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)

The full Bayesian signi/cance test (FBST) for precise hypotheses is presented, with some illustrative applications. In the FBST we compute the evidence against the precise hypothesis. We discuss some of the theoretical properties of the FBST, and provide an invariant formulation for coordinate transformations, provided a reference density has been established. This evidence is the probability of the highest relative surprise set, “tangential” to the sub-manifold (of the parameter space) that defines the null hypothesis.

Mathematicians often speak of conjectures as being confirmed by evidence that falls short of proof. For their own conjectures, evidence justifies further work in looking for a proof. Those conjectures of mathematics that have long resisted proof, such as the Riemann hypothesis, have had to be considered in terms of the evidence for and against them. In recent decades, massive increases in computer power have permitted the gathering of huge amounts of numerical evidence, both for conjectures in pure mathematics and (...) for the behavior of complex applied mathematical models and statistical algorithms. Mathematics has therefore become (among other things) an experimental science (though that has not diminished the importance of proof in the traditional style). We examine how the evaluation of evidence for conjectures works in mathematical practice. We explain the (objective) Bayesian view of probability, which gives a theoretical framework for unifying evidence evaluation in science and law as well as in mathematics. Numerical evidence in mathematics is related to the problem of induction; the occurrence of straightforward inductive reasoning in the purely logical material of pure mathematics casts light on the nature of induction as well as of mathematical reasoning. (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)

Abstract: The Pull Bayesian Significance Test (FBST) for precise hy- potheses is applied to a Multivariate Normal Structure (MNS) model. In the FBST we compute the evidence against the precise hypothesis. This evi- dence is the probability of the Highest Relative Surprise Set (HRSS) tangent to the sub-manifold (of the parameter space) that defines the null hypothesis. The MNS model we present appears when testing equivalence conditions for genetic expression measurements, using micro-array technology.

Bayesian models can be related to cognitive processes in a variety of ways that can be usefully understood in terms of Marr's distinction among three levels of explanation: computational, algorithmic and implementation. In this note, we discuss how an integrated probabilistic account of the different levels of explanation in cognitive science is resulting, at least for the current research practice, in a sort of unpredicted epistemological shift with respect to Marr's original proposal.

Bayesian epistemologists support the norms of probabilism and conditionalization using Dutch book and accuracy arguments. These arguments assume that rationality requires agents to maximize practical or epistemic value in every doxastic state, which is evaluated from a subjective point of view (e.g., the agent’s expectancy of value). The accuracy arguments also presuppose that agents are opinionated. The goal of this paper is to discuss the assumptions of these arguments, including the measure of epistemic value. I have designed AI agents (...) based on the Bayesian model and a nonmonotonic framework and tested how they achieve practical and epistemic value in conditions in which an alternative set of assumptions holds. In one of the tested conditions, the nonmonotonic agent, which is not opinionated and fulfills neither probabilism nor conditionalization, outperforms the Bayesian in the measure of epistemic value that I argue for in the paper (α-value). I discuss the consequences of these results for the epistemology of rationality. (shrink)

Conditional independence tests have received special attention lately in machine learning and computational intelligence related literature as an important indicator of the relationship among the variables used by their models. In the field of probabilistic graphical models, which includes Bayesian network models, conditional independence tests are especially important for the task of learning the probabilistic graphical model structure from data. In this paper, we propose the full Bayesian significance test for tests of conditional independence for discrete datasets. The (...) full Bayesian significance test is a powerful Bayesian test for precise hypothesis, as an alternative to the frequentist’s significance tests (characterized by the calculation of the p-value). (shrink)

Statistical tests that detect and measure deviation from the Hardy-Weinberg equilibrium (HWE) have been devised but are limited when testing for deviation at multiallelic DNA loci is attempted. Here we present the full Bayesian significance test (FBST) for the HWE. This test depends neither on asymptotic results nor on the number of possible alleles for the particular locus being evaluated. The FBST is based on the computation of an evidence index in favor of the HWE hypothesis. A great (...) deal of forensic inference based on DNA evidence assumes that the HWE is valid for the genetic loci being used. We applied the FBST to genotypes obtained at several multiallelic short tandem repeat loci during routine parentage testing; the locus Penta E exemplifies those clearly in HWE while others such as D10S1214 and D19S253 do not appear to show this. (shrink)

The Fully Bayesian Significance Test (FBST) is a coherent Bayesian significance test for sharp hypotheses. This paper explores the FBST as a model selection tool for general mixture models, and gives some computational experiments for Multinomial-Dirichlet-Normal-Wishart models.

