probabilistic specification and quality indicators were elicited from project advisory groups, including people with learning disability, and took into account a pilot survey of 30 individuals. A subsequent survey of 1,461 supported employees was used to update the model and to provide actual assessments of quality of placement. RESULTS: We present the BBN methodology in some detail, as novel to this discipline. We show how the model was constructed, and its implications for supported employment. We derive indices for quality of placement, taking into account the views of clients. We show how survey and individual results can be used to update the model. Use of the model suggests that quality of placement is, on average, relatively high, with small differences between groups with differing primary disability. CONCLUSIONS: The BBN is the appropriate methodology to model complex relationships and interventions for problems such as these. The model developed in this study can be used to assess and improve the fit between people and jobs, both at the individual level and for groups of employees, and can take into account different kinds of quality for different stakeholders.

Adult↗
PubMed2005

Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data.

MOTIVATION: The classification of high-dimensional data is always a challenge to statistical machine learning. We propose a novel method named shallow feature selection that assigns each feature a probability of being selected based on the structure of training data itself. Independent of particular classifiers, the high dimension of biodata can be fleetly reduced to an applicable case for consequential processing. Moreover, to improve both efficiency and performance of classification, these prior probabilities are further used to specify the distributions of top-level hyperparameters in hierarchical models of Bayesian neural network (BNN), as well as the parameters in Gaussian process models. RESULTS: Three BNN approaches were derived and then applied to identify ovarian cancer from NCI's high-resolution mass spectrometry data, which yielded an excellent performance in 1000 independent k-fold cross validations (k = 2,...,10). For instance, indices of average sensitivity and specificity of 98.56 and 98.42%, respectively, were achieved in the 2-fold cross validations. Furthermore, only one control and one cancer were misclassified in the leave-one-out cross validation. Some other popular classifiers were also tested for comparison. AVAILABILITY: The programs implemented in MatLab, R and Neal's fbm.2004-11-10.

Bayes Theorem↗
PubMed2006

Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles.

We propose a computational strategy for discovering gene networks affected by a chemical compound. Two kinds of DNA microarray data are assumed to be used: One dataset is short time-course data that measure responses of genes following an experimental treatment. The other dataset is obtained by several hundred single gene knock-downs. These two datasets provide three kinds of information; (i) A gene network is estimated from time-course data by the dynamic Bayesian network model, (ii) Relationships between the knocked-down genes and their regulatees are estimated directly from knock-down microarrays and (iii) A gene network can be estimated by gene knock-down data alone using the Bayesian network model. We propose a method that combines these three kinds of information to provide an accurate gene network that most strongly relates to the mode-of-action of the chemical compound in cells. This information plays an essential role in pharmacogenomics. We illustrate this method with an actual example where human endothelial cell gene networks were generated from a novel time course of gene expression following treatment with the drug fenofibrate, and from 270 novel gene knock-downs. Finally, we succeeded in inferring the gene network related to PPAR-alpha, which is a known target of fenofibrate.

Bayes Theorem↗
PubMed2005

Modularized learning of genetic interaction networks from biological annotations and mRNA expression data.

MOTIVATION: Inferring the genetic interaction mechanism using Bayesian networks has recently drawn increasing attention due to its well-established theoretical foundation and statistical robustness. However, the relative insufficiency of experiments with respect to the number of genes leads to many false positive inferences. RESULTS: We propose a novel method to infer genetic networks by alleviating the shortage of available mRNA expression data with prior knowledge. We call the proposed method 'modularized network learning' (MONET). Firstly, the proposed method divides a whole gene set to overlapped modules considering biological annotations and expression data together. Secondly, it infers a Bayesian network for each module, and integrates the learned subnetworks to a global network. An algorithm that measures a similarity between genes based on hierarchy, specificity and multiplicity of biological annotations is presented. The proposed method draws a global picture of inter-module relationships as well as a detailed look of intra-module interactions. We applied the proposed method to analyze Saccharomyces cerevisiae stress data, and found several hypotheses to suggest putative functions of unclassified genes. We also compared the proposed method with a whole-set-based approach and two expression-based clustering approaches.

Algorithms↗
PubMed2003

A Bayesian neural network approach for modelling censored data with an application to prognosis after surgery for breast cancer.

