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)

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)

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 (...) class='Hi'>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)

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 (...) class='Hi'>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)

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)

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.

In this paper we compare causal models with reason models in the construction of Bayesian networks for legal evidence. In causal models, arrows in the network are drawn from causes to effects. In a reason model, the arrows are instead drawn towards the evidence, from factum probandum to factum probans. We explore the differences between causal models and reason models and observe several distinct advantages with reason models. Reason models are better aligned with the philosophy (...) of Bayesian inference, as they model reasons for up-dating beliefs. Reason models are better suited for measuring the combined support of the evidence, and a prior probability of guilt that reflects the number of possible perpetrators is accommodated more easily with reason models. (shrink)

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)

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)

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)

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)

The Recursive Bayesian Net (RBN) 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)

This paper has two main parts. In the first part, we motivate a kind of indeterminate, suppositional credences by discussing the prospect for a subjective interpretation of a causal Bayesian network, an important tool for causal reasoning in artificial intelligence. A CBN consists of a causal graph and a collection of interventional probabilities. The subjective interpretation in question would take the causal graph in a CBN to represent the causal structure that is believed (...) by an agent, and interventional probabilities in a CBN to represent suppositional credences. We review a difficulty noted in the literature with such an interpretation, and suggest that a natural way to address the challenge is to go for a generalization of CBN that allows indeterminate credences. In the second part, we develop a decision-theoretic foundation for such indeterminate suppositional credences, by generalizing a theory of coherent choice functions to accommodate some form of act-state dependence. The upshot is a decision-theoretic framework that is not only rich enough to, so to speak, ground the probabilities in a subjectively interpreted causal network, but also interesting in its own right, in that it accommodates both act-state dependence and imprecise probabilities. (shrink)

Bayesian networks are computer programs which represent probabilitistic relationships graphically as directed acyclic graphs, and which can use those graphs to reason probabilistically , often at relatively low computational cost. Almost every expert system in the past tried to support probabilistic reasoning, but because of the computational difficulties they took approximating short-cuts, such as those afforded by MYCIN's certainty factors. That all changed with the publication of Judea Pearl's Probabilistic Reasoning in Intelligent Systems, in 1988, which synthesized a decade (...) of research making accurate graphical probabilistic reasoning computationally achievable.Bayesian network technology is now one of the fastest growing fields of research in artificial intelligence. That it has become a publication industry in its own right is shown by a search on Google scholar :This development, together with a parallel related growth in the use of causal discovery algorithms which automate the learning of Bayesian networks from sample data, has generated considerable interest, and controversy, within the philosophy-of-science community.Three central questions bringing together AI researchers and philosophers of science are: Are Bayesian networks Bayesian? What is the relation between probability and causality? Are the assumptions behind causal discovery of Bayesian networks realistic or fantastical?Jon Williamson, as a philosopher of science with a keen interest in the technology, asks and answers these questions in his new book. Although it is self-contained, his book is not very likely as an introduction to the technology , nor is it optimal even as an introduction to the philosophical problems in interpreting Bayesian networks . Rather Williamson's book is an attempt to move the debate forward by solving the central problems of the …. (shrink)

We clarify the status of the so-called causal minimality condition in the theory of causal Bayesian networks, which has received much attention in the recent literature on the epistemology of causation. In doing so, we argue that the condition is well motivated in the interventionist (or manipulability) account of causation, assuming the causal Markov condition which is essential to the semantics of causal Bayesian networks. Our argument has two parts. First, we show that the (...) causal minimality condition, rather than an add-on methodological assumption of simplicity, necessarily follows from the substantive interventionist theses, provided that the actual probability distribution is strictly positive. Second, we demonstrate that the causal minimality condition can fail when the actual probability distribution is not positive, as is the case in the presence of deterministic relationships. But we argue that the interventionist account still entails a pragmatic justification of the causal minimality condition. Our argument in the second part exemplifies a general perspective that we think commendable: when evaluating methods for inferring causal structures and their underlying assumptions, it is relevant to consider how the inferred causal structure will be subsequently used for counterfactual reasoning. (shrink)

