We appeal to the theory of Bayesian Networks to model different strategies for obtaining confirmation for a hypothesis from experimental test results provided by less than fully reliable instruments. In particular, we consider (i) repeated measurements of a single test consequence of the hypothesis, (ii) measurements of multiple test consequences of the hypothesis, (iii) theoretical support for the reliability of the instrument, and (iv) calibration procedures. We evaluate these strategies on their relative merits under idealized conditions and show some (...) surprising repercussions on the variety-of-evidence thesis and the Duhem-Quine thesis. (shrink)

In a criminal trial, evidence is used to draw conclusions about what happened concerning a supposed crime. Traditionally, the three main approaches to modeling reasoning with evidence are argumentative, narrative and probabilistic approaches. Integrating these three approaches could arguably enhance the communication between an expert and a judge or jury. In previous work, techniques were proposed to represent narratives in a Bayesian network and to use narratives as a basis for systematizing the construction of a Bayesian (...) class='Hi'>network for a legal case. In this paper, these techniques are combined to form a design method for constructing a Bayesian network based on narratives. This design method is evaluated by means of an extensive case study concerning the notorious Dutch case of the Anjum murders. (shrink)

There is a long philosophical tradition of addressing questions in philosophy of science and epistemology by means of the tools of Bayesian probability theory (see Earman (1992) and Howson and Urbach (1993)). In the late '70s, an axiomatic approach to conditional independence was developed within a Bayesian framework. This approach in conjunction with developments in graph theory are the two pillars of the theory of Bayesian Networks, which is a theory of probabilistic reasoning in artificial intelligence. The (...) theory has been very successful over the last two decades and has found a wide array of applications ranging from medical diagnosis to safety systems for hazardous industries. (shrink)

This article considers the extent to which Bayesian networks with imprecise probabilities, which are used in statistics and computer science for predictive purposes, can be used to represent causal structure. It is argued that the adequacy conditions for causal representation in the precise context—the Causal Markov Condition and Minimality—do not readily translate into the imprecise context. Crucial to this argument is the fact that the independence relation between random variables can be understood in several different ways when the joint (...) probability distribution over those variables is imprecise, none of which provides a compelling basis for the causal interpretation of imprecise Bayes nets. I conclude that there are serious limits to the use of imprecise Bayesian networks to represent causal structure. (shrink)

In a criminal trial, a judge or jury needs to reason about what happened based on the available evidence, often including statistical evidence. While a probabilistic approach is suitable for analysing the statistical evidence, a judge or jury may be more inclined to use a narrative or argumentative approach when considering the case as a whole. In this paper we propose a combination of two approaches, combining Bayesian networks with scenarios. Whereas a Bayesian network is a popular (...) tool for analysing parts of a case, constructing and understanding a network for an entire case is not straightforward. We propose an explanation method for understanding a Bayesian network in terms of scenarios. This method builds on a previously proposed construction method, which we slightly adapt with the use of scenario schemes for the purpose of explaining. The resulting structure is explained in terms of scenarios, scenario quality and evidential support. A probabilistic interpretation of scenario quality is provided using the concept of scenario schemes. Finally, the method is evaluated by means of a case study. (shrink)

Lexical ambiguity can be syntactic if it involves more than one grammatical category for a single word, or semantic if more than one meaning can be associated with a word. In this article we discuss the application of a Bayesian‐network model in the resolution of lexical ambiguities of both types. The network we propose comprises a parsing subnetwork, which can be constructed automatically for any context‐free grammar, and a subnetwork for semantic analysis, which, in the spirit of (...) Fillmore's (1968) case grammars, seeks to fulfill the required cases of all candidates for verb of the sentence. Solving for the highest joint probability of the variables conditioned upon the evidences to the network yields the most likely candidate with its meaning, along with its cases and respective meanings. This is achieved by fixing the values of all evidence nodes concurrently, and then performing a stochastic simulation in which the remaining nodes are updated probabilistically with a high degree of parallelism. The process of disambiguation is directed neither by the syntax nor the semantics, but rather by the interrelation between the two subnetworks. The use of a Bayesian‐network model allows us to express this interrelation between the two subnetworks and among their constituents in a rather direct and rigorous way that, in connection with the convergence properties of the stochastic simulation, reveals a very robust model. (shrink)

By identifying and pursuing analogies between causal and logical influence I show how the Bayesian network formalism can be applied to reasoning about logical deductions.

