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PubMed2005

The evaluation of evidence in the forensic investigation of fire incidents. Part II. Practical examples of the use of Bayesian networks.

This paper extends a previous discussion of the use of Bayesian networks for evaluating evidence in the forensic investigation of fire incidents. Bayesian networks are proposed for two casework examples and the practical implications studied in detail. Such networks were found to provide precious support in addressing some of the wide range of issues that affect the coherent evaluation of evidence.

Journal Article↗
PubMed2006

A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae.

The transcriptional response to exogenously supplied nitric oxide in Saccharomyces cerevisiae was modeled using an integrated framework of Bayesian network learning and experimental feedback. A Bayesian network learning algorithm was used to generate network models of transcriptional output, followed by model verification and revision through experimentation. Using this framework, we generated a network model of the yeast transcriptional response to nitric oxide and a panel of other environmental signals. We discovered two environmental triggers, the diauxic shift and glucose repression, that affected the observed transcriptional profile. The computational method predicted the transcriptional control of yeast flavohemoglobin YHB1 by glucose repression, which was subsequently experimentally verified. A freely available software application, ExpressionNet, was developed to derive Bayesian network models from a combination of gene expression profile clusters, genetic information and experimental conditions.

Algorithms↗
PubMed2004

Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data.

We propose a dynamic Bayesian network and nonparametric regression model for constructing a gene network from time series microarray gene expression data. The proposed method can overcome a shortcoming of the Bayesian network model in the sense of the construction of cyclic regulations. The proposed method can analyze the microarray data as a continuous data and can capture even nonlinear relations among genes. It can be expected that this model will give a deeper insight into complicated biological systems. We also derive a new criterion for evaluating an estimated network from Bayes approach. We conduct Monte Carlo experiments to examine the effectiveness of the proposed method. We also demonstrate the proposed method through the analysis of the Saccharomyces cerevisiae gene expression data.

Bayes Theorem↗
PubMed2005

Identification of transcription factor binding sites with variable-order Bayesian networks.

MOTIVATION: We propose a new class of variable-order Bayesian network (VOBN) models for the identification of transcription factor binding sites (TFBSs). The proposed models generalize the widely used position weight matrix (PWM) models, Markov models and Bayesian network models. In contrast to these models, where for each position a fixed subset of the remaining positions is used to model dependencies, in VOBN models, these subsets may vary based on the specific nucleotides observed, which are called the context. This flexibility turns out to be of advantage for the classification and analysis of TFBSs, as statistical dependencies between nucleotides in different TFBS positions (not necessarily adjacent) may be taken into account efficiently--in a position-specific and context-specific manner. RESULTS: We apply the VOBN model to a set of 238 experimentally verified sigma-70 binding sites in Escherichia coli. We find that the VOBN model can distinguish these 238 sites from a set of 472 intergenic 'non-promoter' sequences with a higher accuracy than fixed-order Markov models or Bayesian trees. We use a replicated stratified-holdout experiment having a fixed true-negative rate of 99.9%. We find that for a foreground inhomogeneous VOBN model of order 1 and a background homogeneous variable-order Markov (VOM) model of order 5, the obtained mean true-positive (TP) rate is 47.56%. In comparison, the best TP rate for the conventional models is 44.39%, obtained from a foreground PWM model and a background 2nd-order Markov model. As the standard deviation of the estimated TP rate is approximately 0.01%, this improvement is highly significant.

Algorithms↗
PubMed2006

Predicting the outcome of pregnancies of unknown location: Bayesian networks with expert prior information compared to logistic regression.

BACKGROUND: As women present at earlier gestations to early pregnancy units (EPUs), the number of women diagnosed with a pregnancy of unknown location (PUL) increases. Some of these women will have an ectopic pregnancy (EP), and it is this group in the PUL population that poses the greatest concern. The aim of this study was to develop Bayesian networks to predict EPs in the PUL population. METHODS: Data were gathered in a single EPU from all women with a PUL. This data set was divided into a model-building (599 women with 44 EPs) and a validation (257 women with 22 EPs) data set and consisted of the following variables: vaginal bleeding, fluid in the pouch of Douglas, midline echo, lower abdominal pain, age, endometrial thickness, gestation days, the ratio of HCG at 48 and 0 h, progesterone levels (0 and 48 h) and the clinical outcome of the PUL. We developed Bayesian networks with expert information using this data set to predict EPs. RESULTS: The best Bayesian network used the gestational age, HCG ratio and the progesterone level at 48 h and had an area under the receiver operator characteristic curve (AUC) of 0.88 for predicting EPs when tested prospectively. CONCLUSIONS: Discrete-valued Bayesian networks are more complex to build than, for example, logistic regression. Nevertheless, we have demonstrated that such models can be used to predict EPs in a PUL population. Prospective interventional multicentre studies are needed to validate the use of such models in clinical practice.