In this paper, the notion of degree of inconsistency is introduced as a tool to evaluate the sensitivity of the Full Bayesian Significance Test (FBST) value of evidence with respect to changes in the prior or reference density. For that, both the definition of the FBST, a possibilistic approach to hypothesis testing based on Bayesian probability procedures, and the use of bilattice structures, as introduced by Ginsberg and Fitting, in paraconsistent logics, are reviewed. The computational and theoretical advantages (...) of using the proposed degree of inconsistency based sensitivity evaluation as an alternative to traditional statistical power analysis is also discussed. (shrink)

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

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.

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

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)

The notion of an ideal reasoner has several uses in epistemology. Often, ideal reasoners are used as a parameter of (maximum) rationality for finite reasoners (e.g. humans). However, the notion of an ideal reasoner is normally construed in such a high degree of idealization (e.g. infinite/unbounded memory) that this use is unadvised. In this dissertation, I investigate the conditions under which an ideal reasoner may be used as a parameter of rationality for finite reasoners. In addition, I present and justify (...) the research program of computational epistemology, which investigates the parameter of maximum rationality for finite reasoners using computer simulations. (shrink)

The Full Bayesian Significance Test (FBST) for precise hypotheses is presented, with some applications relevant to reliability theory. The FBST is an alternative to significance tests or, equivalently, to p-ualue.s. In the FBST we compute the evidence of the precise hypothesis. This evidence is the probability of the complement of a credible set "tangent" to the sub-manifold (of the para,rreter space) that defines the null hypothesis. We use the FBST in an application requiring a quality control of used components, (...) based on remaining life statistics. (shrink)

Like Lewis, many philosophers hold reductionist accounts of chance (on which claims about chance are to be understood as claims that certain patterns of events are instantiated) and maintain that rationality requires that credence should defer to chance (in the sense that under certain circumstances one's credence in an event must coincide with the chance of that event). It is a shortcoming of an account of chance if it implies that this norm of rationality is unsatisfiable by computable agents. This (...) shortcoming is more common than one might have hoped. (shrink)

According to data provided by CRAN, in November 2023, the number of downloads of the bayesvl program reached 293, showing an increase of +57.5% compared to the previous month.

The Internet of Things (IoT) infrastructure forms a gigantic network of interconnected and interacting devices. This infrastructure involves a new generation of service delivery models, more advanced data management and policy schemes, sophisticated data analytics tools, and effective decision making applications. IoT technology brings automation to a new level wherein nodes can communicate and make autonomous decisions in the absence of human interventions. IoT enabled solutions generate and process enormous volumes of heterogeneous data exchanged among billions of nodes. This results (...) in Big Data congestion, data management, storage issues and various inefficiencies. Fog Computing aims at solving the issues with data management as it includes intelligent computational components and storage closer to the data sources. Often, an IoT-enabled infrastructure is shared among many users with various requirements. Sharing resources, sharing operational costs and collective decision making (consensus) among many stakeholders is frequently neglected. This research addresses an essential requirement for adaptive, autonomous and consensus-based Fog computational solutions which are able to support distributed and in-network schemes and policies. These network schemes and policies need to meet the requirements of many users. In this work, innovative consensus-based computational solutions are investigated. These proposed solutions aim to correlate and organise data for effective management and decision making in Fog. Instead of individual decision making, the algorithms aim to aggregate several decisions into a consensus decision representing a collective agreement, benefiting from the individuals variant knowledge and meeting multiple stakeholders requirements. In order to validate the proposed solutions, hybrid research methodology is involved that includes the design of a test-bed and the execution of several experiments. In order to investigate the effectiveness of the paradigm, three experiments were designed and validated. Real-life sensor data and synthetic statistical data was collected, processed and analysed. Bayesian Machine Learning models and Analytics were used to consolidate the design and evaluate the performance of the algorithms. In the Fog environment, the first scenario tests the Aggregation by Distribution algorithm. The solution contribute in achieving a notable efficiency of data delivery obtained with a minimal loss in precision. The second scenario validates the merits of the approach in predicting the activities of high mobility IoT applications. The third scenario tests the applications related to smart home IoT. All proposed Consensus algorithms use statistical analysis to support effective decision making in Fog and enable data aggregation for optimal storage, data transmission, processing and analytics. The final results of all experiments showed that all the implemented consensus approaches surpass the individual ones in different performance terms. Formal results also showed that the paradigm is a good fit in many IoT environments and can be suitable for different scenarios when applying data analysis to correlate data with the design. Finally, the design demonstrates that Fog Computing can compete with Cloud Computing in terms of accuracy with an added preference of locality. (shrink)

