According to a growing trend in theoretical neuroscience, the human perceptual system is akin to a Bayesian machine. The aim of this article is to clearly articulate the claims that perception can be considered Bayesian inference and that the brain can be considered a Bayesian machine, some of the epistemological challenges to these claims; and some of the implications of these claims. We address two questions: (i) How are Bayesian models used in theoretical neuroscience? (ii) From (...) the use of Bayesian models in theoretical neuroscience, have we learned or can we hope to learn that perception is Bayesian inference or that the brain is a Bayesian machine? From actual practice in theoretical neuroscience, we argue for three claims. First, currently Bayesian models do not provide mechanistic explanations; instead they are useful devices for predicting and systematizing observational statements about people's performances in a variety of perceptual tasks. That is, currently we should have an instrumentalist attitude towards Bayesian models in neuroscience. Second, the inference typically drawn from Bayesian behavioural performance in a variety of perceptual tasks to underlying Bayesian mechanisms should be understood within the three-level framework laid out by David Marr ( [1982] ). Third, we can hope to learn that perception is Bayesian inference or that the brain is a Bayesian machine to the extent that Bayesian models will prove successful in yielding secure and informative predictions of both subjects' perceptual performance and features of the underlying neural mechanisms. (shrink)

Bayesian models of legal arguments generally aim to produce a single integrated model, combining each of the legal arguments under consideration. This combined approach implicitly assumes that variables and their relationships can be represented without any contradiction or misalignment, and in a way that makes sense with respect to the competing argument narratives. This paper describes a novel approach to compare and ‘average’ Bayesian models of legal arguments that have been built independently and with no attempt to make (...) them consistent in terms of variables, causal assumptions or parameterization. The approach involves assessing whether competing models of legal arguments are explained or predict facts uncovered before or during the trial process. Those models that are more heavily disconfirmed by the facts are given lower weight, as model plausibility measures, in the Bayesian model comparison and averaging framework adopted. In this way a plurality of arguments is allowed yet a single judgement based on all arguments is possible and rational. (shrink)

Cancer treatment decisions should be based on all available evidence. But this evidence is complex and varied: it includes not only the patient’s symptoms and expert knowledge of the relevant causal processes, but also clinical databases relating to past patients, databases of observations made at the molecular level, and evidence encapsulated in scientific papers and medical informatics systems. Objective Bayesian nets offer a principled path to knowledge integration, and we show in this chapter how they can be applied to (...) integrate various kinds of evidence in the cancer domain. This is important from the systems biology perspective, which needs to integrate data that concern different levels of analysis, and is also important from the point of view of medical informatics. (shrink)

The target article provides important theoretical contributions to psychology and Bayesian modeling. Despite the article's excellent points, we suggest that it succumbs to a few misconceptions about evolutionary psychology (EP). These include a mischaracterization of evolutionary psychology's approach to optimality; failure to appreciate the centrality of mechanism in EP; and an incorrect depiction of hypothesis testing. An accurate characterization of EP offers more promise for successful integration with Bayesian modeling.

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)

Cancer treatment decisions should be based on all available evidence. But this evidence is complex and varied: it includes not only the patient’s symptoms and expert knowledge of the relevant causal processes, but also clinical databases relating to past patients, databases of observations made at the molecular level, and evidence encapsulated in scientific papers and medical informatics systems. Objective Bayesian nets offer a principled path to knowledge integration, and we show in this chapter how they can be applied to (...) integrate various kinds of evidence in the cancer domain. This is important from the systems biology perspective, which needs to integrate data that concern different levels of analysis, and is also important from the point of view of medical informatics. (shrink)

In most decision-making situations, there is a plethora of information potentially available to people. Deciding what information to gather and what to ignore is no small feat. How do decision makers determine in what sequence to collect information and when to stop? In two experiments, we administered a version of the German cities task developed by Gigerenzer and Goldstein (1996), in which participants had to decide which of two cities had the larger population. Decision makers were not provided with the (...) names of the cities, but they were able to collect different kinds of cues for both response alternatives (e.g., “Does this city have a university?”) before making a decision. Our experiments differed in whether participants were free to determine the number of cues they examined. We demonstrate that a novel model, using hierarchical latent mixtures and Bayesian inference (Lee & Newell, 2011) provides a more complete description of the data from both experiments than simple conventional strategies, such as the take–the–best or the Weighted Additive heuristics. (shrink)