Adolescent↗
PubMed2001

A Bayesian network for diagnosis of primary bone tumors.

The authors developed a Bayesian network to differentiate among five benign and five malignant neoplasms of the appendicular skeleton using the patient's age and sex and 17 radiographic characteristics. In preliminary evaluation with physicians in training, the model identified the correct diagnosis in 19 cases (68%), and included the correct diagnosis among the two most probable diagnoses in 25 cases (89%). Bayesian networks can capture and apply knowledge of primary bone neoplasms. Further testing and refinement of the model are underway.

Bayes Theorem↗
PubMed2004

A general approach to Bayesian networks for the interpretation of evidence.

Bayesian networks (BNs) are mathematically and statistically rigorous techniques for handling uncertainty. The field of forensic science has recently attributed increased attention to the many advantages of this graphical method for assisting the evaluation of scientific evidence. However, the majority of contributions that relate to this topic restrict themselves to the presentation of already "constructed" BNs, and often, only a few explanations are given as to how one obtains a specific BN structure for a given problem. Based on several examples, the present paper will therefore attempt to explain in more detail some guiding considerations that might be helpful for the elicitation of appropriate structures for BNs.

Bayes Theorem↗
PubMed2004

A comparison of learning algorithms for Bayesian networks: a case study based on data from an emergency medical service.

Due to the uncertainty of many of the factors that influence the performance of an emergency medical service, we propose using Bayesian networks to model this kind of system. We use different algorithms for learning Bayesian networks in order to build several models, from the hospital manager's point of view, and apply them to the specific case of the emergency service of a Spanish hospital. This first study of a real problem includes preliminary data processing, the experiments carried out, the comparison of the algorithms from different perspectives, and some potential uses of Bayesian networks for management problems in the health service.

Algorithms↗
PubMed1994

A Bayesian network model for radiological diagnosis and procedure selection: work-up of suspected gallbladder disease.

Bayesian networks, a technique for reasoning under uncertainty, currently are being developed for application to medical decision making. To explore their usefulness for radiologic decision support, a Bayesian belief network was constructed in the domain of hepatobiliary disease. The network model's nodes represent diagnoses, physical findings, laboratory test results, and imaging study findings. The connections between nodes incorporate conditional probabilities, such as sensitivity and specificity, to represent probabilistic influences. Statistical data were abstracted from peer-reviewed journal articles on hepatobiliary disease, and a network was created to reflect the data. The network successfully determined the a priori probabilities of various diseases, and incorporated laboratory and imaging results to calculate the a posteriori probabilities. The most informative examination was identified, that is, the laboratory study or imaging procedure that led to the greatest diagnostic certainty. Bayesian networks represent a very promising technique for decision support in radiology: they can assist physicians in formulating diagnoses and in selecting imaging procedures.

Adult↗
PubMed2006

Insights into protein-protein interfaces using a Bayesian network prediction method.

Identifying the interface between two interacting proteins provides important clues to the function of a protein, and is becoming increasing relevant to drug discovery. Here, surface patch analysis was combined with a Bayesian network to predict protein-protein binding sites with a success rate of 82% on a benchmark dataset of 180 proteins, improving by 6% on previous work and well above the 36% that would be achieved by a random method. A comparable success rate was achieved even when evolutionary information was missing, a further improvement on our previous method which was unable to handle incomplete data automatically. In a case study of the Mog1p family, we showed that our Bayesian network method can aid the prediction of previously uncharacterised binding sites and provide important clues to protein function. On Mog1p itself a putative binding site involved in the SLN1-SKN7 signal transduction pathway was detected, as was a Ran binding site, previously characterized solely by conservation studies, even though our automated method operated without using homologous proteins. On the remaining members of the family (two structural genomics targets, and a protein involved in the photosystem II complex in higher plants) we identified novel binding sites with little correspondence to those on Mog1p. These results suggest that members of the Mog1p family bind to different proteins and probably have different functions despite sharing the same overall fold. We also demonstrated the applicability of our method to drug discovery efforts by successfully locating a number of binding sites involved in the protein-protein interaction network of papilloma virus infection. In a separate study, we attempted to distinguish between the two types of binding site, obligate and non-obligate, within our dataset using a second Bayesian network. This proved difficult although some separation was achieved on the basis of patch size, electrostatic potential and conservation. Such was the similarity between the two interacting patch types, we were able to use obligate binding site properties to predict the location of non-obligate binding sites and vice versa.