Proponents of various causal exclusion arguments claim that for any given event, there is often a unique level of granularity at which that event is caused. Against these causal exclusion arguments, causal ecumenists argue that the same event or phenomenon can be caused at multiple levels of granularity. This paper argues that the Bayesian network approach to representing the causal structure of target systems is consistent with causal ecumenism. Given the ubiquity of Bayesian networks as a tool (...) for representing causal structure in both philosophy of science and science itself, this result speaks in favor of the ecumenical view, and against rival exclusionary accounts. Gebharter’s (Philos Phenomenol Res 95(2):353–375, 2017) argument that the Bayes nets formalism is consistent with causal exclusion is considered and rebutted. (shrink)

The coherentist theory of justification provides a response to the sceptical challenge: even though the independent processes by which we gather information about the world may be of dubious quality, the internal coherence of the information provides the justification for our empirical beliefs. This central canon of the coherence theory of justification is tested within the framework of Bayesian networks, which is a theory of probabilistic reasoning in artificial intelligence. We interpret the independence of the information gathering processes (IGPs) (...) in terms of conditional independences, construct a minimal sufficient condition for a coherence ranking of information sets and assess whether the confidence boost that results from receiving information through independent IGPs is indeed a positive function of the coherence of the information set. There are multiple interpretations of what constitute IGPs of dubious quality. Do we know our IGPs to be no better than randomization processes? Or, do we know them to be better than randomization processes but not quite fully reliable, and if so, what is the nature of this lack of full reliability? Or, do we not know whether they are fully reliable or not? Within the latter interpretation, does learning something about the quality of some IGPs teach us anything about the quality of the other IGPs? The Bayesian-network models demonstrate that the success of the coherentist canon is contingent on what interpretation one endorses of the claim that our IGPs are of dubious quality. (shrink)

Chronic myeloid leukemia (CML) is a cancer of the hematopoietic system initiated by a single genetic mutation which results in the oncogenic fusion protein Bcr-Abl. Untreated, patients pass through different phases of the disease beginning with the rather asymptomatic chronic phase and ultimately culminating into blast crisis, an acute leukemia resembling phase with a very high mortality. Although many processes underlying the chronic phase are well understood, the exact mechanisms of disease progression to blast crisis are not yet revealed. In (...) this paper we develop a mathematical model of CML based on causal Bayesian networks in order to study possible disease progression mechanisms. Our results indicate that an increase of Bcr-Abl levels alone is not sufficient to explain the phenotype of blast crisis and that secondary changes such as additional mutations are necessary to explain disease progression and the poor therapy response of patients in blast crisis. (shrink)

We construct a probabilistic coherence measure for information sets which determines a partial coherence ordering. This measure is applied in constructing a criterion for expanding our beliefs in the face of new information. A number of idealizations are being made which can be relaxed by an appeal to Bayesian Networks.