This paper applies Bayesian theories to critically analyse and offer reforms of intelligence analysis, collection, analysis, and decision making on the basis of Human Intelligence, Signals Intelligence, and Communication Intelligence. The article criticises the reliabilities of existing intelligence methodologies to demonstrate the need for Bayesian reforms. The proposed epistemic reform program for intelligence analysis should generate more reliable inferences. It distinguishes the transmission of knowledge from its generation, and consists of Bayesian three stages modular model for the (...) generation of reliable intelligence from multiple coherent and independent testimonial sources, and for the tracing and analysis of intelligence failures. The paper concludes with suggestions for further research, the development of artificial intellignce that may measure coherence and reliability of HUMINT sources and infer intelligence following the outlined general modular model. (shrink)

Compared with traditional statistics, only a few social scientists employ Bayesian analyses. The existing software programs for implementing Bayesian analyses such as OpenBUGS, WinBUGS, JAGS, and rstanarm can be daunting given that their complex computer codes involve a steep learning curve. In contrast, this paper introduces a new open software for implementing Bayesian network modelling and analysis: the bayesvl R package. The package aims at providing an intuitive gateway for beginners of Bayesian statistics to construct and (...) analyse mathematical models in social sciences... (shrink)

Experimental studies of speech production involving compensations for auditory and somatosensory perturbations and adaptation after training suggest that both types of sensory information are considered to plan and monitor speech production. Interestingly, individual sensory preferences have been observed in this context: subjects who compensate less for somatosensory perturbations compensate more for auditory perturbations, and \textit{vice versa}. We propose to integrate this sensory preference phenomenon in a model of speech motor planning using a probabilistic model in which speech units are characterized (...) both in auditory and somatosensory terms. Sensory preference is implemented in the model according to two approaches. In the first approach, which is often used in motor control models accounting for sensory integration, sensory preference is attributed to the relative precision (i.e., inverse of the variance) of the sensory characterization of the speech motor goals associated with phonological units (which are phonemes in the context of this paper). In the second, ``more original’’ variant, sensory preference is implemented by modulating the sensitivity of the comparison between the predicted sensory consequences of motor commands and the sensory characterizations of the phonemes. We present simulation results using these two variants, in the context of the adaptation to an auditory perturbation, implemented in a 2-dimensional biomechanical model of the tongue. Simulation results show that both variants lead to qualitatively similar results. Distinguishing them experimentally would require precise analyses of partial compensation patterns. However, the second proposed variant implements sensory preference without changing the sensory characterizations of the phonemes. This dissociates sensory preference and sensory characterizations of the phonemes, and makes the account of sensory preference more flexible. Indeed, in the second variant the sensory characterizations of the phonemes can remain stable, when sensory preference varies as a response to cognitive or attentional control. This opens new perspectives for capturing speech production variability associated with aging, disorders and speaking conditions. (shrink)

We agree with Jones & Love (J&L) that much of Bayesian modeling has taken a fundamentalist approach to cognition; but we do not believe in the potential of Bayesianism to provide insights into psychological processes. We discuss the advantages of associative explanations over Bayesian approaches to causal induction, and argue that Bayesian models have added little to our understanding of human causal reasoning.

It has been argued recently that dogmatism in epistemology is incompatible with Bayesianism. That is, it has been argued that dogmatism cannot be modelled using traditional techniques for Bayesian modelling. I argue that our response to this should not be to throw out dogmatism, but to develop better modelling techniques. I sketch a model for formal learning in which an agent can discover a posteriori fundamental epistemic connections. In this model, there is no formal objection to dogmatism.

A widely shared view in the cognitive sciences is that discovering and assessing explanations of cognitive phenomena whose production involves uncertainty should be done in a Bayesian framework. One assumption supporting this modelling choice is that Bayes provides the best approach for representing uncertainty. However, it is unclear that Bayes possesses special epistemic virtues over alternative modelling frameworks, since a systematic comparison has yet to be attempted. Currently, it is then premature to assert that cognitive phenomena involving uncertainty are (...) best explained within the Bayesian framework. As a forewarning, progress in cognitive science may be hindered if too many scientists continue to focus their efforts on Bayesian modelling, which risks to monopolize scientific resources that may be better allocated to alternative approaches. (shrink)