Causal models provide a framework for precisely representing complex causal structures, where specific models can be used to efficiently predict, infer, and explain the world. At the same time, we often do not know the full causal structure a priori and so must learn it from data using a causal model search algorithm. This chapter provides a general overview of causal models and their uses, with a particular focus on causal graphical models (the most (...) commonly used causal modeling framework) and methods for learning such models from observational and experimental data. The chapter concludes with two examples of productive causal search and modeling in experimental philosophy. (shrink)

Independence of Conditionals (IC) has recently been proposed as a basic rule for causal structure learning. If a Bayesian network represents the causal structure, its Conditional Probability Distributions (CPDs) should be algorithmically independent. In this paper we compare IC with causal faithfulness (FF), stating that only those conditional independences that are implied by the causal Markov condition hold true. The latter is a basic postulate in common approaches to causal structure learning. The common (...) spirit of FF and IC is to reject causal graphs for which the joint distribution looks ‘non-generic’. The difference lies in the notion of genericity: FF sometimes rejects models just because one of the CPDs is simple, for instance if the CPD describes a deterministic relation. IC does not behave in this undesirable way. It only rejects a model when there is a non-generic relation between different CPDs although each CPD looks generic when considered separately. Moreover, it detects relations between CPDs that cannot be captured by conditional independences. IC therefore helps in distinguishing causal graphs that induce the same conditional independences (i.e., they belong to the same Markov equivalence class). The usual justification for FF implicitly assumes a prior that is a probability density on the parameter space. IC can be justified by Solomonoff’s universal prior, assigning non-zero probability to those points in parameter space that have a finite description. In this way, it favours simple CPDs, and therefore respects Occam’s razor. Since Kolmogorov complexity is uncomputable, IC is not directly applicable in practice. We argue that it is nevertheless helpful, since it has already served as inspiration and justification for novel causal inference algorithms. (shrink)

Recent work on the interpretation of counterfactual conditionals has paid much attention to the role of causal independencies. One influential idea from the theory of Causal Bayesian Networks is that counterfactual assumptions are made by intervention on variables, leaving all of their causal non-descendants unaffected. But intervention is not applicable across the board. For instance, backtracking counterfactuals, which involve reasoning from effects to causes, cannot proceed by intervention in the strict sense, for otherwise they would be (...) equivalent to their consequents. We discuss these and similar cases, focusing on two factors which play a role in determining whether and which causal parents of the manipulated variable are affected: Speakers' need for an explanation of the hypothesized state of affairs, and differences in the ‘resilience’ of beliefs that are independent of degrees of certainty. We describe the relevant theoretical notions in some detail and provide experimental evidence that these factors do indeed affect speakers' interpretation of counterfactuals. (shrink)

The application of the formal framework of causal Bayesian Networks to children’s causal learning provides the motivation to examine the link between judgments about the causal structure of a system, and the ability to make inferences about interventions on components of the system. Three experiments examined whether children are able to make correct inferences about interventions on different causal structures. The first two experiments examined whether children’s causal structure and intervention judgments were consistent with (...) one another. In Experiment 1, children aged between 4 and 8 years made causal structure judgments on a three-component causal system followed by counterfactual intervention judgments. In Experiment 2, children’s causal structure judgments were followed by intervention judgments phrased as future hypotheticals. In Experiment 3, we explicitly told children what the correct causal structure was and asked them to make intervention judgments. The results of the three experiments suggest that the representations that support causal structure judgments do not easily support simple judgments about interventions in children. We discuss our findings in light of strong interventionist claims that the two types of judgments should be closely linked. (shrink)

Causal reasoning is primarily concerned with what would happen to a system under external interventions. In particular, we are often interested in predicting the probability distribution of some random variables that would result if some other variables were forced to take certain values. One prominent approach to tackling this problem is based on causal Bayesian networks, using directed acyclic graphs as causal diagrams to relate post-intervention probabilities to pre-intervention probabilities that are estimable from observational data. However, (...) such causal diagrams are seldom fully testable given observational data. In consequence, many causal discovery algorithms based on data-mining can only output an equivalence class of causal diagrams. This paper is concerned with causal reasoning given an equivalence class of causal diagrams, represented by a ancestral graph. We present two main results. The first result extends Pearl 's celebrated do-calculus to the context of ancestral graphs. In the second result, we focus on a key component of Pearl's calculus---the property of invariance under interventions, and give stronger graphical conditions for this property than those implied by the first result. The second result also improves the earlier, similar results due to Spirtes et al. (shrink)

