The exponential growth of social data both in volume and complexity has increasingly exposed many of the shortcomings of the conventional frequentist approach to statistics. The scientific community has called for careful usage of the approach and its inference. Meanwhile, the alternative method, Bayesian statistics, still faces considerable barriers toward a more widespread application. The bayesvl R package is an open program, designed for implementing Bayesian modeling and analysis using the Stan language’s no-U-turn (NUTS) sampler. The package combines (...) the ability to construct Bayesian network models using directed acyclic graphs (DAGs), the Markov chain Monte Carlo (MCMC) simulation technique, and the graphic capability of the ggplot2 package. As a result, it can improve the user experience and intuitive understanding when constructing and analyzing Bayesian network models. A case example is offered to illustrate the usefulness of the package for Big Data analytics and cognitive computing. (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 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)

: Most work done in philosophy of experiment has focused on experiments taken from the domain of physics. The present essay tests whether Allan Franklin's (1984, 1986, 1989, 1990) philosophy of experiment developed in the context of high energy physics can be extended to include examples from evolutionary biology, such as H. B. D. Kettlewell's (1955, 1956, 1958) famous studies of industrial melanism in the peppered moth, Biston betularia. The analysis demonstrates that many of the techniques used by evolutionary (...) biologists exemplify the strategies Franklin lists, and identifies an additional strategy that can likewise be justified by appeal to Bayes's Theorem. (shrink)

This paper presents an effort to induce a Bayesian belief network (BBN) from crime data, namely the national crime victimization survey (NCVS). This BBN defines a joint probability distribution over a set of variables that were employed to record a set of crime incidents, with particular focus on characteristics of the victim. The goals are to generate a BBN to capture how characteristics of crime incidents are related to one another, and to make this information available to domain specialists. (...) The novelty associated with the study reported in this paper lies in the use of a Bayesian network to represent a complex data set to non-experts in a way that facilitates automated analysis. Validation of the BBN’s ability to approximate the joint probability distribution over the set of variables entailed in the NCVS data set is accomplished through a variety of sources including mathematical techniques and human experts for appropriate triangulation. Validation results indicate that the BBN induced from the NCVS data set is a good joint probability model for the set of attributes in the domain, and accordingly can serve as an effective query tool. (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)

Probability updating via Bayes' rule often entails extensive informational and computational requirements. In consequence, relatively few practical applications of Bayesian adaptive control techniques have been attempted. This paper discusses an alternative approach to adaptive control, Bayesian in spirit, which shifts attention from the updating of probability distributions via transitional probability assessments to the direct updating of the criterion function, itself, via transitional utility assessments. Results are illustrated in terms of an adaptive reinvestment two-armed bandit problem.

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)

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)

Decoupling is a general principle that allows us to separate simple components in a complex system. In statistics, decoupling is often expressed as independence, no association, or zero covariance relations. These relations are sharp statistical hypotheses, that can be tested using the FBST - Full Bayesian Significance Test. Decoupling relations can also be introduced by some techniques of Design of Statistical Experiments, DSEs, like randomization. This article discusses the concepts of decoupling, randomization and sparsely connected statistical models in (...) the epistemological framework of cognitive constructivism. (shrink)

Gene clustering is a useful exploratory technique to group together genes with similar expression levels under distinct cell cycle phases or distinct conditions. It helps the biologist to identify potentially meaningful relationships between genes. In this study, we propose a clustering method based on multivariate normal mixture models, where the number of clusters is predicted via sequential hypothesis tests: at each step, the method considers a mixture model of m components (m = 2 in the first step) and tests if (...) in fact it should be m - 1. If the hypothesis is rejected, m is increased and a new test is carried out. The method continues (increasing m) until the hypothesis is accepted. The theoretical core of the method is the full Bayesian significance test, an intuitive Bayesian approach, which needs no model complexity penalization nor positive probabilities for sharp hypotheses. Numerical experiments were based on a cDNA microarray dataset consisting of expression levels of 205 genes belonging to four functional categories, for 10 distinct strains of Saccharomyces cerevisiae. To analyze the method’s sensitivity to data dimension, we performed principal components analysis on the original dataset and predicted the number of classes using 2 to 10 principal components. Compared to Mclust (model-based clustering), our method shows more consistent results. (shrink)