The mechanisms by which delusion and anxiety affect the tendency to make hasty decisions (Jumping-to-Conclusions bias) remain unclear. This paper proposes a Bayesian computational model that explores the assignment of evidence weights as a potential explanation of the Jumping-to-Conclusions bias using the Beads Task. We also investigate the Beads Task as a repeated measure by varying the key aspects of the paradigm. The Bayesian model estimations from two online studies showed that higher delusional ideation promoted reduced belief updating (...) but the impact of general and social anxiety on evidence weighting was inconsistent. The altered evidence weighting as a result of a psychopathological trait appeared insufficient in contributing to the Jumping-to-Conclusions bias. Variations in Beads Task aspects significantly affected subjective certainty at the point of decisions but not the number of draws to decisions. Repetitions of the Beads Task are feasible if one assesses the Jumping-to-Conclusions bias using number of draws to decisions. (shrink)

Kyburg’s opposition to the subjective Bayesian theory, and in particular to its advocates’ indiscriminate and often questionable use of Dutch Book arguments, is documented and much of it strongly endorsed. However, it is argued that an alternative version, proposed by both de Finetti at various times during his long career, and by Ramsey, is less vulnerable to Kyburg’s misgivings. This is a logical interpretation of the formalism, one which, it is argued, is both more natural and also avoids other, (...) widely-made objections to Bayesianism. (shrink)

As is clear to any user of software, quality control of software has not reached the same levels of sophistication as it has with traditional manufacturing. In this paper we argue that this is because insufficient thought is being given to the methods of reasoning under uncertainty that are appropriate to this domain. We then describe how we have built a large-scale Bayesian network to overcome the difficulties that have so far been met in software quality control. This exploits (...) a number of recent advances in tool support for constructing large networks. We end the paper by describing how the network was validated and illustrate the range of reasoning styles that can be modelled with this tool. (shrink)

Schurz (Synthese 164:201–234, 2008) proposed a justification of creative abduction on the basis of the Reichenbachian principle of the common cause. In this paper we take up the idea of combining creative abduction with causal principles and model instances of successful creative abduction within a Bayes net framework. We identify necessary conditions for such inferences and investigate their unificatory power. We also sketch several interesting applications of modeling creative abduction Bayesian style. In particular, we discuss use-novel predictions, confirmation, (...) and the problem of underdetermination in the context of abductive inferences. (shrink)

A large and growing body of research in computational psychiatry draws on Bayesian modelling to illuminate the dysfunctions and aberrations that underlie psychiatric disorders. After identifying the chief attractions of this research programme, we argue that its typical focus on abstract, domain-general inferential processes is likely to obscure many of the distinctive ways in which the human mind can break down and malfunction. We illustrate this by appeal to psychosis and the social phenomenology of delusions.

We give an overview of the practice of developing and using complex climate models, as seen from experiences in a major climate modelling center and through participation in the Coupled Model Intercomparison Project. We discuss the construction and calibration of models; their evaluation, especially through use of out-of-sample tests; and their exploitation in multi-model ensembles to identify biases and make predictions. We stress that adequacy or utility of climate models is best assessed via their skill against more naïve predictions. The (...) framework we use for making inferences about reality using simulations is naturally Bayesian, and has many points of contact with more familiar examples of scientific epistemology. While the use of complex simulations in science is a development that changes much in how science is done in practice, we argue that the concepts being applied fit very much into traditional practices of the scientific method, albeit those more often associated with laboratory work. (shrink)

Michael G. Titelbaum presents a new Bayesian framework for modeling rational degrees of belief—the first of its kind to represent rational requirements on agents who undergo certainty loss.

In classifications of vocabulary knowledge, vocabulary size and depth have often been separately conceptualized (Schmitt, 2014). Although size and depth are known to be substantially correlated, it is not clear whether they are a single construct or two separate components of vocabulary knowledge (Yanagisawa & Webb, 2020). This issue has not been addressed extensively in the literature and can be better examined using structural equation modeling (SEM), with measurement error modeled separately from the construct of interest. The current study (...) reports on conventional and Bayesian SEM approaches (e.g., Muthén & Asparouhov, 2012) to examine the factor structure of the size and depth of second language vocabulary knowledge of Japanese adult learners of English. A total of 255 participants took five vocabulary tests. One test was designed to measure vocabulary size in terms of the number of words known, while the remaining four were designed to measure vocabulary depth in terms of word association, polysemy, and collocation. All tests used a multiple-choice format. The size test was divided into three subtests according to word frequency. Results from conventional and Bayesian SEM show that a correlated two-factor model of size and depth with three and four indicators, respectively, fit better than a single-factor model of size and depth. In the two-factor model, vocabulary size and depth were strongly correlated (r =.945 for conventional SEM and.943 for Bayesian SEM with cross loadings), but they were distinct. The implications of these findings are discussed. (shrink)