Decision-making typically requires judgments about causal relations: we need to know the causal effects of our actions and the causal relevance of various environmental factors. We investigate how several individuals' causal judgments can be aggregated into collective causal judgments. First, we consider the aggregation of causal judgments via the aggregation of probabilistic judgments, and identify the limitations of this approach. We then explore the possibility of aggregating causal judgments independently of probabilistic ones. Formally, (...) we introduce the problem of causal-network aggregation. Finally, we revisit the aggregation of probabilistic judgments when this is constrained by prior aggregation of qualitative causal judgments. (shrink)

Mechanistic philosophy of science views a large part of scientific activity as engaged in modelling mechanisms. While science textbooks tend to offer qualitative models of mechanisms, there is increasing demand for models from which one can draw quantitative predictions and explanations. Casini et al. (Theoria 26(1):5–33, 2011) put forward the Recursive Bayesian Networks (RBN) formalism as well suited to this end. The RBN formalism is an extension of the standard Bayesian net formalism, an extension that allows for modelling (...) the hierarchical nature of mechanisms. Like the standard Bayesian net formalism, it models causal relationships using directed acyclic graphs. Given this appeal to acyclicity, causal cycles pose a prima facie problem for the RBN approach. This paper argues that the problem is a significant one given the ubiquity of causal cycles in mechanisms, but that the problem can be solved by combining two sorts of solution strategy in a judicious way. (shrink)

While standard procedures of causal reasoning as procedures analyzing causal Bayesian networks are custom-built for (non-deterministic) probabilistic struc- tures, this paper introduces a Boolean procedure that uncovers deterministic causal structures. Contrary to existing Boolean methodologies, the procedure advanced here successfully analyzes structures of arbitrary complexity. It roughly involves three parts: first, deterministic dependencies are identified in the data; second, these dependencies are suitably minimalized in order to eliminate redundancies; and third, one or—in case of ambiguities—more than (...) one causal structure is assigned to the minimalized deterministic dependencies. (shrink)

Bayesian approaches to legal reasoning propose causal models of the relation between evidence, the credibility of evidence, and ultimate hypotheses, or verdicts. They assume that legal reasoning is the process whereby one infers the posterior probability of a verdict based on observed evidence, or facts. In practice, legal reasoning does not operate quite that way. Legal reasoning is also an attempt at inferring applicable rules derived from legal precedents or statutes based on the facts at hand. To make (...) such an inference, legal reasoning follows syllogistic logic and first order transitivity. This paper proposes a Bayesian model of legal syllogistic reasoning that complements existing Bayesian models of legal reasoning using a Bayesian network whose variables correspond to legal precedents, statutes, and facts. We suggest that legal reasoning should be modelled as a process of finding the posterior probability of precedents and statutes based on available facts. (shrink)

Recent work on the interpretation of counterfactual conditionals has paid much attention to the role of causal independencies. One influential idea from the theory of Causal Bayesian Networks is that counterfactual assumptions are made by intervention on variables, leaving all of their causal non‐descendants unaffected. But intervention is not applicable across the board. For instance, backtracking counterfactuals, which involve reasoning from effects to causes, cannot proceed by intervention in the strict sense, for otherwise they would be (...) equivalent to their consequents. We discuss these and similar cases, focusing on two factors which play a role in determining whether and which causal parents of the manipulated variable are affected: Speakers' need for an explanation of the hypothesized state of affairs, and differences in the ‘resilience’ of beliefs that are independent of degrees of certainty. We describe the relevant theoretical notions in some detail and provide experimental evidence that these factors do indeed affect speakers' interpretation of counterfactuals. (shrink)