A Bayesian framework is introduced to carry out Automatic Relevance Determination (ARD) in feedforward neural networks to model censored data. A procedure to identify and interpret the prognostic group allocation is also described. These methodologies are applied to 1616 records routinely collected at Christie Hospital, in a monthly cohort study with 5-year follow-up. Two cohort studies are presented, for low- and high-risk patients allocated by standard clinical staging. The results of contrasting the Partial Logistic Artificial Neural Network (PLANN)-ARD model with the proportional hazards model are that the two are consistent, but the neural network may be more specific in the allocation of patients into prognostic groups. With automatic model selection, the regularised neural network is more conservative than the default stepwise forward selection procedure implemented by SPSS with the Akaike Information Criterion.

Bayes Theorem↗
PubMed2002

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.

MOTIVATION: Our goal is to construct a model for genetic regulatory networks such that the model class: (i) incorporates rule-based dependencies between genes; (ii) allows the systematic study of global network dynamics; (iii) is able to cope with uncertainty, both in the data and the model selection; and (iv) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes. RESULTS: We introduce Probabilistic Boolean Networks (PBN) that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty. We show how the dynamics of these networks can be studied in the probabilistic context of Markov chains, with standard Boolean networks being special cases. Then, we discuss the relationship between PBNs and Bayesian networks--a family of graphical models that explicitly represent probabilistic relationships between variables. We show how probabilistic dependencies between a gene and its parent genes, constituting the basic building blocks of Bayesian networks, can be obtained from PBNs. Finally, we present methods for quantifying the influence of genes on other genes, within the context of PBNs. Examples illustrating the above concepts are presented throughout the paper.

Cell Cycle↗
PubMed2002

A Bayesian attractor network with incremental learning.

A realtime online learning system with capacity limits needs to gradually forget old information in order to avoid catastrophic forgetting. This can be achieved by allowing new information to overwrite old, as in a so-called palimpsest memory. This paper describes an incremental learning rule based on the Bayesian confidence propagation neural network that has palimpsest properties when employed in an attractor neural network. The network does not suffer from catastrophic forgetting, has a capacity dependent on the learning time constant and exhibits faster convergence for newer patterns.

Bayes Theorem↗
PubMed2004

A biological network describing infection with Mycoplasma hyopneumoniae in swine herds.

We have made a biological model based on a Bayesian network for risk factors for infection with Mycoplasma hyopneumoniae (Mycoplasma) in slaughter pigs; prevalence of infection is based on veterinary examinations. The model is a probabilistic/stochastic determination based on the inherent biological uncertainty of the severity of infection with Mycoplasma and the derived stochastic effects on productivity for the herd. The conditional probabilities in the Bayesian network are based on published studies and expert opinions. We used the model to calculate how the risk factors and our evidence about the herd influenced our view on the severity of Mycoplasma, and how our view changed when we had more veterinary evidence. We also show how one can use the model to deal with conflicting examinations.

Abattoirs↗
PubMed1997

DIAS--the diabetes advisory system: an outline of the system and the evaluation results obtained so far.

The present paper gives a description of the Diabetes Advisory System (DIAS), and the evaluation results obtained so far. DIAS is a decision support system for the management of insulin dependent diabetes. The core of the system is a compartment model of the human carbohydrate metabolism implemented as a causal probabilistic network (CPN or Bayesian network), which gives it the ability to handle the uncertainty, for example, in blood glucose measurements or physiological variations in glucose metabolism. The evaluation results suggest that, at least in our hands, DIAS can generate advice that is safe and of a quality that is at least comparable to what is available from experienced clinicians.

Bayes Theorem↗
PubMed2003

A multi-agent intelligent environment for medical knowledge.

AMPLIA is a multi-agent intelligent learning environment designed to support training of diagnostic reasoning and modelling of domains with complex and uncertain knowledge. AMPLIA focuses on the medical area. It is a system that deals with uncertainty under the Bayesian network approach, where learner-modelling tasks will consist of creating a Bayesian network for a problem the system will present. The construction of a network involves qualitative and quantitative aspects. The qualitative part concerns the network topology, that is, causal relations among the domain variables. After it is ready, the quantitative part is specified. It is composed of the distribution of conditional probability of the variables represented. A negotiation process (managed by an intelligent MediatorAgent) will treat the differences of topology and probability distribution between the model the learner built and the one built-in in the system. That negotiation process occurs between the agents that represent the expert knowledge domain (DomainAgent) and the agent that represents the learner knowledge (LearnerAgent).

Artificial Intelligence↗
PubMed1999

Using probabilistic and decision-theoretic methods in treatment and prognosis modeling.