ObjectiveTo compare techniques for computing clustering and switching scores in terms of agreement, correlation, and empirical value as predictors of incident cognitive impairment.MethodsWe transcribed animal and letter F fluency recordings on 640 cases of ICI and matched controls from a national epidemiological study, amending each transcription with word timings. We then calculated clustering and switching scores, as well as scores indexing speed of responses, using techniques described in the literature. We evaluated agreement among the techniques with Cohen’s (...) κ and calculated correlations among the scores. After fitting a base model with raw scores, repetitions, and intrusions, we fit a series of Bayesian logistic regression models adding either clustering and switching scores or speed scores, comparing the models in terms of several metrics. We partitioned the ICI cases into acute and progressive cases and repeated the regression analysis for each group.ResultsFor animal fluency, we found that models with speed scores derived using the slope difference algorithm achieved the best values of the Watanabe–Akaike Information Criterion, but with good net reclassification improvement only for the progressive group. For letter fluency, different models excelled for prediction of acute and progressive cases. For acute cases, NRI was best for speed scores derived from a network model, while for progressive cases, the best model used clustering and switching scores derived from the same network model. Combining variables from the best animal and letter F models led to marginal improvements in model fit and NRI only for the all-cases and acute-cases analyses.ConclusionSpeed scores improve a base model for predicting progressive cognitive impairment from animal fluency. Letter fluency scores may provide complementary information. (shrink)

The use of transcranial Electrical Stimulation in the modulation of cognitive brain functions to improve neuropsychiatric conditions has extensively increased over the decades. tES techniques have also raised new challenges associated with study design, stimulation protocol, functional specificity, and dose-response relationship. In this paper, we addressed challenges through the emerging methodology to investigate the dose-response relationship of High Definition-transcranial Direct Current Stimulation, identifying the role of negative valence in tinnitus perception. In light of the neurofunctional testable framework and tES (...) application, hypotheses were formulated to measure clinical and surrogate endpoints. We posited that conscious pairing adequately pleasant stimuli with tinnitus perception results in correction of the loudness misperception and would be reinforced by concurrent active HD-tDCS on the left Dorsolateral Prefrontal Cortex. The dose-response relationship between HD-tDCS specificity and the loudness perception is also modeled. We conducted a double-blind, randomized crossover pilot study with six recruited tinnitus patients. Accrued data was utilized to design a well-controlled adaptive seamless Bayesian dose-response study. The sample size and optimum interims were anticipated for adaptive decision-making about efficacy, safety, and single session dose parameters. Furthermore, preliminary pilot study results were sufficient to show a significant difference within the longitudinally detected self-report tinnitus loudness between before and under positive emotion induction. This study demonstrated a research methodology used to improve emotion regulation in tinnitus patients. In the projected method, positive emotion induction is essential for promoting functional targeting under HD-tDCS anatomical specificity to indicate the efficacy and facilitate the dose-finding process. The continuous updating of prior knowledge about efficacy and dose during the exploratory stage adapts the anticipated dose-response model. Consequently, the effective dose range to make superiority neuromodulation in correcting loudness misperception of tinnitus will be redefined. Highly effective dose adapts the study to a standard randomized trial and transforms it into the confirmatory stage in which active HD-tDCS protocol is compared with a sham trial. Establishing the HD-tDCS intervention protocols relying on this novel method provides reliable evidence for regulatory agencies to approve or reject the efficacy and safety. Furthermore, this paper supports a technical report for designing multimodality data-driven complementary investigations in emotion regulation, including EEG-driven neuro markers, Stroop-driven attention biases, and neuroimaging-driven brain network dynamics. (shrink)

The statistical evidence for the detrimental effect of exposure to low levels of lead on the cognitive capacities of children has been debated for several decades. In this paper I describe how two techniques from artificial intelligence and statistics help make the statistical evidence for the accepted epidemiological conclusion seem decisive. The first is a variable-selection routine in TETRAD III for finding causes, and the second a Bayesian estimation of the parameter reflecting the causal influence of Actual Lead (...) Exposure, a latent variable, on the measured IQ score of middle class suburban children. (shrink)

With small to modest sample sizes and complex models, maximum likelihood estimation of confirmatory factor analysis models can show serious estimation problems such as non-convergence or parameter estimates outside the admissible parameter space. In this article, we distinguish different Bayesian estimators that can be used to stabilize the parameter estimates of a CFA: the mode of the joint posterior distribution that is obtained from penalized maximum likelihood estimation, and the mean, median, or mode of the marginal posterior distribution that (...) are calculated by using Markov Chain Monte Carlo methods. In two simulation studies, we evaluated the performance of the Bayesian estimators from a frequentist point of view. The results show that the EAP produced more accurate estimates of the latent correlation in many conditions and outperformed the other Bayesian estimators in terms of root mean squared error. We also argue that it is often advantageous to choose a parameterization in which the main parameters of interest are bounded, and we suggest the four-parameter beta distribution as a prior distribution for loadings and correlations. Using simulated data, we show that selecting weakly informative four-parameter beta priors can further stabilize parameter estimates, even in cases when the priors were mildly misspecified. Finally, we derive recommendations and propose directions for further research. (shrink)