Modular approaches to the architecture of the mind claim that some mental mechanisms, such as sensory input processes, operate in special-purpose subsystems that are functionally independent from the rest of the mind. This assumption of modularity seems to be in tension with recent claims that the mind has a predictive architecture. Predictive approaches propose that both sensory processing and higher-level processing are part of the same Bayesian information-processing hierarchy, with no clear boundary between perception and cognition. Furthermore, it is (...) not clear how any part of the predictive architecture could be functionally independent, given that each level of the hierarchy is influenced by the level above. Both the assumption of continuity across the predictive architecture and the seeming non-isolability of parts of the predictive architecture seem to be at odds with the modular approach. I explore and ultimately reject the predictive approach’s apparent commitments to continuity and non-isolation. I argue that predictive architectures can be modular architectures, and that we should in fact expect predictive architectures to exhibit some form of modularity. (shrink)

Academia is a competitive environment. Early Career Researchers (ECRs) are limited in experience and resources and especially need achievements to secure and expand their careers. To help with these issues, this book offers a new approach for conducting research using the combination of mindsponge innovative thinking and Bayesian analytics. This is not just another analytics book. 1. A new perspective on psychological processes: Mindsponge is a novel approach for examining the human mind’s information processing mechanism. This conceptual framework is (...) used to construct models in studies. The framework is highly flexible and widely applicable for many different types of information processes. The mindsponge approach can help researchers discover interesting ideas or even formulate their very own theories when investigating psychosocial phenomena. This approach brings a fresh wind to the current landscape of social sciences and humanities (SSH). 2. Easy-to-follow analysis protocol: The Bayesian Mindsponge Framework (BMF analytics) is useful in terms of computing and visualizing power but also easy to learn and apply. Contrary to being intimidating, the Bayesian analytics section of this book is presented in a reader-friendly manner with a detailed yet clear step-by-step procedure. Examples are from published BMF articles, allowing readers to immediately practice the method and quickly create their own applications. With educational purposes in mind, the book is very suitable for ECRs who are looking to innovate their research methods. 3. Advocating for low-cost, high-quality research: Doing science can be very costly. Mindsponge innovative thinking and BMF analytics help produce impactful studies using openly available data on online repositories. This is based on the authors’ previous works and experiences. The book presents examples of employing the open R package bayesvl on secondary data from different sources. With less financial constraints, researchers can have more freedom of thought to pursue their curiosity and creativity. ECRs in low- and middle-income countries may find this aspect crucial in their careers. 4. Support and collaboration: The authors share their insights from experiences in the academic publishing system to help readers get through the processes of manuscript writing and peer-reviewing more easily. The authors are also ready to support other researchers with further inquiries and collaboration opportunities at the following website, mindsponge(dot)info. This book is for: a) ECRs whose only abundant resources are their innovation capacity and strength of will; b) Researchers in SSH who want to explore a novel approach to thinking and study conducting; c) Low- and middle-income countries’ researchers looking for a cost-effective research protocol; and, d) Innovative thinkers who want to turn their interesting thoughts into good publications. (shrink)

Mental representations remain the central posits of psychology after many decades of scrutiny. However, there is no consensus about the representational format(s) of biological cognition. This paper provides a survey of evidence from computational cognitive psychology, perceptual psychology, developmental psychology, comparative psychology, and social psychology, and concludes that one type of format that routinely crops up is the language-of-thought (LoT). We outline six core properties of LoTs: (i) discrete constituents; (ii) role-filler independence; (iii) predicate–argument structure; (iv) logical operators; (v) inferential (...) promiscuity; and (vi) abstract content. These properties cluster together throughout cognitive science. Bayesian computational modeling, compositional features of object perception, complex infant and animal reasoning, and automatic, intuitive cognition in adults all implicate LoT-like structures. Instead of regarding LoT as a relic of the previous century, researchers in cognitive science and philosophy-of-mind must take seriously the explanatory breadth of LoT-based architectures. We grant that the mind may harbor many formats and architectures, including iconic and associative structures as well as deep-neural-network-like architectures. However, as computational/representational approaches to the mind continue to advance, classical compositional symbolic structures – that is, LoTs – only prove more flexible and well-supported over time. (shrink)