There are two distinct approaches to Bayesian modelling in cognitive science. Black-box approaches use Bayesian theory to model the relationship between the inputs and outputs of a cognitive system without reference to the mediating causal processes; while mechanistic approaches make claims about the neural mechanisms which generate the outputs from the inputs. This paper concerns the relationship between these two approaches. We argue that the dominant trend in the philosophical literature, which characterizes the relationship between black-box and mechanistic (...) approaches to Bayesian cognitive science in terms of the dichotomy between instrumentalism and realism, is misguided. We propose that the two distinctions are orthogonal: black-box and mechanistic approaches to Bayesian modelling can each be given either an instrumentalist or a realist interpretation. We argue that the current tendency to conflate black-box approaches with instrumentalism and mechanistic approaches with realism stems from unwarranted assumptions about the nature of scientific explanation, the ontological commitments of scientific theories, and the role of abstraction and idealization in scientific models. We challenge each of these assumptions to reframe the debates over Bayesian modelling in cognitive science. (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)

According to the Bayesian paradigm in the psychology of reasoning, the norms by which everyday human cognition is best evaluated are probabilistic rather than logical in character. Recently, the Bayesian paradigm has been applied to the domain of argumentation, where the fundamental norms are traditionally assumed to be logical. Here, we present a major generalisation of extant Bayesian approaches to argumentation that (i)utilizes a new class of Bayesian learning methods that are better suited to modelling dynamic (...) and conditional inferences than standard Bayesian conditionalization, (ii) is able to characterise the special value of logically valid argument schemes in uncertain reasoning contexts, (iii) greatly extends the range of inferences and argumentative phenomena that can be adequately described in a Bayesian framework, and (iv) undermines some influential theoretical motivations for dual function models of human cognition. We conclude that the probabilistic norms given by the Bayesian approach to rationality are not necessarily at odds with the norms given by classical logic. Rather, the Bayesian theory of argumentation can be seen as justifying and enriching the argumentative norms of classical logic. (shrink)

The prominence of Bayesian modeling of cognition has increased recently largely because of mathematical advances in specifying and deriving predictions from complex probabilistic models. Much of this research aims to demonstrate that cognitive behavior can be explained from rational principles alone, without recourse to psychological or neurological processes and representations. We note commonalities between this rational approach and other movements in psychology – namely, Behaviorism and evolutionary psychology – that set aside mechanistic explanations or make use of optimality (...) assumptions. Through these comparisons, we identify a number of challenges that limit the rational program's potential contribution to psychological theory. Specifically, rational Bayesian models are significantly unconstrained, both because they are uninformed by a wide range of process-level data and because their assumptions about the environment are generally not grounded in empirical measurement. The psychological implications of most Bayesian models are also unclear. Bayesian inference itself is conceptually trivial, but strong assumptions are often embedded in the hypothesis sets and the approximation algorithms used to derive model predictions, without a clear delineation between psychological commitments and implementational details. Comparing multiple Bayesian models of the same task is rare, as is the realization that many Bayesian models recapitulate existing (mechanistic level) theories. Despite the expressive power of current Bayesian models, we argue they must be developed in conjunction with mechanistic considerations to offer substantive explanations of cognition. We lay out several means for such an integration, which take into account the representations on which Bayesian inference operates, as well as the algorithms and heuristics that carry it out. We argue this unification will better facilitate lasting contributions to psychological theory, avoiding the pitfalls that have plagued previous theoretical movements. (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)

We consider the use of interventions for resolving a problem of unidentified statistical models. The leading examples are from latent variable modelling, an influential statistical tool in the social sciences. We first explain the problem of statistical identifiability and contrast it with the identifiability of causal models. We then draw a parallel between the latent variable models and Bayesian networks with hidden nodes. This allows us to clarify the use of interventions for dealing with unidentified statistical models. We end (...) by discussing the philosophical and methodological import of our result. (shrink)

