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At least 289 records · Page 16Linked to original sources
PubMed2007

Issues in applied statistics for public health bioterrorism surveillance using multiple data streams: research needs.

The objective of this report is to provide a basis to inform decisions about priorities for developing statistical research initiatives in the field of public health surveillance for emerging threats. Rapid information system advances have created a vast opportunity of secondary data sources for information to enhance the situational and health status awareness of populations. While the field of medical informatics and initiatives to standardize healthcare-seeking encounter records continue accelerating, it is necessary to adapt analytic and statistical methodologies to mature in sync with sibling information science technologies. One major right-of-passage for statistical inference is to advance the optimal application of analytic methodologies for using multiple data streams in detecting and characterizing public health population events of importance. This report first describes the problem in general and the data context, then delineates more specifically the practical nature of the problem and the related issues. Approaches currently applied to data with time-series, statistical process control and traditional inference concepts are described with examples in the section on Statistics and the Role of the Analytic Surveillance Data Monitor. These are the techniques that are providing substance to surveillance professionals and enabling use of multiple data streams. The next section describes use of a more complex approach that takes temporal as well as spatial dimensions into consideration for detection and situational awareness regarding event distributions. The space-time statistic has successfully been used to detect and track public health events of interest. Important research questions which are summarized at the end of this report are described in more detail with respect to the methodological application in the respective sections. This was thought to help elucidate the research requirements as summarized later in the report. Following the description of the space-time scan statistical application; this report extends to a less traditional area of promise given what has been observed in recent application of analytic methods. Bayesian networks (BNs) represent a conceptual step with advantages of flexibility for the public health surveillance community. Progression from traditional to the more extending statistical concepts in the context of the dynamic status quo of responsibility and challenge, leads to a conclusion consisting of categorical research needs. The report is structured by design to inform judgment about how to build on practical systems to achieve better analytic outcomes for public health surveillance. There are references to research issues throughout the sections with a summarization at the end, which also includes items previously unmentioned in the report.

Algorithms↗
PubMed1994

The design and construction of a medical simulation model.

This paper describes the design, construction and validation of a probabilistic simulation model of patients who present with abdominal pain. The model incorporates text-book medical knowledge, clinical judgment, and statistics collected from real cases. The knowledge representation combines techniques of Bayesian network modelling with ideas of logistic discrimination. The model is shown to generate convincing, realistic cases; large numbers of artificial cases with no missing observations can be generated quickly. This should make the model a useful tool for investigating factors which limit achievable computer accuracy in the diagnosis of abdominal pain.

Abdominal Pain↗
PubMed2004

Feature inference and the causal structure of categories.

The purpose of this article was to establish how theoretical category knowledge-specifically, knowledge of the causal relations that link the features of categories-supports the ability to infer the presence of unobserved features. Our experiments were designed to test proposals that causal knowledge is represented psychologically as Bayesian networks. In five experiments we found that Bayes' nets generally predicted participants' feature inferences quite well. However, we also observed a pervasive violation of one of the defining principles of Bayes' nets-the causal Markov condition-because the presence of characteristic features invariably led participants to infer yet another characteristic feature. We argue that this effect arises from a domain-general bias to assume the presence of underlying mechanisms associated with the category. Specifically, people take an exemplar to be a "well functioning" category member when it has most or all of the category's characteristic features, and thus are likely to infer a characteristic value on an unobserved dimension.

Analysis of Variance↗
PubMed2005

Probabilistic prediction of protein-protein interactions from the protein sequences.

Prediction of protein-protein interactions is very important for several bioinformatics tasks though it is not a straightforward problem. In this paper, employing only protein sequence information, a framework is presented to predict protein-protein interactions using a probabilistic-based tree augmented nai ve (TAN) Bayesian network. Our framework also provides a confidence level for every predicted interaction, which is useful for further analysis by the biologists. The framework is applied to the yeast interaction datasets for predicting interactions and it is shown that our framework gives better performance than support vector machine (SVM). The framework is implemented as a webserver and is available for prediction.

Artificial Intelligence↗
PubMed2005

Prediction of methylated CpGs in DNA sequences using a support vector machine.