Standard models in quantitative linguistics assume that word usage follows a fixed frequency distribution, often Zipf's law or a close relative. This view, however, does not capture the near daily variations in topics of conversation, nor the short-term dynamics of language change. In order to understand the dynamics of human language use, we present a corpus of daily word frequency variation scraped from online news sources every 20 min for more than 2 years. We construct a simple time-varying model with (...) a latent state, which is observed via word frequency counts. We use Bayesian techniques to infer the parameters of this model for 20,000 words, allowing us to convert complex word-frequency trajectories into low-dimensional parameters in word usage. By analyzing the inferred parameters of this model, we quantify the relative mobility and drift of words on a day-to-day basis, while accounting for sampling error. We quantify this variation and show evidence against “rich-get-richer” models of word use, which have been previously hypothesized to explain statistical patterns in language. (shrink)

For a long while Bayesian techniques in statistics in general, and decision theory in particular, were considered suspect at best, and to be avoided; but now along comes Jeffrey with a system of subjective probability and utility functions determined by the individual's preferences, and a strongly Bayesian approach to decision-making, and by so doing puts the whole matter in a new light and makes it quite important to reassess the prior rejection of Bayesian methods. There are (...) twelve chapters, each with exercises, which begin with the model of deliberation, progress though scaling and ranking desirability, preference and propositional attitudes, thence to probability and measurement of desirability, and finally to induction and confirmation. The author's theory bears some resemblances to that sketched by Ramsey, but it draws somewhat on the later work of Von Neumann and Morgenstern. The author examines probability as viewed both statically—when the agent's attitudes are constant—and dynamically-when desirability and, consequently, probability assignments change. This text is one of the small but growing library of works whose interest is induction and probability theory; in that library, it will occupy an important place.—P. J. M. (shrink)

This research employs the Bayesian network modeling approach, and the Markov chain Monte Carlo technique, to learn about the role of lies and violence in teachings of major religions, using a unique dataset extracted from long-standing Vietnamese folktales. The results indicate that, although lying and violent acts augur negative consequences for those who commit them, their associations with core religious values diverge in the final outcome for the folktale characters. Lying that serves a religious mission of either Confucianism or (...) Taoism (but not Buddhism) brings a positive outcome to a character (βT_and_Lie_O= 2.23; βC_and_Lie_O= 1.47; βT_and_Lie_O= 2.23). A violent act committed to serving Buddhist missions results in a happy ending for the committer (βB_and_Viol_O= 2.55). What is highlighted here is a glaring double standard in the interpretation and practice of the three teachings: the very virtuous outcomes being preached, whether that be compassion and meditation in Buddhism, societal order in Confucianism, or natural harmony in Taoism, appear to accommodate two universal vices—violence in Buddhism and lying in the latter two. These findings contribute to a host of studies aimed at making sense of contradictory human behaviors, adding the role of religious teachings in addition to cognition in belief maintenance and motivated reasoning in discounting counterargument. (shrink)

Inference to the Best Explanation and Bayesianism have both been proposed as descriptions of the way that people make inferences. This paper argues that one result from cognitive psychology, the "feminist bank teller" experiment, suggests that people use Inference to the Best Explanation rather than Bayesian techniques.

In this article, we consider estimation of the parameters of a generalized Pareto distribution and some lifetime indices such as those relating to reliability and hazard rate functions when the failure data are progressive first-failure censored. Both classical and Bayesian techniques are obtained. In the Bayesian framework, the point estimations of unknown parameters under both symmetric and asymmetric loss functions are discussed, after having been estimated using the conjugate gamma and discrete priors for the shape and scale (...) parameters, respectively. In addition, both exact and approximate confidence intervals as well as the exact confidence region for the estimators are constructed. A practical example using a simulated data set is analyzed. Finally, the performance of Bayes estimates is compared with that of maximum likelihood estimates through a Monte Carlo simulation study. (shrink)

Genetic Programming is a powerful optimization algorithm, which employs the crossover for genetic operation. Because the crossover operator in GP randomly selects sub-trees, the building blocks may be destroyed by the crossover. Recently, algorithms called PMBGPs based on probabilistic techniques have been proposed in order to improve the problem mentioned above. We propose a new PMBGP employing Bayesian network for generating new individuals with a special chromosome called expanded parse tree, which much reduces a number of possible symbols (...) at each node. Although the large number of symbols gives rise to the large conditional probability table and requires a lot of samples to estimate the interactions among nodes, a use of the expanded parse tree overcomes these problems. Computational experiments on two subjects demonstrate that our new PMBGP is much superior to prior probabilistic models. (shrink)