We present three experiments using a novel problem in which participants update their estimates of propensities when faced with an uncertain new instance. We examine this using two different causal structures (common cause/common effect) and two different scenarios (agent‐based/mechanical). In the first, participants must update their estimate of the propensity for two warring nations to successfully explode missiles after being told of a new explosion on the border between both nations. In the second, participants must update their estimate of (...) the accuracy of two early warning tests for cancer when they produce conflicting reports about a patient. Across both experiments, we find two modal responses, representing around one‐third of participants each. In the first, “Categorical” response, participants update propensity estimates as if they were certain about the single event, for example, certain that one of the nations was responsible for the latest explosion, or certain about which of the two tests is correct. In the second, “No change” response, participants make no update to their propensity estimates at all. Across the three experiments, the theory is developed and tested that these two responses in fact have a single representation of the problem: because the actual outcome is binary (only one of the nations could have launched the missile; the patient either has cancer or not), these participants believe it is incorrect to update propensities in a graded manner. They therefore operate on a “certainty threshold” basis, whereby, if they are certain enough about the single event, they will make the “Categorical” response, and if they are below this threshold, they will make the “No change” response. Ramifications are considered for the “categorical” response in particular, as this approach produces a positive‐feedback dynamic similar to that seen in the belief polarization/confirmation bias literature. (shrink)

Using Bayesian network causal models, we provide a simple general account of probabilistic causal interaction. We also detail problems in the leading accounts by Ellery Eells, and any others which require valence reversals, contextual unanimity, or average effects.

As a compact representation of joint probability distributions over a dependence graph of random variables, and a tool for modelling and reasoning in the presence of uncertainty, Bayesian networks are of great importance for artificial intelligence to combine domain knowledge, capture causal relationships, or learn from incomplete datasets. Known as a NP-hard problem in a classical setting, Bayesian inference pops up as a class of algorithms worth to explore in a quantum framework. This paper explores such a (...) research direction and improves on previous proposals by a judicious use of the utility function in an entangled configuration. It proposes a completely quantum mechanical decision-making process with a proven computational advantage. A prototype implementation in Qiskit (a Python-based program development kit for the IBM Q machine) is discussed as a proof-of-concept. (shrink)

Discovering high-level causal relations from low-level data is an important and challenging problem that comes up frequently in the natural and social sciences. In a series of papers, Chalupka etal. (2015, 2016a, 2016b, 2017) develop a procedure forcausal feature learning (CFL) in an effortto automate this task. We argue that CFL does not recommend coarsening in cases where pragmatic considerations rule in favor of it, and recommends coarsening in cases where pragmatic considerations rule against it. We propose a new (...) technique, pragmatic causal feature learning (PCFL), which extends the original CFL algorithm in useful and intuitive ways. We show that PCFL has the same attractive measure-theoretic properties as the original CFL algorithm. We compare the performance of both methods through theoretical analysis and experiments. (shrink)

We propose a causal model theory to explain asymmetries in judgments of the intentionality of a foreseen side-effect that is either negative or positive (Knobe, 2003). The theory is implemented as a Bayesian network relating types of mental states, actions, and consequences that integrates previous hypotheses. It appeals to two inferential routes to judgment about the intentionality of someone else's action: bottom-up from action to desire and top-down from character and disposition. Support for the theory comes from (...) three experiments that test the prediction that bottom-up inference should occur only when the actor's primary objective is known. The model fits intentionality judgments reasonably well with no free parameters. (shrink)

Much of the recent work on the epistemology of causation has centered on two assumptions, known as the Causal Markov Condition and the Causal Faithfulness Condition. Philosophical discussions of the latter condition have exhibited situations in which it is likely to fail. This paper studies the Causal Faithfulness Condition as a conjunction of weaker conditions. We show that some of the weaker conjuncts can be empirically tested, and hence do not have to be assumed a priori. Our (...) results lead to two methodologically significant observations: (1) some common types of counterexamples to the Faithfulness condition constitute objections only to the empirically testable part of the condition; and (2) some common defenses of the Faithfulness condition do not provide justification or evidence for the testable parts of the condition. It is thus worthwhile to study the possibility of reliable causal inference under weaker Faithfulness conditions. As it turns out, the modification needed to make standard procedures work under a weaker version of the Faithfulness condition also has the practical effect of making them more robust when the standard Faithfulness condition actually holds. This, we argue, is related to the possibility of controlling error probabilities with finite sample size (“uniform consistency”) in causal inference. (shrink)