DNA methylation plays a key role in the regulation of gene expression. The most common type of DNA modification consists of the methylation of cytosine in the CpG dinucleotide. At the present time, there is no method available for the prediction of DNA methylation sites. Therefore, in this study we have developed a support vector machine (SVM)-based method for the prediction of cytosine methylation in CpG dinucleotides. Initially a SVM module was developed from human data for the prediction of human-specific methylation sites. This module achieved a MCC and AUC of 0.501 and 0.814, respectively, when evaluated using a 5-fold cross-validation. The performance of this SVM-based module was better than the classifiers built using alternative machine learning and statistical algorithms including artificial neural networks, Bayesian statistics, and decision trees. Additional SVM modules were also developed based on mammalian- and vertebrate-specific methylation patterns. The SVM module based on human methylation patterns was used for genome-wide analysis of methylation sites. This analysis demonstrated that the percentage of methylated CpGs is higher in UTRs as compared to exonic and intronic regions of human genes. This method is available on line for public use under the name of Methylator at http://bio.dfci.harvard.edu/Methylator/.

Algorithms↗
PubMed2005

A probabilistic approach to the joint evaluation of firearm evidence and gunshot residues.

The present paper addresses issues that affect both the separate as well as the joint evaluation of firearm evidence (i.e., marks) and gunshot residues (GSR). Mark evidence will be used as a basis to discriminate among barrels through which a bullet in question might have been shot whereas GSR will be used to draw inferences about the distance of firing. Particular attention is drawn to the coherent handling of uncertainties associated with the various parameters considered within each item of evidence. The proposed analysis relies on a probabilistic viewpoint that uses graphical models (i.e., Bayesian networks) as an aid to cope with the complexity induced by the number of variables considered. The paper discusses how an approach based on a probabilistic network environment can be used for the formal analysis and construction of arguments. Emphasis is made on the gain of insight into structural dependencies that may be uncovered when the evaluative process is extended beyond single items of scientific evidence.

Bayes Theorem↗
PubMed2006

Handling manipulated evidence.

Bayesian Networks have been advocated as useful tools to describe the relations of dependence/independence among random variables and relevant hypotheses in a crime case. Moreover, they have been applied to help the investigator structure the problem and evaluate the impact of the observed evidence, typically with respect to the hypothesis of guilt of a suspect. In this paper we describe a model to handle the possibility that one or more pieces of evidence have been manipulated in order to mislead the investigations. This method is based on causal inference models, although it is developed in a different, specific framework.

Bayes Theorem↗
PubMed2005

Methods for reasoning from geometry about anatomic structures injured by penetrating trauma.

This paper presents the methods used for three-dimensional (3D) reasoning about anatomic structures affected by penetrating trauma in TraumaSCAN-Web, a platform-independent decision support system for evaluating the effects of penetrating trauma to the chest and abdomen. In assessing outcomes for an injured patient, TraumaSCAN-Web utilizes 3D models of anatomic structures and 3D models of the regions of damage associated with stab and gunshot wounds to determine the probability of injury to anatomic structures. Probabilities estimated from 3D reasoning about affected anatomic structures serve as input to a Bayesian network which calculates posterior probabilities of injury based on these initial probabilities together with available information about patient signs, symptoms and test results. In addition to displaying textual descriptions of conditions arising from penetrating trauma to a patient, TraumaSCAN-Web allows users to visualize the anatomy suspected of being injured in 3D, in this way providing a guide to its reasoning process.

Artificial Intelligence↗
PubMed2006

User modeling and adaptation in health promotion dialogs with an animated character.

In this paper, we describe our experience with the design and implementation of an embodied conversational agent (ECA) that converses with users to change their dietary behavior. Our intent is to develop a system that dynamically models the agent and the user and adapts the agent's counseling dialog accordingly. Towards this end, we discuss our efforts to automatically determine the user's dietary behavior stage of change and attitude towards the agent on the basis of unconstrained typed text dialog, first with another person and then with an ECA controlled by an experimenter in a wizard of Oz study. We describe how the results of these studies have been incorporated into an algorithm that combines the results from simple parsing rules together with contextual features using a Bayesian network to determine user stage and attitude automatically.