According to classical arguments, language learning is both facilitated and constrained by cognitive biases. These biases are reflected in linguistic typology—the distribution of linguistic patterns across the world's languages—and can be probed with artificial grammar experiments on child and adult learners. Beginning with a widely successful approach to typology (Optimality Theory), and adapting techniques from computational approaches to statistical learning, we develop a Bayesian model of cognitive biases and show that it accounts for the detailed pattern of results (...) of artificial grammar experiments on noun-phrase word order (Culbertson, Smolensky, & Legendre, 2012). Our proposal has several novel properties that distinguish it from prior work in the domains of linguistic theory, computational cognitive science, and machine learning. This study illustrates how ideas from these domains can be synthesized into a model of language learning in which biases range in strength from hard (absolute) to soft (statistical), and in which language-specific and domain-general biases combine to account for data from the macro-level scale of typological distribution to the micro-level scale of learning by individuals. (shrink)

Temporal regularities in speech, such as interdependencies in the timing of speech events, are thought to scaffold early acquisition of the building blocks in speech. By providing on-line clues to the location and duration of upcoming syllables, temporal structure may aid segmentation and clustering of continuous speech into separable units. This hypothesis tacitly assumes that learners exploit predictability in the temporal structure of speech. Existing measures of speech timing tend to focus on first-order regularities among adjacent units, and are overly (...) sensitive to idiosyncrasies in the data they describe. Here, we compare several statistical methods on a sample of 18 languages, testing whether syllable occurrence is predictable over time. Rather than looking for differences between languages, we aim to find across languages (using clearly defined acoustic, rather than orthographic, measures), temporal predictability in the speech signal which could be exploited by a language learner. First, we analyse distributional regularities using two novel techniques: a Bayesian ideal learner analysis, and a simple distributional measure. Second, we model higher-order temporal structure—regularities arising in an ordered series of syllable timings—testing the hypothesis that non-adjacent temporal structures may explain the gap between subjectively-perceived temporal regularities, and the absence of universally-accepted lower-order objective measures. Together, our analyses provide limited evidence for predictability at different time scales, though higher-order predictability is difficult to reliably infer. We conclude that temporal predictability in speech may well arise from a combination of individually weak perceptual cues at multiple structural levels, but is challenging to pinpoint. (shrink)

Many clinical and psychological constructs are conceptualized to have multivariate higher-order constructs that give rise to multidimensional lower-order traits. Although recent measurement models and computing algorithms can accommodate item response data with a higher-order structure, there are few measurement models and computing techniques that can be employed in the context of complex research synthesis, such as meta-analysis of individual participant data or integrative data analysis. The current study was aimed at modeling complex item responses that can arise when underlying (...) domain-specific, lower-order traits are hierarchically related to multiple higher-order traits for individual participant data from multiple studies. We formulated a multi-group, multivariate higher-order item response theory (HO-IRT) model from a Bayesian perspective and developed a new Markov chain Monte Carlo (MCMC) algorithm to simultaneously estimate the (a) structural parameters of the first- and second-order latent traits across multiple groups and (b) item parameters of the model. Results from a simulation study support the feasibility of the MCMC algorithm. From the analysis of real data, we found that a bivariate HO-IRT model with different correlation/covariance structures for different studies fit the data best, compared to a univariate HO-IRT model or other alternate models with unreasonable assumptions (i.e., the same means and covariances across studies). Although more work is needed to further develop the method and to disseminate it, the multi-group multivariate HO-IRT model holds promise to derive a common metric for individual participant data from multiple studies in research synthesis studies for robust inference and for new discoveries. (shrink)

Cognitive architectures have often been applied to data from individual experiments. In this paper, I develop an ACT-R reader that can model a much larger set of data, eye-tracking corpus data. It is shown that the resulting model has a good fit to the data for the considered low-level processes. Unlike previous related works, the model achieves the fit by estimating free parameters of ACT-R using Bayesian estimation and Markov-Chain Monte Carlo techniques, rather than by relying on the (...) mix of manual selection + default values. The method used in the paper is generalizable beyond this particular model and data set and could be used on other ACT-R models. (shrink)