According to certain normative theories in epistemology, rationality requires us to be logically omniscient. Yet this prescription clashes with our ordinary judgments of rationality. How should we resolve this tension? In this paper, I focus particularly on the logical omniscience requirement in Bayesian epistemology. Building on a key insight by Hacking :311–325, 1967), I develop a version of Bayesianism that permits logical ignorance. This includes: an account of the synchronic norms that govern a logically ignorant individual at any given (...) time; an account of how we reduce our logical ignorance by learning logical facts and how we should update our credences in response to such evidence; and an account of when logical ignorance is irrational and when it isn’t. At the end, I explain why the requirement of logical omniscience remains true of ideal agents with no computational, processing, or storage limitations. (shrink)

A consistent finding in research on conditional reasoning is that individuals are more likely to endorse the valid modus ponens (MP) inference than the equally valid modus tollens (MT) inference. This pattern holds for both abstract task and probabilistic task. The existing explanation for this phenomenon within a Bayesian framework (e.g., Oaksford & Chater, 2008) accounts for this asymmetry by assuming separate probability distributions for both MP and MT. We propose a novel explanation within a computational-level Bayesian account (...) of reasoning according to which “argumentation is learning”. We show that the asymmetry must appear for certain prior probability distributions, under the assumption that the conditional inference provides the agent with new information that is integrated into the existing knowledge by minimizing the Kullback-Leibler divergence between the posterior and prior probability distribution. We also show under which conditions we would expect the opposite pattern, an MT-MP asymmetry. (shrink)

The Gompertz distribution is commonly used in biology for modeling fatigue and mortality. This paper studies a class of models proposed by Adham and Walker, featuring a Gompertz type distribution where the dependence structure is modeled by a lognormal distribution, and develops a new multivariate formulation that facilitates several numerical and computational aspects. This paper also implements the FBST, the Full Bayesian Significance Test for pertinent sharp (precise) hypotheses on the lognormal covariance structure. The FBST’s e-value, ev(H), gives the (...) epistemic value of hypothesis, H, or the value of evidence in the observed in support of H. (shrink)

Knill, Kersten, & Mamassian (Chapter 6) provide an interesting discussion of how the Bayesian formulation can be used to help investigate human vision. In their view, computational theories can be based on an ideal observer that uses Bayesian inference to make optimal use of available information. Four factors are important here: the image information used, the output structures estimated, the priors assumed (i.e., knowledge about the structure of the world), and the likelihood function used (i.e., knowledge about the (...) projection of the world onto the sensors). Knill & Kersten argue that such a framework not only helps analyze a perceptual task, but can also help investigators to define it. Two examples are provided (the interpretation of surface contour and the perception of moving shadows) to show how this approach can be used in practice. As the authors admit, most (if not all) perceptual processes are ill-suited to a "strong" Bayesian approach based on a single consistent model of the world. Instead, they argue for a "weak" variant that assumes Bayesian inference to be carried out in modules of more limited scope. But how weak is "weak"? Are such approaches suitable for only a few relatively low-level tasks, or can they be applied more generally? Could a weak Bayesian approach, for example, explain how we would recognize the return of Elvis Presley? The formal modelling of human perception To help get a fix on things, it is useful to examine the fate of an earlier attempt to formalize human perception: the application of information theory. It was once hoped that this theory—a close cousin of the Bayesian formulation—would provide a way to uncover information-handling laws that were largely independent of physical implementation. In this approach, the human nervous system was assumed to have.. (shrink)

When does it make sense to act randomly? A persuasive argument from Bayesian decision theory legitimizes randomization essentially only in tie-breaking situations. Rational behaviour in humans, non-human animals, and artificial agents, however, often seems indeterminate, even random. Moreover, rationales for randomized acts have been offered in a number of disciplines, including game theory, experimental design, and machine learning. A common way of accommodating some of these observations is by appeal to a decision-maker’s bounded computational resources. Making this suggestion both (...) precise and compelling is surprisingly difficult. Toward this end, I propose two fundamental rationales for randomization, drawing upon diverse ideas and results from the wider theory of computation. The first unifies common intuitions in favour of randomization from the aforementioned disciplines. The second introduces a deep connection between randomization and memory: access to a randomizing device is provably helpful for an agent burdened with a finite memory. Aside from fit with ordinary intuitions about rational action, the two rationales also make sense of empirical observations in the biological world. Indeed, random behaviour emerges more or less where it should, according to the proposal. (shrink)

In the first month of 2024, there was a significant increase in the number of downloads for the Bayesian stats / MCMC computing program, bayesvl, developed by AISDL running on R and Stan. The following RDocumentation (CRAN) graph illustrates the noticeable leap in data for January 2024.