Bayesian cognitive science is a research programme that relies on modelling resources from Bayesian statistics for studying and understanding mind, brain, and behaviour. Conceiving of mental capacities as computing solutions to inductive problems, Bayesian cognitive scientists develop probabilistic models of mental capacities and evaluate their adequacy based on behavioural and neural data generated by humans (or other cognitive agents) performing a pertinent task. The overarching goal is to identify the mathematical principles, algorithmic procedures, and causal mechanisms that (...) enable cognitive agents to take uncertainty into account and weigh it appropriately in producing adaptive behaviour. -/- The appeal of Bayesian cognitive science derives from its transparency, normativity, and unifying power. Resources from Bayesian statistics allow cognitive scientists to characterise transparently, in terms of random variables and probabilistic dependencies between them, the inductive problems that many mental capacities are presumed to solve. Given this characterisation, researchers can define an upper bound on one’s performance on that problem and use it as a benchmark for interpreting experimental results, formulating hypotheses about why and when deviations from optimal performance should be expected, and seeking explanations of mental capacities within one encompassing theoretical framework. -/- Although critics question the testability, explanatory power, and plausibility of Bayesian models of mental capacities, Bayesian cognitive science has proved itself to be an incredibly fruitful research programme. Fuelled by empirical and theoretical results from psychology, neuroscience, philosophy, computer science, artificial intelligence, and evolution, Bayesian cognitive science has: advanced our understanding of why cognitive systems should keep track of uncertainty and use it to facilitate adaptive behaviour; clarified how the brain might encode information about the uncertainty of its stimuli and perform computations with probability distributions; and crystallised the insight that cognitive agents’ management of uncertainty might be grounded in predictive processes aimed at avoiding surprising exchanges with the environment. (shrink)

Children acquiring languages with noun classes have ample statistical information available that characterizes the distribution of nouns into these classes, but their use of this information to classify novel nouns differs from the predictions made by an optimal Bayesian classifier. We use rational analysis to investigate the hypothesis that children are classifying nouns optimally with respect to a distribution that does not match the surface distribution of statistical features in their input. We propose three ways in which children's apparent (...) statistical insensitivity might arise, and find that all three provide ways to account for the difference between children's behavior and the optimal classifier. A fourth model combines two of these proposals and finds that children's insensitivity is best modeled as a bias to ignore certain features during classification, rather than an inability to encode those features during learning. These results provide insight into children's developing knowledge of noun classes and highlight the complex ways in which statistical information from the input interacts with children's learning processes. (shrink)

Bayesian non-parametric (BNP) modeling has been developed and proven to be a powerful tool to analyze messy data with complex structures. Despite the increasing popularity of BNP modeling, it also faces challenges. One challenge is the estimation of the precision parameter in the Dirichlet process mixtures. In this study, we focus on a BNP growth curve model and investigate how non-informative prior, weakly informative prior, accurate informative prior, and inaccurate informative prior affect the model convergence, parameter estimation, (...) and computation time. A simulation study has been conducted. We conclude that the non-informative prior for the precision parameter is less preferred because it yields a much lower convergence rate, and growth curve parameter estimates are not sensitive to informative priors. (shrink)

Recently, there has been an increased interest in developing statistical methodologies for analyzing single case experimental design data to supplement visual analysis. Some of these are simulation-driven such as Bayesian methods because Bayesian methods can compensate for small sample sizes, which is a main challenge of SCEDs. Two simulation-driven approaches: Bayesian unknown change-point model and simulation modeling analysis were compared in the present study for three real datasets that exhibit “clear” immediacy, “unclear” immediacy, and delayed effects. (...) Although SMA estimates can be used to answer some aspects of functional relationship between the independent and the outcome variables, they cannot address immediacy or provide an effect size estimate that considers autocorrelation as required by the What Works Clearinghouse Standards. BUCP overcomes these drawbacks of SMA. In final analysis, it is recommended that both visual and statistical analyses be conducted for a thorough analysis of SCEDs. (shrink)