This book is a clear, concise, and conceptually unified treatment of various problems, both formal and philosophical, of inductive logic and probability. Ackermann's main concern throughout the book is the problem of adducing inductive support for various hypotheses, and of deciding between two competing hypotheses which is more reasonable given the available evidence. The author begins with a general consideration of the criteria to be met by satisfactory rules of inductive inference: accordance with intuitive notions of reasonableness in simple cases, (...) sensitivity to the given evidence, capacity for unambiguous intersubjective application. Ackermann quickly disposes of the argument that valid inductive rules must be made to rest upon a "postulate of the uniformity of nature": "If past projections of regularities suddenly begin to go wrong, nondeductive rules satisfying the criteria suggested above will begin to select regularities other than the ones which have failed." This clears the way for a consideration of the general problem of evidential support or confirmation, with its well-known paradoxes and difficulties. Ackermann, like Goodman, locates the source of these in problems bearing on the semantics of scientific language, and cautiously points to Goodman's theory of projection and entrenchment as the way out of most of the muddle. Succeeding chapters deal with the notion of probability of hypotheses, statistical inference, and the application of Bayesian techniques and decision theory to science. A well-chosen bibliography completes this modest but rewarding little book.—H. P. K. (shrink)

This article introduces a new hybrid intake procedure developed for posttraumatic stress disorder (PTSD) screening, which combines an automated textual assessment of respondents’ self-narratives and item-based measures that are administered consequently. Text mining technique and item response modeling were used to analyze long constructed response (i.e., self-narratives) and responses to standardized questionnaires (i.e., multiple choices), respectively. The whole procedure is combined in a Bayesian framework where the textual assessment functions as prior information for the estimation of the PTSD latent (...) trait. The purpose of this study is twofold: first, to investigate whether the combination model of textual analysis and item-based scaling could enhance the classification accuracy of PTSD, and second, to examine whether the standard error of estimates could be reduced through the use of the narrative as a sort of routing test. With the sample at hand, the combination model resulted in a reduction in the misclassification rate, as well as a decrease of standard error of latent trait estimation. These findings highlight the benefits of combining textual assessment and item-based measures in a psychiatric screening process. We conclude that the hybrid test design is a promising approach to increase test efficiency and is expected to be applicable in a broader scope of educational and psychological measurement in the future. (shrink)

*PSA 2016, symposium on “Data in Time: Epistemology of Historical Data” organized by Sabina Leonelli, 5 November 2016* *See published version: "Radiocarbon Dating in Archaeology: Triangulation and Traceability" in Data Journeys in the Sciences (2020) - link below* Archaeologists put a premium on pressing “legacy data” into service, given the notoriously selective and destructive nature of their practices of data capture. Legacy data consist of material and records that been assembled over decades, sometimes centuries, often by means and for purposes (...) long since discredited or superseded. The primary strategies by which archaeologists put the data to work for new purposes are, I argue, secondary retrieval, recontextualization, and experimental modelling. I focus here on a particularly telling and complex example of secondary retrieval: the extraction of new data from old by means of radiocarbon dating. This is by no means a straightforward process of retrieving physical samples from legacy data to which 14C techniques can be applied that can, on their own, decisively settle chronological questions. When Libby’s post-war radiocarbon revolution got under way, it was expected to establish an absolute chronology that would render obsolete the local and relative chronologies on which archaeologists had long relied. Transformative though it has been, bringing these tools of physical dating to bear on archaeological problems has been a long, tortuous process, now described as proceeding through two subsequent radiocarbon revolutions. The second was an extended process of calibration by which 14C chronologies were corrected and refined, often against the very lines of evidence they were meant to displace. The most recent, a “pragmatic Bayesian” approach to archaeological dating, is motivated by concern that, no matter how much it is refined, radiocarbon dating cannot on its own resolve the chronological problems that archaeologists address; the challenge, its advocates argue, is to ‘fully integrate archaeological information with 14C dating in order to address archaeologically relevant timescales and episodes’. This is a genre of “robustness” reasoning that illustrates its epistemic risks as well as its appeal. As recent philosophical debate makes clear, it depends on appeals to the convergence of independent lines of evidence that may have more rhetorical than epistemic force and that may be spurious. Drawing on this philosophical literature I identify a set of conditions that must be met if these risks are to be avoided, all of which are an explicit focus of debate in cases of contestation about and reconciliation of chronologies based on legacy data. (shrink)

Bayesian decision theory, in its classical or strict form, requires agents to have a determinate probability function. In recent years many decision theorists have come to think that this requirement should be weakened to allow for cases in which the agent makes indeterminate probability judgments. It has been claimed that this weakening makes the theory more realistic, and that it makes the theory more tenable as a normative ideal. This paper shows that the usual technique for weakening strict Bayesianism (...) has neither of these claimed advantages. (shrink)

Bayesian modeling techniques have proven remarkably successful at representing rational constraints on agents’ degrees of belief. Yet Frank Arntzenius’s “Shangri-La” example shows that these techniques fail for stories involving forgetting. This paper presents a formalized, expanded Bayesian modeling framework that generates intuitive verdicts about agents’ degrees of belief after losing information. The framework’s key result, called Generalized Conditionalization, yields applications like a version of Bas van Fraassen’s Reflection Principle for forgetting. These applications lead to questions about (...) why agents should coordinate their doxastic states over time, and about the commitments an agent can make by assigning degrees of belief. (shrink)

Bayesian theory now incorporates a vast body of mathematical, statistical and computational techniques that are widely applied in a panoply of disciplines, from artificial intelligence to zoology. Yet Bayesians rarely agree on the basics, even on the question of what Bayesianism actually is. This book is about the basics e about the opportunities, questions and problems that face Bayesianism today.