When visual attention is directed away from a stimulus, neural processing is weak and strength and precision of sensory data decreases. From a computational perspective, in such situations observers should give more weight to prior expectations in order to behave optimally during a discrimination task. Here we test a signal detection theoretic model that counter-intuitively predicts subjects will do just the opposite in a discrimination task with two stimuli, one attended and one unattended: when subjects are probed to discriminate the (...) unattended stimulus, they rely less on prior information about the probed stimulus’ identity. The model is in part inspired by recent findings that attention reduces trial-by-trial variability of the neuronal population response and that they use a common criterion for attended and unattended trials. In five different visual discrimination experiments, when attention was directed away from the target stimulus, subjects did not adjust their response bias in reaction to a change in stimulus presentation frequency despite being fully informed and despite the presence of performance feedback and monetary and social incentives. This indicates that subjects did not rely more on the priors under conditions of inattention as would be predicted by a Bayes-optimal observer model. These results inform and constrain future models of Bayesian inference in the human brain. (shrink)

The aim of this study is to justify the belief that there are biological normative mechanisms that fulfill non-trivial causal roles in the explanations (as formulated by researchers) of actions and behaviors present in specific systems. One example of such mechanisms is the predictive mechanisms described and explained by predictive processing (hereinafter PP), which (1) guide actions and (2) shape causal transitions between states that have specific content and fulfillment conditions (e.g. mental states). Therefore, I am guided by a specific (...) theoretical goal associated with the need to indicate those conditions that should be met by the non-trivial theory of normative mechanisms and the specific models proposed by PP supporters. In this work, I use classical philosophical methods, such as conceptual analysis and critical reflection. I also analyze selected studies in the field of cognitive science, cognitive psychology, neurology, information theory and biology in terms of the methodology, argumentation and language used, in accordance with their theoretical importance for the issues discussed in this study. In this sense, the research presented here is interdisciplinary. My research framework is informed by the mechanistic model of explanation, which defines the necessary and sufficient conditions for explaining a given phenomenon. The research methods I chose are therefore related to the problems that I intend to solve. In the introductory chapter, “The concept of predictive processing”, I discuss the nature of PP as well as its main assumptions and theses. I also highlight the key concepts and distinctions for this research framework. Many authors argue that PP is a contemporary version of Kantianism and is exposed to objections similar to those made against the approach of Immanuel Kant. I discuss this thesis and show that it is only in a very general sense that the PP framework is neo-Kantian. Here we are not dealing with transcendental deduction nor with the application of transcendental arguments. I argue that PP is based on reverse engineering and abduction inferences. In the second part of this chapter, I respond to the objection formulated by Dan Zahavi, who directly accuses this research framework of anti-realistic consequences. I demonstrate that the position of internalism, present in the so-called conservative PP, does not imply anti-realism, and that, due to the explanatory role played in it by structural representations directed at real patterns, it is justified to claim that PP is realistic. In this way, I show that PP is a non-trivial research framework, having its subject, specific methods and its own epistemic status. Finally, I discuss positions classified as the socalled radical PP. In the chapter “Predictive processing as a Bayesian explanatory model” I justify the thesis according to which PP offers Bayesian modeling. Many researchers claim that the brain is an implemented statistical probabilistic network that is an approximation of the Bayesian 7 rule. In practice, this means that all cognitive processes are to apply Bayes' rule and can be described in terms of probability distributions. Such a solution arouses objections among many researchers and is the subject of wide criticism. The purpose of this chapter is to justify the thesis that Bayesian PP is a non-trivial research framework. For this purpose, I argue that it explains certain phenomena not only at the computational level described by David Marr, but also at the level of algorithms and implementation. Later in this chapter I demonstrate that PP is normative modeling. Proponents of the use of Bayesian models in psychology or decision theory argue that they are normative because they allow the formulation of formal rules of action that show what needs to be done to make a given action optimal. Critics of this approach emphasize that such thinking about the normativity of Bayesian modeling is unjustified and that science should shift from prescriptive to descriptive positions. In a polemic with Shira Elqayam and Jonathan Evans (2011), I show that the division they propose into prescriptivism and Bayesian descriptivism is apparent, because, as I argue, there are two forms of prescriptivism, i.e. the weak and the strong. I argue that the weak version is epistemic and can lead to anti-realism, while the strong version is ontic and allows one to justify realism in relation to Bayesian models. I argue that a weak version of prescriptivism is valid for PP. It allows us to adopt anti-realism in relation to PP. In practice, this means that you can explain phenomena using Bayes' rule. This does not, however, imply that they are Bayesian in nature. However, the full justification of realism in relation to the Bayesian PP presupposes the adoption of strong prescriptivism. This position assumes that phenomena are explained by Bayesian rule because they are Bayesian as such. If they are Bayesian in nature, then they should be explained using Bayesian modeling. This thesis will be substantiated in the chapters “Normative functions and mechanisms in the context of predictive processing” and “Normative mechanisms and actions in predictive processing”. In the chapter “The Free Energy Principle in predictive processing”, I discuss the Free Energy Principle (hereinafter FEP) formulated