Animals↗
PubMed1997

BANTER: a Bayesian network tutoring shell.

We present an educational tool for bringing the information contained in a Bayesian network to the end user in an easily intelligible form. The BANTER shell is designed to tutor users in evaluation of hypotheses and selection of optimal diagnostic procedures. BANTER can be used with any Bayesian network containing nodes that can be classified into hypotheses, observations, and diagnostic procedures. The system enables one to present various types of queries to the network, to test one's ability to select optimal diagnostic procedures, and the request explanations. We describe the system's capabilities by illustrating how it functions with two structurally different network models of real-world medical problems.

Adult↗
PubMed2005

Bayesian network learning with feature abstraction for gene-drug dependency analysis.

Combined analysis of the microarray and drug-activity datasets has the potential of revealing valuable knowledge about various relations among gene expressions and drug activities in the malignant cell. In this paper, we apply Bayesian networks, a tool for compact representation of the joint probability distribution, to such analysis. For the alleviation of data dimensionality problem, the huge datasets were condensed using a feature abstraction technique. The proposed analysis method was applied to the NCI60 dataset (http://discover.nci.nih.gov) consisting of gene expression profiles and drug activity patterns on human cancer cell lines. The Bayesian networks, learned from the condensed dataset, identified most of the salient pairwise correlations and some known relationships among several features in the original dataset, confirming the effectiveness of the proposed feature abstraction method. Also, a survey of the recent literature confirms the several relationships appearing in the learned Bayesian network to be biologically meaningful.

Algorithms↗
PubMed2006

Applying dynamic Bayesian networks to perturbed gene expression data.

BACKGROUND: A central goal of molecular biology is to understand the regulatory mechanisms of gene transcription and protein synthesis. Because of their solid basis in statistics, allowing to deal with the stochastic aspects of gene expressions and noisy measurements in a natural way, Bayesian networks appear attractive in the field of inferring gene interactions structure from microarray experiments data. However, the basic formalism has some disadvantages, e.g. it is sometimes hard to distinguish between the origin and the target of an interaction. Two kinds of microarray experiments yield data particularly rich in information regarding the direction of interactions: time series and perturbation experiments. In order to correctly handle them, the basic formalism must be modified. For example, dynamic Bayesian networks (DBN) apply to time series microarray data. To our knowledge the DBN technique has not been applied in the context of perturbation experiments. RESULTS: We extend the framework of dynamic Bayesian networks in order to incorporate perturbations. Moreover, an exact algorithm for inferring an optimal network is proposed and a discretization method specialized for time series data from perturbation experiments is introduced. We apply our procedure to realistic simulations data. The results are compared with those obtained by standard DBN learning techniques. Moreover, the advantages of using exact learning algorithm instead of heuristic methods are analyzed. CONCLUSION: We show that the quality of inferred networks dramatically improves when using data from perturbation experiments. We also conclude that the exact algorithm should be used when it is possible, i.e. when considered set of genes is small enough.

Algorithms↗
PubMed2005

Risk analysis of a patient monitoring system using Bayesian Network modeling.

In a modern technological environment where information systems are characterized by complexity, situations of non-effective operation should be anticipated. Often system failures are a result of insufficient planning or equipment malfunction, indicating that it is essential to develop techniques for predicting and addressing a system failure. Particularly for safety-critical applications such as the healthcare information systems, which are dealing with human health, risk analysis should be considered a necessity. This paper presents a new method for performing a risk analysis study of health information systems. Specifically, the CCTA Risk Analysis and Management Methodology (CRAMM) has been utilized for identifying and valuating the assets, threats, and vulnerabilities of the information system, followed by a graphical modeling of their interrelationships using Bayesian Networks. The proposed method exploits the results of the CRAMM-based risk analysis for developing a Bayesian Network model, which presents concisely all the interactions of the undesirable events for the system. Based on "what-if" studies of system operation, the Bayesian Network model identifies and prioritizes the most critical events. The proposed risk analysis framework has been applied to a vital signs monitoring information system for homecare telemedicine, namely the VITAL-Home System, developed and maintained for a private medical center (Medical Diagnosis and Treatment S.A.).