Causal probabilistic networks, also called Bayesian networks, allow both qualitative knowledge about the structure of a problem and quantitative knowledge, derived from case databases, expert opinion and literature to be exploited in the construction of decision support systems for diagnosis, treatment and prognosis. This mixing of qualitative and quantitative knowledge will be illustrated, using the selection of antibiotics for a subset of patients with severe infections. The subset consists of patients where bacteria or fungi have been found in the blood. A simple pathophysiological model of infection is used to calculate a prognosis, dependent on the choice of antibiotics. A decision-theoretic approach is used to balance the therapeutic benefit of antibiotic treatment against the cost of antibiotics in the form of direct monetary cost, side effects and ecological cost. A retrospective trial on patients with bacteria or fungi in the blood stemming from the urinary tract indicates that with this approach, it may be possible to suggest balanced choices of antibiotics that not only achieve greater therapeutic benefit, but also reduce the cost of therapy.

Anti-Bacterial Agents↗
PubMed1999

Medical data mining using evolutionary computation.

In this paper, we introduce a system for discovering medical knowledge by learning Bayesian networks and rules. Evolutionary computation is used as the search algorithm. The Bayesian networks can provide an overall structure of the relationships among the attributes. The rules can capture detailed and interesting patterns in the database. The system is applied to real-life medical databases for limb fracture and scoliosis. The knowledge discovered provides insights to and allows better understanding of these two medical domains.

Algorithms↗
PubMed2003

Connective molecular pathways of experimental bladder inflammation.

Inflammation is an inherent response of the organism that permits its survival despite constant environmental challenges. The process normally leads to recovery from injury and to healing. However, if targeted destruction and assisted repair are not properly phased, chronic inflammation can result in persistent tissue damage. To better understand the inflammatory process, we recently introduced a profiling methodology to identify common genes involved in bladder inflammation. The method represents a complementation to the classic quantification of inflammation and provides information regarding the early, intermediate, and late events in gene regulation. However, gene profiling fails to describe the molecular pathways and their interconnections involved in the particular inflammatory response. The present work introduces a new statistical technique for inferring functional interconnections between inflammatory pathways underlying classic models of bladder inflammation and permits the modeling of the inflammatory network. This new statistical method is based on variants of cluster analysis, Boolean networking, differential equations, Bayesian networking, and partial correlation. By applying partial correlation analysis, we developed mosaics of gene expression that permitted a global visualization of common and unique pathways elicited by different stimuli. The significance of these processes was tested from both biological and statistical viewpoints. We propose that connective mosaic may represent the necessary simplification step to visualize cDNA array results.

Animals↗
PubMed2025

Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

BACKGROUND: Inflammation is a key driver of atherosclerosis, yet the mechanisms sustaining inflammation in human plaques remain poorly understood. This study uses a network-based approach to identify immune gene programs involved in the transition from low- to high-risk (rupture-prone) human atherosclerotic plaques. METHODS: Expression data from human carotid artery plaques, both stable (low-risk, n = 16) and unstable (high-risk, n = 27), were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA). Bayesian network inference, operated on the eigengene values from the WGCNA, further extended the WGCNA analysis, and similarity to the signature of T cell subsets was validated in single-cell RNA sequencing data of human plaques, and a loss-of-function study in a mouse model of atherosclerosis. In silico drug repurposing was performed to identify potential therapeutic targets. RESULTS: Our analysis revealed a distinct gene module with a prominent T cell signature, particularly in unstable plaques. Key regulatory factors, RUNX3, IRF7 and in particular PRDM1, were significantly downregulated in plaque T cells from symptomatic versus asymptomatic patients, indicating a protective role. Additionally, as PRDM1 is downstream of IRF7, we opted for PRDM1 as a key target. T cell-specific Prdm1 deficiency in Western-type diet fed Ldlr knockout mice featured accelerated plaque progression. Finally, as PRDM1 targeting drugs are not yet available, we performed in silico drug repurposing, identifying EGFR inhibitors as promising therapeutic candidates. CONCLUSIONS: This study highlights a PRDM1-regulated T cell network that distinguishes high-risk from low-risk plaques and demonstrates the regulatory role of T cell PRDM1 in controlling atherosclerosis, positioning this pathway as a promising therapeutic target.