by Karl Friston and some of its implications. According to this principle, all biological systems (defined in terms of Markov blankets) minimize the free energy of their internal states in order to maintain homeostasis. Some researchers believe that PP is a special case of applying this principle to cognition, and that predictive mechanisms are homeostatic mechanisms that minimize free energy. The discussion of FEP is important due to the fact that some authors consider it to be important for explanatory purposes and normative. If this is the case, then FEP turns out to be crucial in explaining normative predictive mechanisms and, in general, any normative biological mechanisms. To define the explanatory possibilities of this principle, I refer to the discussion of its supporters on the issue they define as the problem of continuity and discontinuity between life and mind. A critical analysis of this discussion and the additional arguments I have formulated have allowed me to revise the explanatory ambitions of FEP. I also reject the belief that this principle is necessary to explain the nature of predictive mechanisms. I argue that the principle formulated and defended by Friston is an important research heuristic for PP analysis. 8 In the chapter “Normative functions and mechanisms in predictive processing”, I start my analyzes by formulating an answer to the question about the normative nature of homeostatic mechanisms. I demonstrate that predictive mechanisms are not homeostatic. I defend the view that a full explanation of normative mechanisms presupposes an explanation of normative functions. I discuss the most important proposals for understanding the normativity of a function, both from a systemic and teleosemantic perspective. I conclude that the non-trivial concept of a function must meet two requirements which I define as explanatory and normative. I show that none of the theories I have invoked satisfactorily meets both of these requirements. Instead, I propose a model of normativity based on Bickhard's account, but supplemented by a mechanistic perspective. I argue that a function is normative when: (1) it allows one to explain the dysfunction of a given mechanism; (2) it contributes to the maintenance of the organism's stability by shaping and limiting possible relations, processes and behaviors of a given system; and when (3) (according to the representational and predictive functions) it enables explaining the attribution of logical values of certain representations / predictions. In such an approach, a mechanism is normative when it performs certain normative functions and when it is constitutive for a specific action or behavior, despite the fact that for some reason it cannot realize it either currently or in the long-term. Such an understanding of the normativity of mechanisms presupposes the acceptance of the epistemic hypothesis. I argue that this hypothesis is not cognitively satisfactory, and therefore the ontic hypothesis should be justified, which is directly related to adopting the position of ontic prescriptivism. For this reason, referring to the mechanistic theory of scientific explanations, I formulate an ontical interpretation of the concept of a normative mechanism. According to this approach, a mechanism or a function is normative when they perform such and such causal roles in explaining certain actions and behaviors. With regard to the normative properties of predictive mechanisms and functions, this means that they are the causes of specific actions an organism carries out in the environment. In this way, I justify the necessity of accepting the ontic hypothesis and rejecting the epistemic hypothesis. The fifth chapter, “Normative mechanisms and actions in predictive processing”, is devoted to the dark room problem and the related exploration-exploitation trade-off. A dark room is the state that an agent could be in if it minimized the sum of all potential prediction errors. I demonstrate that, in accordance with the basic assumption of PP about the need for continuous and long-term minimization of prediction errors, such a state should be desirable for the agent. Is it really so? Many authors believe it is not. I argue that the test of the value of PP is the possibility of a non-trivial solution of this problem, which can be reduced to the choice between active and uncertainty-increasing exploration and safe and easily predictable exploitation. I show that the solution proposed by PP supporters present in the literature does not enable a fully satisfactory explanation of this dilemma. Then I defend the position according to which the full explanation of the normative mechanisms, and, subsequently, the solution to the dilemma of exploration and exploitation, involves reference to the existence of constraints present in the environment. The constraints 9 include elements of the environment that make a given mechanism not only causal but also normative. They are therefore key to explaining the predictive mechanisms. They do not only play the role of the context in which the mechanism is implemented, but, above all, are its constitutive component. I argue that the full explanation of the role of constraints in normative predictive mechanisms presupposes the integration of individual models of specific cognitive phenomena, because only the mechanistic integration of PP with other models allows for a non-trivial explanation of the nature of normative predictive mechanisms that would have a strong explanatory value. The explanatory monism present in many approaches to PP makes it impossible to solve the problem of the dark room. Later in this chapter, I argue that the Bayesian PP is normative not because it enables the formulation of such and such rules of action, but because the predictive mechanisms themselves are normative. They are normative because they condition the choice of such and such actions by agents. In this way, I justify the hypothesis that normative mechanisms make it possible to explain the phenomenon of agent motivation, which is crucial for solving the dark room problem. In the last part of the chapter, I formulate the hypothesis of distributed normativity, which assumes that the normative nature of certain mechanisms, functions or objects is determined by the relations into which these mechanisms, functions or objects enter. This means that what is normative (in the primary sense) is the relational structure that constitutes the normativity of specific items included in it. I suggest that this hypothesis opens up many areas of research and makes it possible to rethink many problems. In the “Conclusion”, I summarize the results of my research and indicate further research perspectives. (shrink)