Folklore has a critical role as a cultural transmitter, all the while being a socially accepted medium for the expressions of culturally contradicting wishes and conducts. In this study of Vietnamese folktales, through the use of Bayesian multilevel modeling and the Markov chain Monte Carlo technique, we offer empirical evidence for how the interplay between religious teachings (Confucianism, Buddhism, and Taoism) and deviant behaviors (lying and violence) could affect a folktale’s outcome. The findings indicate that characters who lie and/or (...) commit violent acts tend to have bad endings, as intuition would dictate, but when they are associated with any of the above Three Teachings, the final endings may vary. Positive outcomes are seen in cases where characters associated with Confucianism lie and characters associated with Buddhism act violently. The results supplement the worldwide literature on discrepancies between folklore and real-life conduct, as well as on the contradictory human behaviors vis-à-vis religious teachings. Overall, the study highlights the complexity of human decision-making, especially beyond the folklore realm. (shrink)

In recent years, simultaneous localization and mapping based on stochastic state-transition / observation models and Bayesian estimation technique has been the mainstream of the mobile robot mapping research. In contrast to this trend, we present an alternative formulation of the map building problem from the viewpoint of non-linear dimensionality reduction or manifold learning. In this framework, the robot map building is interpreted as a problem of reconstructing the coordinates of objects so that proximities between them in the space of (...) robot's observation history as faithfully as possible. Based on this insight, we generalize the covisibility-based mapping method which was established in previous studies into the map building based on dimensionality reduction of historical visibility data. We applied latest non-linear dimensionality reduction techniques to this framework, and compared them with classical techniques such as PCA and MDS in experimental studies. (shrink)

Acoustic emission technique is a common approach to identify the damage of the refractories; however, there is a complex problem since there are as many as fifteen involved parameters, which calls for effective data processing and classification algorithms to reduce the level of complexity. In this paper, experiments involving three-point bending tests of refractories were conducted and AE signals were collected. A new data processing method of merging the similar parameters in the description of the damage and reducing the dimension (...) was developed. By means of the principle component analysis for dimension reduction, the fifteen related parameters can be reduced to two parameters. The parameters were the linear combinations of the fifteen original parameters and taken as the indexes for damage classification. Based on the proposed approach, the Gaussian mixture model was integrated with the Bayesian information criterion to group the AE signals into two damage categories, which accounted for 99% of all damage. Electronic microscope scanning of the refractories verified the two types of damage. (shrink)

Forms of justification for inductive machine learning techniques are discussed and classified into four types. This is done with a view to introduce some of these techniques and their justificatory guarantees to the attention of philosophers, and to initiate a discussion as to whether they must be treated separately or rather can be viewed consistently from within a single framework.

This research employs the Bayesian network modeling approach, and the Markov chain Monte Carlo technique, to learn about the role of lies and violence in teachings of major religions, using a unique dataset extracted from long-standing Vietnamese folktales. The results indicate that, although lying and violent acts augur negative consequences for those who commit them, their associations with core religious values diverge in the outcome for the folktale characters. Lying that serves a religious mission of either Confucianism or Taoism (...) (but not Buddhism) brings a positive outcome to a character. A violent act committed to serving Buddhist mission results in a happy ending for the committer. (shrink)

The finding of fractal scaling (FS) in behavioral sequences has raised a debate on whether FS is a pervasive property of the cognitive system or is the result of specific processes. Inferences about the origins of properties in time sequences are causal. That is, as opposed to correlational inferences reflecting instantaneous symmetrical relations, causal inferences concern asymmetric relations lagged in time. Here, I integrate Granger‐causality with inferences about FS. Four simulations illustrate that causal analyses can isolate distinct FS sources, whereas (...) correlational techniques cannot. I then analyze three simultaneous sequences of responses from a database of word‐naming trials. I find that two, or perhaps three, distinct sources account for the presence of FS in these sequences, but FS is not a general property of the system. This suggests that FS arises due to the properties of a limited number of identifiable psychological and/or neural processes. Finally, I reanalyze a previously published dataset of acoustic frequency spectra using the new tools. The causality/criticality combination introduced here offers a new important perspective in the study of cognition. (shrink)