Artificial Intelligence↗
PubMed1997

Efficient temporal probabilistic reasoning via context-sensitive model construction.

We present a language for representing context-sensitive temporal probabilistic knowledge. Context constraints allow inference to be focused on only the relevant portions of the probabilistic knowledge. We provide a declarative semantics for our language. We present a sound and complete algorithm for computing posterior probabilities of temporal queries, as well as an efficient implementation of the algorithm. Throughout we illustrate the approach with the problem of reasoning about the effects of medications and interventions on the state of a patient in cardiac arrest. We empirically evaluate the efficiency of our system by comparing its inference times on problems in this domain with those of standard Bayesian network representations of the problems.

Algorithms↗
PubMed2003

Precaution, uncertainty and causation in environmental decisions.

What measures of uncertainty and what causal analysis can improve the management of potentially severe, irreversible or dreaded environmental outcomes? Environmental choices show that policies intended to be precautionary (such as adding MTBE to petrol) can cause unanticipated harm (by mobilizing benzene, a known leukemogen, in the ground water). Many environmental law principles set the boundaries of what should be done but do not provide an operational construct to answer this question. Those principles, ranging from the precautionary principle to protecting human health from a significant risk of material health impairment, do not explain how to make environmental management choices when incomplete, inconsistent and complex scientific evidence characterizes potentially adverse environmental outcomes. Rather, they pass the task to lower jurisdictions such as agencies or authorities. To achieve the goals of the principle, those who draft it must deal with scientific casual conjectures, partial knowledge and variable data. In this paper we specifically deal with the qualitative and quantitative aspects of the European Union's (EU) explanation of consistency and on the examination of scientific developments relevant to variability and uncertain data and causation. Managing hazards under the precautionary principle requires inductive, empirical methods of assessment. However, acting on a scientific conjecture can also be socially unfair, costly, and detrimental when applied to complex environmental choices. We describe a constructive framework rationally to meet the command of the precautionary principle using alternative measures of uncertainty and recent statistical methods of causal analysis. These measures and methods can bridge the gap between conjectured future irreversible or severe harm and scant scientific evidence, thus leading to more confident and resilient social choices. We review two sets of measures and computational systems to deal with uncertainty and link them to causation through inductive empirical methods such as Bayesian Networks. We conclude that primary legislation concerned with large uncertainties and potential severe or dreaded environmental outcomes can produce accurate and efficient choices. To do so, primary legislation should specifically indicate what measures can represent uncertainty and how to deal with uncertain causation thus providing guidance to an agency's rulemaking or to an authority's writing secondary legislation. A corollary conclusion with legal, scientific and probabilistic implications concerns how to update past information when the state of information increases because a failure to update can result in regretting past choices. Elected legislators have the democratic mandate to formulate precautionary principles and are accountable. To preserve that mandate, imbedding formal methods to represent uncertainty in the statutory language of the precautionary principle enhances subsequent judicial review of legislative actions. The framework that we propose also reduces the Balkanized views and interpretations of probabilities, possibilities, likelihood and uncertainty that exists in environmental decision-making.

Bayes Theorem↗
PubMed1997

DIAVAL, a Bayesian expert system for echocardiography.

DIAVAL is an expert system for the diagnosis of heart diseases, including several kinds of data, mainly from echocardiography. The first part of this paper is devoted to the causal probabilistic model which constitutes the knowledge base of the expert system in the form of a Bayesian network, emphasizing the importance of the OR gate. The second part deals with the process of diagnosis, which consists of computing the a posteriori probabilities, selecting the most probable and most relevant diagnoses, and generating a written report. It also describes the results of the evaluation of the program.

Artificial Intelligence↗
PubMed2005

Quantitative risk modelling for new pharmaceutical compounds.