Predictive processing (PP) has been repeatedly presented as a unificatory account of perception, action, and cognition. In this paper, we argue that this is premature: As a unifying theory, PP fails to deliver general, simple, homogeneous, and systematic explanations. By examining its current trajectory of development, we conclude that PP remains only loosely connected both to its computational framework and to its hypothetical biological underpinnings, which makes its fundamentals unclear. Instead of offering explanations that refer to the same set of (...) principles, we observe systematic equivocations in PP‐based models, or outright contradictions with its avowed principles. To make matters worse, PP‐based models are seldom empirically validated, and they are frequently offered as mere just‐so stories. The large number of PP‐based models is thus not evidence of theoretical progress in unifying perception, action, and cognition. On the contrary, we maintain that the gap between theory and its biological and computational bases contributes to the arrested development of PP as a unificatory theory. Thus, we urge the defenders of PP to focus on its critical problems instead of offering mere re‐descriptions of known phenomena, and to validate their models against possible alternative explanations that stem from different theoretical assumptions. Otherwise, PP will ultimately fail as a unified theory of cognition. (shrink)

The framework of Solomonoff prediction assigns prior probability to hypotheses inversely proportional to their Kolmogorov complexity. There are two well-known problems. First, the Solomonoff prior is relative to a choice of Universal Turing machine. Second, the Solomonoff prior is not computable. However, there are responses to both problems. Different Solomonoff priors converge with more and more data. Further, there are computable approximations to the Solomonoff prior. I argue that there is a tension between these two responses. This is because computable (...) approximations to Solomonoff prediction do not always converge. (shrink)

Clearing algorithms are at the core of modern payment systems, facilitating the settling of multilateral credit messages with (near) minimum transfers of currency. Traditional clearing procedures use batch processing based on MILP - mixed-integer linear programming algorithms. The MILP approach demands intensive computational resources; moreover, it is also vulnerable to operational risks generated by possible defaults during the inter-batch period. This paper presents TORC3 - the Token-Ring Clearing Algorithm for Currency Circulation. In contrast to the MILP approach, TORC3 is a (...) real time heuristic procedure, demanding modest computational resources, and able to completely shield the clearing operation against the participating agents’ risk of default. (shrink)

This chapter explores to what extent some core ideas of predictive processing can be applied to the phenomenology of time consciousness. The focus is on the experienced continuity of consciously perceived, temporally extended phenomena (such as enduring processes and successions of events). The main claim is that the hierarchy of representations posited by hierarchical predictive processing models can contribute to a deepened understanding of the continuity of consciousness. Computationally, such models show that sequences of events can be represented as states (...) of a hierarchy of dynamical systems. Phenomenologically, they suggest a more fine-grained analysis of the perceptual contents of the specious present, in terms of a hierarchy of temporal wholes. Visual perception of static scenes not only contains perceived objects and regions but also spatial gist; similarly, auditory perception of temporal sequences, such as melodies, involves not only perceiving individual notes but also slightly more abstract features (temporal gist), which have longer temporal durations (e.g., emotional character or rhythm). Further investigations into these elusive contents of conscious perception may be facilitated by findings regarding its neural underpinnings. Predictive processing models suggest that sensorimotor areas may influence these contents. (shrink)