The past 15 years occasioned an extraordinary blossoming of research into the cognitive and affective mechanisms that support moral judgment and behavior. This growth in our understanding of moral mechanisms overshadowed a crucial and complementary question, however: How are they learned? As this special issue of the journal Cognition attests, a new crop of research into moral learning has now firmly taken root. This new literature draws on recent advances in formal methods developed in other domains, such as Bayesian (...) inference, reinforcement learning and other machine learning techniques. Meanwhile, it also demonstrates how learning and deciding in a social domain—and especially in the moral domain—sometimes involves specialized cognitive systems. We review the contributions to this special issue and situate them within the broader contemporary literature. Our review focuses on how we learn moral values and moral rules, how we learn about personal moral character and relationships, and the philosophical implications of these emerging models. (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)

Cancer research is experiencing ‘paradigm instability’, since there are two rival theories of carcinogenesis which confront themselves, namely the somatic mutation theory and the tissue organization field theory. Despite this theoretical uncertainty, a huge quantity of data is available thanks to the improvement of genome sequencing techniques. Some authors think that the development of new statistical tools will be able to overcome the lack of a shared theoretical perspective on cancer by amalgamating as many data as possible. We think (...) instead that a deeper understanding of cancer can be achieved by means of more theoretical work, rather than by merely accumulating more data. To support our thesis, we introduce the analytic view of theory development, which rests on the concept of plausibility, and make clear in what sense plausibility and probability are distinct concepts. Then, the concept of plausibility is used to point out the ineliminable role played by the epistemic subject in the development of statistical tools and in the process of theory assessment. We then move to address a central issue in cancer research, namely the relevance of computational tools developed by bioinformaticists to detect driver mutations in the debate between the two main rival theories of carcinogenesis. Finally, we briefly extend our considerations on the role that plausibility plays in evidence amalgamation from cancer research to the more general issue of the divergences between frequentists and Bayesians in the philosophy of medicine and statistics. We argue that taking into account plausibility-based considerations can lead to clarify some epistemological shortcomings that afflict both these perspectives. (shrink)

When radiocarbon dating techniques were applied to archaeological material in the 1950s they were hailed as a revolution. At last archaeologists could construct absolute chronologies anchored in temporal data backed by immutable laws of physics. This would make it possible to mobilize archaeological data across regions and time-periods on a global scale, rendering obsolete the local and relative chronologies on which archaeologists had long relied. As profound as the impact of 14C dating has been, it has had a long (...) and tortuous history now described as proceeding through three revolutions, each of which addresses distinct challenges of capturing, processing and packaging radiogenic data for use in resolving chronological puzzles with which archaeologists has long wrestled. In practice, mobilizing radiogenic data for archaeological use is a hard-won achievement; it involves multiple transformations that, at each step of the way, depend upon a diverse array of technical expertise and background knowledge. I focus on strategies of triangulation and traceability that establish the integrity of these data and their relevance as anchors for evidential reasoning in archaeology. (shrink)

Can self-locating beliefs be relevant to non-self-locating claims? Traditional Bayesian modeling techniques have trouble answering this question because their updating rule fails when applied to situations involving contextsensitivity. This essay develops a fully general framework for modeling stories involving context-sensitive claims. The key innovations are a revised conditionalization rule and a principle relating models of the same story with different modeling languages. The essay then applies the modeling framework to the Sleeping Beauty Problem, showing that when Beauty awakens (...) her degree of belief in heads should be one-third. This demonstrates that it can be rational for an agent who gains only self-locating beliefs between two times to alter her degree of belief in a non-self-locating claim. (shrink)

Franklin and Pickering agree that scientists in an experimental sequence, like the one to be discussed here, choose to accept certain experiments and their results as crucial, but disagree as to whether such choice can be justified in terms of an on-line estimate of evidential reliability. This paper suggests that it is possible to define a position between Franklin 's Bayesian objectivism and Pickering's social constructivism. This position depends on considering the sequence of improvement in material technique and instrumentation (...) as more important than any measure of reliability determined merely from such factors as evidential spread in relevant sequences, a factor that neither Franklin nor Pickering takes sufficiently into account. (shrink)

En este trabajo analizamos cómo se articula la justificación estadística de las conclusiones obtenidas en los ensayos clínicos aleatorizados con sus condiciones de aceptabilidad ética y política. Pretendemos mostrar cómo varía tal justificación dependiendo de nuestra concepción de la probabilidad y, correlativamente, qué argumentos éticos se pueden ofrecer sobre cada una de ellas. Veremos cómo los enfoques frecuentista y bayesiano resultan defendibles en el ámbito de los ensayos clínicos y defenderemos que, para su aceptación pública, se les debe exigir garantías (...) de imparcialidad cuyo mejor ejemplo es la propia técnica de aleatorización. /// This paper analyses how to combine the statistical justification of the results obtained in a randomised clinical trial and the ethical and social arguments that support its implementation. It aims at showing how this justification varies according to the view on probability we adopt and the different ethical cases that can be made to sustain it. Both the frequentist and the Bayesian approaches to the design of clinical trials will be seen as equally defensible on these grounds. To be socially acceptable both approaches must meet an impartiality requirement, which is best served by the technique of randomisation. (shrink)