Through their transcript products genes regulate the rates at which an immense variety of transcripts and subsequent proteins occur. Understanding the mechanisms that determine which genes are expressed, and when they are expressed, is one of the keys to genetic manipulation for many purposes, including the development of new treatments for disease. Viewing each gene in a genome as a distinct variable that is either on or off, or more realistically as a continuous variable, the values of some of these (...) variables influence the values of others through the regulatory proteins they express, including, of course, the possibility that the rate of expression of a gene at one time may, in various circumstances, influence the rate of expression of that same gene at a later time. If we imagine an arrow drawn from each gene expression variable at a given time to a gene variable whose expression it influences a short while after, the result is a network, technically a directed acyclic graph. For example, the DAG in Figure 1 is a representation of a system in which the expression level of gene G1 at time 1 ) causes the expression level of G2, which in turn causes the expression level of G3. The arrows in Figure 1 which do not have a variable at their tails are “error terms” which represent all of the causes of a variable other than the ones explicitly represented in the DAG. The DAG describes more than associations—it describes causal connections among gene expression rates. A shock to a cell—by mutation, heating, chemical treatment, etc. may alter the DAG describing the relations among gene expressions, for example by activating a gene that was otherwise not expressed, producing a cascade of new expression effects. Although “knockout” experiments can reveal some of the underlying causal network of gene expression levels, unless guided by information from other sources, such experiments are limited in how much of the network structure they can reveal, due to the sheer number of possible combinations of experimental manipulations of genes necessary to reveal the complete causal network. Recent developments have made it possible to compare quantitatively the expression of tens of thousands of genes in cells from different sources in a single experiment, and to trace gene expression over time in thousands of genes simultaneously. cDNA microarrays are already producing extensive data, much of it available on the web. Thus there are calls for analytic software that can be applied to microarray and other data to help infer regulatory networks. In this paper we will review current techniques that are available for searching for the causal relations between variables, describe algorithmic and data gathering obstacles to applying these techniques to gene expression levels, and describe the prospects for overcoming these obstacles. (shrink)

This paper shows how an efficient and parallel algorithm for inference in Bayesian Networks (BNs) can be built and implemented combining sparse matrix factorization methods with variable elimination algorithms for BNs. This entails a complete separation between a first symbolic phase, and a second numerical phase.

A Bayesian network (BN) is a graphical model of uncertainty that is especially well suited to legal arguments. It enables us to visualize and model dependencies between different hypotheses and pieces of evidence and to calculate the revised probability beliefs about all uncertain factors when any piece of new evidence is presented. Although BNs have been widely discussed and recently used in the context of legal arguments, there is no systematic, repeatable method for modeling legal arguments as BNs. (...) Hence, where BNs have been used in the legal context, they are presented as completed pieces of work, with no insights into the reasoning and working that must have gone into their construction. This means the process of building BNs for legal arguments is ad hoc, with little possibility for learning and process improvement. This article directly addresses this problem by describing a method for building useful legal arguments in a consistent and repeatable way. The method complements and extends recent work by Hepler, Dawid, and Leucari (2007) on object-oriented BNs for complex legal arguments and is based on the recognition that such arguments can be built up from a small number of basic causal structures (referred to as idioms). We present a number of examples that demonstrate the practicality and usefulness of the method. (shrink)

Bayesian networks may either be treated purely formally or be given an interpretation. I argue that current foundations are problematic, and put forward new foundations which involve aspects of both the interpreted and the formal approaches.

Because ports are considered to be the heart of the maritime transportation system, thereby assessing port performance is necessary for a nation’s development and economic success. This study proposes a novel metric, namely, “_port performance index (PPI)_”, to determine the overall performance and utilization of inland waterway ports based on six criteria,_ port facility, port availability, port economics, port service, port connectivity, and port environment_. Unlike existing literature, which mainly ranks ports based on quantitative factors, this study utilizes a (...) class='Hi'>Bayesian Network (BN) model that focuses on both quantitative and qualitative factors to rank a port. The assessment of inland waterway port performance is further analyzed based on different advanced techniques such as sensitivity analysis and belief propagation. Insights drawn from the study show that all the six criteria are necessary to predict PPI. The study also showed that port service has the highest impact while port economics has the lowest impact among the six criteria on PPI for inland waterway ports. (shrink)

We present RAWLSNET, a system for altering Bayesian Network (BN) models to satisfy the Rawlsian principle of fair equality of opportunity (FEO). RAWLSNET's BN models generate aspirational data distributions: data generated to reflect an ideally fair, FEO-satisfying society. FEO states that everyone with the same talent and willingness to use it should have the same chance of achieving advantageous social positions (e.g., employment), regardless of their background circumstances (e.g., socioeconomic status). Satisfying FEO requires alterations to social structures such (...) as school assignments. Our paper describes RAWLSNET, a method which takes as input a BN representation of an FEO application and alters the BN's parameters so as to satisfy FEO when possible, and minimize deviation from FEO otherwise. We also offer guidance for applying RAWLSNET, including on recognizing proper applications of FEO. We demonstrate the use of our system with publicly available data sets. RAWLSNET's altered BNs offer the novel capability of generating aspirational data for FEO-relevant tasks. Aspirational data are free from the biases of real-world data, and thus are useful for recognizing and detecting sources of unfairness in machine learning algorithms besides biased data. (shrink)