Alexander Gebharter has recently proposed to use Bayesian network causal discovery methods to identify the constitutive dependencies that underwrite mechanistic explanations. The proposal depends on using the assumptions of the causal Bayesian network framework to implicitly define mechanistic constitution as a kind of deterministic direct causal dependence. The aim of this paper is twofold. In the first half, we argue that Gebharter’s proposal incurs severe conceptual problems. In the second half, we present an (...) alternative way to bring Bayesian network tools to bear on the issue of understanding mechanistic constitution. More precisely, our proposal interprets constitution as the relation explaining why a target phenomenon has its characteristic causal role in terms of the causal roles of some of its spatiotemporal parts---where the notion of causal role is probabilistically understood. (shrink)

The development of causal modelling since the 1950s has been accompanied by a number of controversies, the most striking of which concerns the Markov condition. Reichenbach's conjunctive forks did satisfy the Markov condition, while Salmon's interactive forks did not. Subsequently some experts in the field have argued that adequate causal models should always satisfy the Markov condition, while others have claimed that non-Markovian causal models are needed in some cases. This paper argues for the second position by (...) considering the multi-causal forks, which are widespread in contemporary medicine (Section 2). A non-Markovian causal model for such forks is introduced and shown to be mathematically tractable (Sections 6, 7, and 8). The paper also gives a general discussion of the controversy about the Markov condition (Section 1), and of the related controversy about probabilistic causality (Sections 3, 4, and 5). (shrink)

We present a new framework for combining logic with probability, and demonstrate the application of this framework to breast cancer prognosis. Background knowledge concerning breast cancer prognosis is represented using logical arguments. This background knowledge and a database are used to build a Bayesian net that captures the probabilistic relationships amongst the variables. Causal hypotheses gleaned from the Bayesian net in turn generate new arguments. The Bayesian net can be queried to help decide when one argument (...) attacks another. The Bayesian net is used to perform the prognosis, while the argumentation framework is used to provide a qualitative explanation of the prognosis. (shrink)

The verbs cause, enable, and prevent express beliefs about the way the world works. We offer a theory of their meaning in terms of the structure of those beliefs expressed using qualitative properties of causal models, a graphical framework for representing causal structure. We propose that these verbs refer to a causal model relevant to a discourse and that “A causes B” expresses the belief that the causal model includes a link from A to B. “A (...) enables/allows B” entails that the model includes a link from A to B, that A represents a category of events necessary for B, and that an alternative cause of B exists. “A prevents B” entails that the model includes a link from A to B and that A reduces the likelihood of B. This theory is able to account for the results of four experiments as well as a variety of existing data on human reasoning. (shrink)

Causal Bayes nets (CBNs) can be used to model causal relationships up to whole mechanisms. Though modelling mechanisms with CBNs comes with many advantages, CBNs might fail to adequately represent some biological mechanisms because—as Kaiser (2016) pointed out—they have problems with capturing relevant spatial and structural information. In this paper we propose a hybrid approach for modelling mechanisms that combines CBNs and cellular automata. Our approach can incorporate spatial and structural information while, at the same time, it comes (...) with all the merits of a CBN representation of mechanisms. (shrink)

This work provides a conceptual foundation for a Bayesian approach to artificial inference and learning. I argue that Bayesian confirmation theory provides a general normative theory of inductive learning and therefore should have a role in any artificially intelligent system that is to learn inductively about its world. I modify the usual Bayesian theory in three ways directly pertinent to an eventual research program in artificial intelligence. First, I construe Bayesian inference rules as defeasible, allowing them (...) to be overridden in certain contexts and therefore allowing them to play a part in a hybrid system, coexisting with non-Bayesian modes of inference. I take seriously the need to find meaningful prior probabilities for hypotheses, and elaborate means for supplying an artificial intelligence with such. And I address the computational complexity of Bayesian inference by reference to simplifications using causal networks and by allowing the probabilistic acceptance of hypotheses and subsequent qualitative inference to supplement Bayesian reasoning. The result is a Pragmatic Bayesian model of induction. (shrink)