The finding of fractal scaling (FS) in behavioral sequences has raised a debate on whether FS is a pervasive property of the cognitive system or is the result of specific processes. Inferences about the origins of properties in time sequences are causal. That is, as opposed to correlational inferences reflecting instantaneous symmetrical relations, causal inferences concern asymmetric relations lagged in time. Here, I integrate Granger-causality with inferences about FS. Four simulations illustrate that causal analyses can isolate distinct FS sources, whereas (...) correlational techniques cannot. I then analyze three simultaneous sequences of responses from a database of word-naming trials. I find that two, or perhaps three, distinct sources account for the presence of FS in these sequences, but FS is not a general property of the system. This suggests that FS arises due to the properties of a limited number of identifiable psychological and/or neural processes. Finally, I reanalyze a previously published dataset of acoustic frequency spectra using the new tools. The causality/criticality combination introduced here offers a new important perspective in the study of cognition. (shrink)

This paper presents an attempt to integrate theories of causal processes—of the kind developed by Wesley Salmon and Phil Dowe—into a theory of causal models using Bayesian networks. We suggest that arcs in causal models must correspond to possible causal processes. Moreover, we suggest that when processes are rendered physically impossible by what occurs on distinct paths, the original model must be restricted by removing the relevant arc. These two techniques suffice to explain cases of late preëmption and (...) other cases that have proved problematic for causal models. (shrink)

Although this issue of the JSE, as usual, contains a diverse cocktail of interesting papers, two of those papers are sufficiently out of the ordinary to deserve a few comments. In this issue, we fearlessly address—for the second time in the JSE’s history—one of the thorniest and most interesting topics in English literature—namely, the debate over Shakespeare authorship. As some current SSE members are undoubtedly aware, many have challenged the orthodox view that the works of Shakespeare were written by the (...) person traditionally identified as the author—that is, William Shaxpere of Stratford-upon-Avon. SSE stalwart (and my editorial predecessor) Peter Sturrock tackled the topic in the JSE in 2008 (Sturrock 2008), and then several years later followed that up with a book on the subject (Sturrock 2013). What Sturrock did brilliantly was to demonstrate how one can invoke Bayesian probability theory to challenge the orthodoxy in a compelling way. For this issue, we reprint that paper and combine it with a penetrating new work on the subject by David Roper. Roper approaches the matter from a different angle than that adopted by Sturrock. He draws on the science of cryptography to argue that the true author of the Shakespeare works was Edward de Vere, the 17th Earl of Oxford. (This is also the conclusion emerging most naturally from Sturrock’s book.) Roper argues that Sixteenth-Century techniques of using codes and ciphers were both common and quite well-developed, and that these permitted concealing secret messages within apparently innocent passages of prose or poetry. Moreover, Roper marshals a great deal of historical evidence for the claim that de Vere and others had good reason to conceal de Vere’s authorship of the works attributed to Shaxpere. So I hope our readers will enjoy this excursion into what should be largely unfamiliar territory for most of them. I know I learned a great deal from these papers, and I’m pleased that the JSE can make a scientific contribution to this venerable debate. As I see it, the papers by Sturrock and Roper together constitute a fascinating and impressive full frontal assault on the orthodox view. (shrink)

Magnetoencephalography is increasingly used for presurgical planning in people with medically refractory focal epilepsy. Localization of interictal epileptiform activity, a surrogate for the seizure onset zone whose removal may prevent seizures, is challenging and depends on the use of multiple complementary techniques. Accurate and reliable localization of epileptiform activity from spontaneous MEG data has been an elusive goal. One approach toward this goal is to use a novel Bayesian inference algorithm—the Champagne algorithm with noise learning—which has shown tremendous (...) success in source reconstruction, especially for focal brain sources. In this study, we localized sources of manually identified MEG spikes using the Champagne algorithm in a cohort of 16 patients with medically refractory epilepsy collected in two consecutive series. To evaluate the reliability of this approach, we compared the performance to equivalent current dipole modeling, a conventional source localization technique that is commonly used in clinical practice. Results suggest that Champagne may be a robust, automated, alternative to manual parametric dipole fitting methods for localization of interictal MEG spikes, in addition to its previously described clinical and research applications. (shrink)