We present computational modeling results based on a self‐paced reading study investigating number attraction effects in Eastern Armenian. We implement three novel computational models of agreement attraction in a Bayesian framework and compare their predictive fit to the data using k‐fold cross‐validation. We find that our data are better accounted for by an encoding‐based model of agreement attraction, compared to a retrieval‐based model. A novel methodological contribution of our study is the use of comprehension questions with open‐ended responses, (...) so that both misinterpretation of the number feature of the subject phrase and misassignment of the thematic subject role of the verb can be investigated at the same time. We find evidence for both types of misinterpretation in our study, sometimes in the same trial. However, the specific error patterns in our data are not fully consistent with any previously proposed model. (shrink)

Models are a principle instrument of modern science. They are built, applied, tested, compared, revised and interpreted in an expansive scientific literature. Throughout this paper, I will argue that models are also a valuable tool for the philosopher of science. In particular, I will discuss how the methodology of Bayesian Networks can elucidate two central problems in the philosophy of science. The first thesis I will explore is the variety-of-evidence thesis, which argues that the more varied the supporting evidence, (...) the greater the degree of confirmation for a given hypothesis. However, when investigated using Bayesian methodology, this thesis turns out not to be sacrosanct. In fact, under certain conditions, a hypothesis receives more confirmation from evidence that is obtained from one rather than more instruments, and from evidence that confirms one rather than more testable consequences of the hypothesis. The second challenge that I will investigate is scientific theory change. This application highlights a different virtue of modeling methodology. In particular, I will argue that Bayesian modeling illustrates how two seemingly unrelated aspects of theory change, namely the (Kuhnian) stability of (normal) science and the ability of anomalies to over turn that stability and lead to theory change, are in fact united by a single underlying principle, in this case, coherence. In the end, I will argue that these two examples bring out some metatheoretical reflections regarding the following questions: What are the differences between modeling in science and modeling in philosophy? What is the scope of the modeling method in philosophy? And what does this imply for our understanding of Bayesianism? (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)

Computational modeling is now ubiquitous in psychology, and researchers who are not modelers may find it increasingly difficult to follow the theoretical developments in their field. This book presents an integrated framework for the development and application of models in psychology and related disciplines. Researchers and students are given the knowledge and tools to interpret models published in their area, as well as to develop, fit, and test their own models. Both the development of models and key features of (...) any model are covered, as are the applications of models in a variety of domains across the behavioural sciences. A number of chapters are devoted to fitting models using maximum likelihood and Bayesian estimation, including fitting hierarchical and mixture models. Model comparison is described as a core philosophy of scientific inference, and the use of models to understand theories and advance scientific discourse is explained. (shrink)

This paper is about the differences between probabilities and beliefs and why reasoning should not always conform to probability laws. Probability is defined in terms of urn models from which probability laws can be derived. This means that probabilities are expressed in rational numbers, they suppose the existence of veridical representations and, when viewed as parts of a probability model, they are determined by a restricted set of variables. Moreover, probabilities are subjective, in that they apply to classes of events (...) that have been deemed (by someone) to be equivalent, rather than to unique events. Beliefs on the other hand are multifaceted, interconnected with all other beliefs, and inexpressible in their entirety. It will be argued that there are not sufficient rational numbers to characterise beliefs by probabilities and that the idea of a veridical set of beliefs is questionable. The concept of a complete probability model based on Fisher's notion of identifiable subsets is outlined. It is argued that to be complete a model must be known to be true. This can never be the case because whatever a person supposes to be true must be potentially modifiable in the light of new information. Thus to infer that an individual's probability estimate is biased it is necessary not only to show that the estimate differs from that given by a probability model, but also to assume that this model is complete, and completeness is not empirically verifiable. It follows that probability models and Bayes theorem are not necessarily appropriate standards for people's probability judgements. The quality of a probability model depends on how reasonable it is to treat some existing uncertainty as if it were equivalent to that in a particular urn model and this cannot be determined empirically. Bias can be demonstrated in estimates of proportions of finite populations such as in the false consensus effect. However the modification of beliefs by ad hoc methods like Tversky and Kahneman's heuristics can be justified, even though this results in biased judgements. This is because of pragmatic factors such as the cost of obtaining and taking account of additional information which are not included even in a complete probability model. Finally, an analogy is drawn between probability models and geometric figures. Both idealisations are useful but qualitatively inadequate characterisations of nature. A difference between the two is that the size of any error can be limited in the case of the geometric figure in a way that is not possible in a probability model. (shrink)