this paper we argue that the formalism can also be applied to modelling the hierarchical structure of physical 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 are vital for prediction, explanation and control respectively, a recursive Bayesian net can be applied to all these tasks. We show how a Recursive Bayesian Net can be used to (...) model mechanisms in cancer science. The highest level of the proposed model will contain variables at the clinical level, while a middle level will map the structure of the DNA damage response mechanism and the lowest level will contain information about gene expression. (shrink)

This article assesses how people reason with categories whose features are related in causal cycles. Whereas models based on causal graphical models have enjoyed success modeling category-based judgments as well as a number of other cognitive phenomena, CGMs are only able to represent causal structures that are acyclic. A number of new formalisms that allow cycles are introduced and evaluated. Dynamic Bayesian networks represent cycles by unfolding them over time. Chain graphs augment CGMs by allowing the (...) presence of undirected links that model feedback relations between variables. Unfolded chain graphs are chain graphs that unfold over time. An existing model of causal cycles is also evaluated. Four experiments in which subjects reason about categories with cyclically related features provided evidence against DBNs and alpha centrality and for the two types of chain graphs. Chain graphs—a mechanism for representing the equilibrium distribution of a dynamic system—may thus be good candidates for modeling how people reason causally with complex systems. Applications of chain graphs to areas of cognition other than category-based judgments are discussed. (shrink)

Judea Pearl (2000) was the first to propose a definition of actual causation using causal models. A number of authors have suggested that an adequate account of actual causation must appeal not only to causal structure but also to considerations of normality. In Halpern and Hitchcock (2011), we offer a definition of actual causation using extended causal models, which include information about both causal structure and normality. Extended causal models are potentially very complex. In this (...) study, we show how it is possible to achieve a compact representation of extended causal models. (shrink)

A main message from the causal modelling literature in the last several decades is that under some plausible assumptions, there can be statistically consistent procedures for inferring (features of) the causal structure of a set of random variables from observational data. But whether we can control the error probabilities with a finite sample size depends on the kind of consistency the procedures can achieve. It has been shown that in general, under the standard causal Markov and Faithfulness (...) assumptions, the procedures can only be pointwise but not uniformly consistent without substantial background knowledge. This implies the impossibility of choosing a finite sample size to control the worst case error probabilities. In this paper, I consider the simpler task of inferring causal directions when the skeleton of the causal structure is known, and establish a similarly negative result concerning the possibility of controlling error probabilities. Although the result is negative in form, it has an interesting positive implication for causal discovery methods. (shrink)

The aim of the paper is to relate Bell’s notion of local causality to the Causal Markov Condition. To this end, first a framework, called local physical theory, will be introduced integrating spatiotemporal and probabilistic entities and the notions of local causality and Markovity will be defined. Then, illustrated in a simple stochastic model, it will be shown how a discrete local physical theory transforms into a Bayesian network and how the Causal Markov Condition arises as (...) a special case of Bell’s local causality and Markovity. (shrink)

Concrete Causation centers about theories of causation, their interpretation, and their embedding in metaphysical-ontological questions, as well as the application of such theories in the context of science and decision theory. The dissertation is divided into four chapters, that firstly undertake the historical-systematic localization of central problems (chapter 1) to then give a rendition of the concepts and the formalisms underlying David Lewis' and Judea Pearl's theories (chapter 2). After philosophically motivated conceptual deliberations Pearl's mathematical-technical framework is drawn on for (...) an epistemic interpretation and for emphasizing the knowledge-organizing aspect of causality in an extension of the interventionist Bayes net account of causation (chapter 3). Integrating causal and non-causal knowledge in unified structures ultimately leads to an approach towards solving problems of (causal) decision theory and at the same time facilitates the representation of logical-mathematical, synonymical, as well as reductive relationships in efficiently structured, operational nets of belief propagation (chapter 4). (shrink)