The process of discovering and developing new drugs is long, costly and risk-laden. Faced with a wealth of newly discovered compounds, industrial scientists need to target resources carefully to discern the key attributes of a drug candidate and to make informed decisions. Here, we describe a quantitative approach to modelling the risk associated with drug development as a tool for scenario analysis concerning the probability of success of a compound as a potential pharmaceutical agent. We bring together the three strands of manufacture, clinical effectiveness and financial returns. This approach involves the application of a Bayesian Network. A simulation model is demonstrated with an implementation in MS Excel using the modelling engine Crystal Ball.

Algorithms↗
PubMed2005

Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia.

Sickle cell anemia (SCA) is a paradigmatic single gene disorder caused by homozygosity with respect to a unique mutation at the beta-globin locus. SCA is phenotypically complex, with different clinical courses ranging from early childhood mortality to a virtually unrecognized condition. Overt stroke is a severe complication affecting 6-8% of individuals with SCA. Modifier genes might interact to determine the susceptibility to stroke, but such genes have not yet been identified. Using Bayesian networks, we analyzed 108 SNPs in 39 candidate genes in 1,398 individuals with SCA. We found that 31 SNPs in 12 genes interact with fetal hemoglobin to modulate the risk of stroke. This network of interactions includes three genes in the TGF-beta pathway and SELP, which is associated with stroke in the general population. We validated this model in a different population by predicting the occurrence of stroke in 114 individuals with 98.2% accuracy.

Anemia, Sickle Cell↗
PubMed2004

Application of influence diagrams to prostate intensity-modulated radiation therapy plan selection.

The purpose is to incorporate clinically relevant factors such as patient-specific and dosimetric information as well as data from clinical trials in the decision-making process for the selection of prostate intensity-modulated radiation therapy (IMRT) plans. The approach is to incorporate the decision theoretic concept of an influence diagram into the solution of the multiobjective optimization inverse planning problem. A set of candidate IMRT plans was obtained by varying the importance factors for the planning target volume (PTV) and the organ-at-risk (OAR) in combination with simulated annealing to explore a large part of the solution space. The Pareto set for the PTV and OAR was analysed to demonstrate how the selection of the weighting factors influenced which part of the solution space was explored. An influence diagram based on a Bayesian network with 18 nodes was designed to model the decision process for plan selection. The model possessed nodes for clinical laboratory results, tumour grading, staging information, patient-specific information, dosimetric information, complications and survival statistics from clinical studies. A utility node was utilized for the decision-making process. The influence diagram successfully ranked the plans based on the available information. Sensitivity analyses were used to judge the reasonableness of the diagram and the results. In conclusion, influence diagrams lend themselves well to modelling the decision processes for IMRT plan selection. They provide an excellent means to incorporate the probabilistic nature of data and beliefs into one model. They also provide a means for introducing evidence-based medicine, in the form of results of clinical trials, into the decision-making process.

Aged↗
PubMed2004

Optimizing exact genetic linkage computations.

Genetic linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the probability of data, which is needed for learning linkage parameters, using exact computation procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper, we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of SUPERLINK, which is a fast genetic linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm and hence enlarge the class of problems that can be handled effectively by exact computations.

Algorithms↗
PubMed2001

Inferring subnetworks from perturbed expression profiles.

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways.

Bayes Theorem↗
PubMed2002

A Bayesian framework for combining gene predictions.

MOTIVATION: Gene identification and gene discovery in new genomic sequences is one of the most timely computational questions addressed by bioinformatics scientists. This computational research has resulted in several systems that have been used successfully in many whole-genome analysis projects. As the number of such systems grows the need for a rigorous way to combine the predictions becomes more essential. RESULTS: In this paper we provide a Bayesian network framework for combining gene predictions from multiple systems. The framework allows us to treat the problem as combining the advice of multiple experts. Previous work in the area used relatively simple ideas such as majority voting. We introduce, for the first time, the use of hidden input/output Markov models for combining gene predictions. We apply the framework to the analysis of the Adh region in Drosophila that has been carefully studied in the context of gene finding and used as a basis for the GASP competition. The main challenge in combination of gene prediction programs is the fact that the systems are relying on similar features such as cod on usage and as a result the predictions are often correlated. We show that our approach is promising to improve the prediction accuracy and provides a systematic and flexible framework for incorporating multiple sources of evidence into gene prediction systems.

Algorithms↗