The Recursive Bayesian Net formalism was originally developed for modelling nested causal relationships. In this paper we argue that the formalism can also be applied to modelling the hierarchical structure of mechanisms. The resulting network contains quantitative information about probabilities, as well as qualitative information about mechanistic structure and causal relations. Since information about probabilities, mechanisms and causal relations is vital for prediction, explanation and control respectively, an RBN can be applied to all these tasks. We show in (...) particular how a simple two-level RBN can be used to model a mechanism in cancer science. The higher level of our model contains variables at the clinical level, while the lower level maps the structure of the cell's mechanism for apoptosis. (shrink)

Discrimination in decision making is prohibited on many attributes, but often present in historical decisions. Use of such discriminatory historical decision making as training data can perpetuate discrimination, even if the protected attributes are not directly present in the data. This work focuses on discovering discrimination in instances and preventing discrimination in classification. First, we propose a discrimination discovery method based on modeling the probability distribution of a class using Bayesian networks. This measures the effect of a protected attribute (...) in a subset of the dataset using the estimated probability distribution. Second, we propose a classification method that corrects for the discovered discrimination without using protected attributes in the decision process. We evaluate the discrimination discovery and discrimination prevention approaches on two different datasets. The empirical results show that a substantial amount of discrimination identified in instances is prevented in future decisions. (shrink)

One of the most challenging tasks when adopting Bayesian networks is the one of learning their structure from data. This task is complicated by the huge search space of possible solutions and by the fact that the problem isNP-hard. Hence, a full enumeration of all the possible solutions is not always feasible and approximations are often required. However, to the best of our knowledge, a quantitative analysis of the performance and characteristics of the different heuristics to solve this problem (...) has never been done before. For this reason, in this work, we provide a detailed comparison of many different state-of-the-art methods for structural learning on simulated data considering both BNs with discrete and continuous variables and with different rates of noise in the data. In particular, we investigate the performance of different widespread scores and algorithmic approaches proposed for the inference and the statistical pitfalls within them. (shrink)

The study of cultural evolution has taken on an increasingly interdisciplinary and diverse approach in explicating phenomena of cultural transmission and adoptions. Inspired by this computational movement, this study uses Bayesian networks analysis, combining both the frequentist and the Hamiltonian Markov chain Monte Carlo (MCMC) approach, to investigate the highly representative elements in the cultural evolution of a Vietnamese city’s architecture in the early 20th century. With a focus on the façade design of 68 old houses in Hanoi’s Old (...) Quarter (based on 78 data lines extracted from 248 photos), the study argues that it is plausible to look at the aesthetics, architecture, and designs of the house façade to find traces of cultural evolution in Vietnam, which went through more than six decades of French colonization and centuries of sociocultural influence from China. The in-depth technical analysis, though refuting the presumed model on the probabilistic dependency among the variables, yields several results, the most notable of which is the strong influence of Buddhism over the decorations of the house façade. Particularly, in the top 5 networks with the best Bayesian Information Criterion (BIC) scores and p<0.05, the variable for decorations (DC) always has a direct probabilistic dependency on the variable B for Buddhism. The paper then checks the robustness of these models using Hamiltonian MCMC method and find the posterior distributions of the models’ coefficients all satisfy the technical requirement. Finally, this study suggests integrating Bayesian statistics in the social sciences in general and for the study of cultural evolution and architectural transformation in particular. (shrink)

When we talk about the coherence of a story, we seem to think of how well its individual pieces fit together—how to explicate this notion formally, though? We develop a Bayesian network based coherence measure with implementation in _R_, which performs better than its purely probabilistic predecessors. The novelty is that by paying attention to the network structure, we avoid simply taking mean confirmation scores between all possible pairs of subsets of a narration. Moreover, we assign special (...) importance to the weakest links in a narration, to improve on the other measures’ results for logically inconsistent scenarios. We illustrate and investigate the performance of the measures in relation to a few philosophically motivated examples, and (more extensively) using the real-life example of the Sally Clark case. (shrink)

La, V. P., & Vuong, Q. H. (2019). bayesvl: Visually learning the graphical structure of Bayesian networks and performing MCMC with ‘Stan’. The Comprehensive R Archive Network (CRAN).