Plaque, Atherosclerotic↗
PubMed2001

Probabilistic neural networks using Bayesian decision strategies and a modified Gompertz model for growth phase classification in the batch culture of Bacillus subtilis.

Probabilistic neural networks (PNNs) were used in conjunction with the Gompertz model for bacterial growth to classify the lag, logarithmic, and stationary phases in a batch process. Using the fermentation time and the optical density of diluted cell suspensions, sampled from a culture of Bacillus subtilis, PNNs enabled a reliable determination of the growth phases. Based on a Bayesian decision strategy, the Gompertz based PNN used newly proposed definition of the lag and logarithmic phases to estimate the latent, logarithmic and stationary phases. This network topology has the potential for use with on-line turbidimeter for the automation and control of cultivation processes.

Journal Article↗
PubMed2006

Cross-species analysis of biological networks by Bayesian alignment.

Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by alignment, which maps bona fide functional relationships between genes in different organisms. Network alignment is based on a scoring function measuring mutual similarities between networks, taking into account their interaction patterns as well as sequence similarities between their nodes. High-scoring alignments and optimal alignment parameters are inferred by a systematic Bayesian analysis. We apply this method to analyze the evolution of coexpression networks between humans and mice. We find evidence for significant conservation of gene expression clusters and give network-based predictions of gene function. We discuss examples where cross-species functional relationships between genes do not concur with sequence similarity.

Algorithms↗
PubMed2004

A Bayesian morphometry algorithm.

Most methods for structure-function analysis of the brain in medical images are usually based on voxel-wise statistical tests performed on registered magnetic resonance (MR) images across subjects. A major drawback of such methods is the inability to accurately locate regions that manifest nonlinear associations with clinical variables. In this paper, we propose Bayesian morphological analysis methods, based on a Bayesian-network representation, for the analysis of MR brain images. First, we describe how Bayesian networks (BNs) can represent probabilistic associations among voxels and clinical (function) variables. Second, we present a model-selection framework, which generates a BN that captures structure-function relationships from MR brain images and function variables. We demonstrate our methods in the context of determining associations between regional brain atrophy (as demonstrated on MR images of the brain), and functional deficits. We employ two data sets for this evaluation: the first contains MR images of 11 subjects, where associations between regional atrophy and a functional deficit are almost linear; the second data set contains MR images of the ventricles of 84 subjects, where the structure-function association is nonlinear. Our methods successfully identify voxel-wise morphological changes that are associated with functional deficits in both data sets, whereas standard statistical analysis (i.e., t-test and paired t-test) fails in the nonlinear-association case.

Aged↗
PubMed1998

A Bayesian neural network method for adverse drug reaction signal generation.

OBJECTIVE: The database of adverse drug reactions (ADRs) held by the Uppsala Monitoring Centre on behalf of the 47 countries of the World Health Organization (WHO) Collaborating Programme for International Drug Monitoring contains nearly two million reports. It is the largest database of this sort in the world, and about 35,000 new reports are added quarterly. The task of trying to find new drug-ADR signals has been carried out by an expert panel, but with such a large volume of material the task is daunting. We have developed a flexible, automated procedure to find new signals with known probability difference from the background data. METHOD: Data mining, using various computational approaches, has been applied in a variety of disciplines. A Bayesian confidence propagation neural network (BCPNN) has been developed which can manage large data sets, is robust in handling incomplete data, and may be used with complex variables. Using information theory, such a tool is ideal for finding drug-ADR combinations with other variables, which are highly associated compared to the generality of the stored data, or a section of the stored data. The method is transparent for easy checking and flexible for different kinds of search. RESULTS: Using the BCPNN, some time scan examples are given which show the power of the technique to find signals early (captopril-coughing) and to avoid false positives where a common drug and ADRs occur in the database (digoxin-acne; digoxin-rash). A routine application of the BCPNN to a quarterly update is also tested, showing that 1004 suspected drug-ADR combinations reached the 97.5% confidence level of difference from the generality. Of these, 307 were potentially serious ADRs, and of these 53 related to new drugs. Twelve of the latter were not recorded in the CD editions of The physician's Desk Reference or Martindale's Extra Pharmacopoea and did not appear in Reactions Weekly online. CONCLUSION: The results indicate that the BCPNN can be used in the detection of significant signals from the data set of the WHO Programme on International Drug Monitoring. The BCPNN will be an extremely useful adjunct to the expert assessment of very large numbers of spontaneously reported ADRs.

Adverse Drug Reaction Reporting Systems↗