Bayes Theorem↗
PubMed1994

Mixed Bayesian networks: a mixture of Gaussian distributions.

Mixed Bayesian networks are probabilistic models associated with a graphical representation, where the graph is directed and the random variables are discrete or continuous. We propose a comprehensive method for estimating the density functions of continuous variables, using a graph structure and a set of samples. The principle of the method is to learn the shape of densities from a sample of continuous variables. The densities are approximated by a mixture of Gaussian distributions. The estimation algorithm is a stochastic version of the Expectation Maximization algorithm (Stochastic EM algorithm). The inference algorithm corresponding to our model is a variant of junction three method, adapted to our specific case. The approach is illustrated by a simulated example from the domain of pharmacokinetics. Tests show that the true distributions seem sufficiently fitted for practical application.

Algorithms↗
PubMed2005

Bayesian networks: computer-assisted diagnosis support in radiology.

Medical knowledge is growing at an explosive rate. While the availability of pertinent data has the potential to make the task of diagnosis more accurate, it is also increasingly overwhelming for physicians to assimilate. Using artificial intelligence techniques, a computer can process large amounts of data to help physicians manage the growing body of medical knowledge and thereby make better decisions. Computer-assisted diagnosis support is of particular interest to the diagnostic imaging community because radiologists must integrate huge amounts of data in order to diagnose disease. Bayesian networks, among the most promising artificial intelligence techniques available, enable computers to store knowledge and estimate the probability of outcomes based on probability theory. The article describes what a Bayesian network is and how it works using a system in mammography for illustration. A comparison of Bayesian networks with other types of artificial intelligence methods, specifically neural networks and case-based reasoning, clarifies the unique features and the potential of these systems to aid radiologists in the decisions they make every day.

Bayes Theorem↗
PubMed2003

Application of a data-mining method based on Bayesian networks to lesion-deficit analysis.

Although lesion-deficit analysis (LDA) has provided extensive information about structure-function associations in the human brain, LDA has suffered from the difficulties inherent to the analysis of spatial data, i.e., there are many more variables than subjects, and data may be difficult to model using standard distributions, such as the normal distribution. We herein describe a Bayesian method for LDA; this method is based on data-mining techniques that employ Bayesian networks to represent structure-function associations. These methods are computationally tractable, and can represent complex, nonlinear structure-function associations. When applied to the evaluation of data obtained from a study of the psychiatric sequelae of traumatic brain injury in children, this method generates a Bayesian network that demonstrates complex, nonlinear associations among lesions in the left caudate, right globus pallidus, right side of the corpus callosum, right caudate, and left thalamus, and subsequent development of attention-deficit hyperactivity disorder, confirming and extending our previous statistical analysis of these data. Furthermore, analysis of simulated data indicates that methods based on Bayesian networks may be more sensitive and specific for detecting associations among categorical variables than methods based on chi-square and Fisher exact statistics.

Algorithms↗
PubMedDate not supplied

Bayesian networks for knowledge discovery in large datasets: basics for nurse researchers.

The growth of nursing databases necessitates new approaches to data analyses. These databases, which are known to be massive and multidimensional, easily exceed the capabilities of both human cognition and traditional analytical approaches. One innovative approach, knowledge discovery in large databases (KDD), allows investigators to analyze very large data sets more comprehensively in an automatic or a semi-automatic manner. Among KDD techniques, Bayesian networks, a state-of-the art representation of probabilistic knowledge by a graphical diagram, has emerged in recent years as essential for pattern recognition and classification in the healthcare field. Unlike some data mining techniques, Bayesian networks allow investigators to combine domain knowledge with statistical data, enabling nurse researchers to incorporate clinical and theoretical knowledge into the process of knowledge discovery in large datasets. This tailored discussion presents the basic concepts of Bayesian networks and their use as knowledge discovery tools for nurse researchers.

Artificial Intelligence↗