Metabolism is a set of chemical reactions, used by living organisms to process chemical compounds in order to take energy and eliminate toxic compounds, for example. Its processes are referred as metabolic pathways. Understanding metabolism is imperative to biology, toxicology and medicine, but the number and complexity of metabolic pathways makes this a difficult task. In our paper, we investigate the use of causal Bayesian networks to model the pathways of yeast saccharomyces cerevisiae metabolism: such a network can (...) be used to draw predictions about the levels of metabolites and enzymes in a particular specimen. We propose a two-stage methodology for causal networks, as follows. First construct a causal network from the network of metabolic pathways. The viability of this causal network depends on the validity of the causal Markov condition. If this condition fails, however, the principle of the common cause motivates the addition of a new causal arrow or a new `hidden' common cause to the network (stage 2 of the model formation process). Algorithms for adding arrows or hidden nodes have been developed separately in a number of papers, and in this paper we combine them, showing how the resulting procedure can be applied to the metabolic pathway problem. Our general approach was tested on neural cell morphology data and demonstrated noticeable improvements in both prediction and network accuracy. (shrink)

Fenton et al. present a Bayesian‐network analysis of the case, using their previously developed set of building blocks (‘idioms’). They claim that these idioms, combined with their opportunity‐based method for estimating the prior probability of guilt, reduce the subjectivity of their analysis. Although their Bayesian model is less cognitively feasible than scenario‐ or argumentation‐based models, they claim that it does model the standard approach to legal proof, which is to continually revise beliefs under new evidence.

Artificial Intelligence (AI) and Philosophy of Science share a fundamental problem—that of understanding causality. Bayesian network techniques have recently been used by Judea Pearl in a new approach to understanding causality and causal processes (Pearl, 2000). Pearl’s approach has great promise, but needs to be supplemented with an explicit account of causal interaction. Thus far, despite considerable interest, philosophy has provided no useful account of causal interaction. Here we provide one, employing the concepts of Bayesian networks. With (...) it we demonstrate the failure of one of philosophy’s more sophisticated attempts to deal with the concept of causal interaction, that of Ellery Eells’ Probabilistic Causality (1991). (shrink)

Artificial Intelligence (AI) and Philosophy of Science share a fundamental problem—understanding causality. Bayesian networks have recently been used by Judea Pearl in a new approach to understanding causality (Pearl, 2000). Part of understanding causality is understanding causal interaction. Bayes nets can represent any degree of causal interaction, and researchers normally try to limit interactions, usually by replacing the full CPT with a noisy-OR function. But we show that noisy-OR and another common model are merely special cases of the general (...) linear systems definition of noninteraction. However, they apply in different situations, and we can measure the degree of causal interaction relative to any such model. (shrink)

Belief polarization is said to occur when two people respond to the same evidence by updating their beliefs in opposite directions. This response is considered to be “irrational” because it involves contrary updating, a form of belief updating that appears to violate normatively optimal responding, as for example dictated by Bayes' theorem. In light of much evidence that people are capable of normatively optimal behavior, belief polarization presents a puzzling exception. We show that Bayesian networks, or Bayes nets, can (...) simulate rational belief updating. When fit to experimental data, Bayes nets can help identify the factors that contribute to polarization. We present a study into belief updating concerning the reality of climate change in response to information about the scientific consensus on anthropogenic global warming. The study used representative samples of Australian and U.S. participants. Among Australians, consensus information partially neutralized the influence of worldview, with free-market supporters showing a greater increase in acceptance of human-caused global warming relative to free-market opponents. In contrast, while consensus information overall had a positive effect on perceived consensus among U.S. participants, there was a reduction in perceived consensus and acceptance of human-caused global warming for strong supporters of unregulated free markets. Fitting a Bayes net model to the data indicated that under a Bayesian framework, free-market support is a significant driver of beliefs about climate change and trust in climate scientists. Further, active distrust of climate scientists among a small number of U.S. conservatives drives contrary updating in response to consensus information among this particular group. (shrink)

This study attempts to analyse the relationship between two key psychological variables associated with performance in sports - Self-Determined Motivation and Competitive Anxiety - through Bayesian Networks analysis. We analysed 674 university students/athletes from 44 universities that competed at the University Games in México, with an average age of 21 years (SD = 2.07) and with a mean of 8.61 years’ (SD = 5.15) experience in sports. Methods: Regarding the data analysis, first a CHAID algorithm was carried out to (...) determine the dependence links between variables, and then a Bayesian networks was developed. The validation of the BN revealed AUC values ranging from 0.5 to 0.92. Subsequently, various instantiations were performed with hypothetical values applied to the “bottom” variables. Results showed two probability trees that have extrinsic motivation and amotivation at the top, while the anxiety/activation due to worries about performance was at the bottom of the probabilities. The instantiations carried out support the existence of these probabilistic relationships, demonstrating their scarce influence on anxiety about competition generated by the intrinsic motivation, and the complex probabilistic effect of introjected and identified regulation regarding the appearance of anxiety due to worry about performance. (shrink)

Bayesian networks (BN) and argumentation diagrams (AD) are two predominant approaches to legal evidential reasoning, that are often treated as alternatives to one another. This paper argues that they are, instead, complimentary and proposes the beginnings of a method to employ them in such a manner. The Bayesian approach tends to be used as a means to analyse the findings of forensic scientists. As such, it constitutes a means to perform evidential reasoning. The design of Bayesian networks (...) that accurately and comprehensively represent the relationships between investigative hypotheses and evidence remains difficult and sometimes contentious, however. Argumentation diagrams are representations of reasoning, and are used as a means to scrutinise reasoning (among other applications). In evidential reasoning, they tend to be used to represent and scrutinise the way humans reason about evidence. This paper examines how argumentation diagrams can be used to scrutinise Bayesian evidential reasoning by developing a method to extract argument diagrams from BN. (shrink)

This paper investigates the relations between causality and propensity. Aparticular version of the propensity theory of probability is introduced, and it is argued that propensities in this sense are not causes. Some conclusions regarding propensities can, however, be inferred from causal statements, but these hold only under restrictive conditions which prevent cause being defined in terms of propensity. The notion of a Bayesian propensity network is introduced, and the relations between such networks and causal networks is investigated. It (...) is argued that causal networks cannot be identified with Bayesian propensity networks, but that causal networks can be a valuable heuristic guide for the construction of Bayesian propensity networks. (shrink)

The appeal to expert opinion is an argument form that uses the verdict of an expert to support a position or hypothesis. A previous scheme-based treatment of the argument form is formalized within a Bayesian network that is able to capture the critical aspects of the argument form, including the central considerations of the expert's expertise and trustworthiness. We propose this as an appropriate normative framework for the argument form, enabling the development and testing of quantitative predictions as (...) to how people evaluate this argument, suggesting that such an approach might be beneficial to argumentation research generally. We subsequently present two experiments as an example of the potential for future research in this vein, demonstrating that participants' quantitative ratings of the convincingness of a proposition that has been supported with an appeal to expert opinion were broadly consistent with the predictions of the Bayesian model. (shrink)

The forensic two-trace problem is a perplexing inference problem introduced by Evett (J Forensic Sci Soc 27:375–381, 1987). Different possible ways of wording the competing pair of propositions (i.e., one proposition advanced by the prosecution and one proposition advanced by the defence) led to different quantifications of the value of the evidence (Meester and Sjerps in Biometrics 59:727–732, 2003). Here, we re-examine this scenario with the aim of clarifying the interrelationships that exist between the different solutions, and in this way, (...) produce a global vision of the problem. We propose to investigate the different expressions for evaluating the value of the evidence by using a graphical approach, i.e. Bayesian networks, to model the rationale behind each of the proposed solutions and the assumptions made on the unknown parameters in this problem. (shrink)