Predictive approaches to the mind claim that perception, cognition, and action can be understood in terms of a single framework: a hierarchy of Bayesian models employing the computational strategy of predictive coding. Proponents of this view disagree, however, over the extent to which perception is direct on the predictive approach. I argue that we can resolve these disagreements by identifying three distinct notions of perceptual directness: psychological, metaphysical, and epistemological. I propose that perception is plausibly construed as psychologically indirect (...) on the predictive approach, in the sense of being constructivist or inferential. It would be wrong to conclude from this, however, that perception is therefore indirect in a metaphysical or epistemological sense on the predictive approach. In the metaphysical case, claims about the inferential properties of constructivist perceptual mechanisms are consistent with both direct and indirect solutions to the metaphysical problem of perception (e.g. naïve realism, representationalism, sense datum theory). In the epistemological case, claims about the inferential properties of constructivist perceptual mechanisms are consistent with both direct and indirect approaches to the justification of perceptual belief. In this paper, I demonstrate how proponents of the predictive approach have conflated these distinct notions of perceptual directness and indirectness, and I propose alternative strategies for developing the philosophical consequences of the approach. (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)

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)

Disagreement about how best to think of the relation between theories and the realities they represent has a longstanding and venerable history. We take up this debate in relation to the free energy principle (FEP) - a contemporary framework in computational neuroscience, theoretical biology and the philosophy of cognitive science. The FEP is very ambitious, extending from the brain sciences to the biology of self-organisation. In this context, some find apparent discrepancies between the map (the FEP) and the territory (target (...) systems) a compelling reason to defend instrumentalism about the FEP. We take this to be misguided. We identify an important fallacy made by those defending instrumentalism about the FEP. We call it the literalist fallacy: this is the fallacy of inferring the truth of instrumentalism based on the claim that the properties of FEP models do not literally map onto real-world, target systems. We conclude that scientific realism about the FEP is a live and tenable option. (shrink)

The new paradigm in the psychology of reasoning draws on Bayesian formal frameworks, and some advocates of the new paradigm think of these formal frameworks as providing a computational-level theory of rational human inference. I argue that Bayesian theories should not be seen as providing a computational-level theory of rational human inference, where by “Bayesian theories” I mean theories that claim that all rational credal states are probabilistically coherent and that rational adjustments of degrees of belief in (...) the light of new evidence must be in accordance with some sort of conditionalization. The problems with the view I am criticizing can best be seen when we look at chains of inferences, rather than single-step inferences. Chains of inferences have been neglected almost entirely within the new paradigm. (shrink)

Well, well, well! Hold onto your hats, folks, because we’ve got some thrilling news from the world of computer downloads! In the wacky world of statistics and software, where numbers have all the fun, here’s a thing: In September 2023, the number of downloads for the bayesvl program by AISDL suddenly increased to 241! But there’s more to the sheer number; it’s 24.9% higher than the previous month’s total of 193. And in case you’re wondering, 241 is nearly as cool (...) as the 246 we saw back in May 2023, when the number started dwindling. It’s like déjà vu. (shrink)

The methodology title on BMF analytics is now in its third year of service to our research community, enabling many researchers to implement their research pursuits. We recently stumbled upon its listing on the Harvard University Library HOLLIS system. Its appearance at the Harvard University HOLLIS helps boost our confidence and strengthen our determination to bring its uses to the community, together with the computing capabilities of the bayesvl R package.

Working in academia is challenging, even more so for those with limited resources and opportunities. Researchers around the world do not have equal working conditions. The paper presents the structure, operation method, and conceptual framework of the SM3D Portal's community coaching method, which is built to help Early Career Researchers (ECRs) and researchers in low-resource settings overcome the obstacle of inequality and start their career progress. The community coaching method is envisioned by three science philosophies (cost-effectiveness, transparency spirit, and proactive (...) attitude) and established and operated based on the Serendipity-Mindsponge-3D knowledge (SM3D) management framework (i.e., mindsponge thinking and Bayesian Mindsponge Framework analytics serve as the coaching program's foundational theory and analytical tools). The coaching method also embraces Open Science's values for lowering the cost of doing science and encouraging the trainees to be transparent, which is expected to facilitate the self-correcting mechanism of science through open data, open review, and open dialogue. Throughout the training process, members are central beneficiaries by gaining research knowledge and skills, acquiring publication as the training's product, and shifting their mindsets from “I can't do it” to “I can do it,” and at the same time transforming a mentee to be ready for a future mentor's role. The coaching method is thus one of the members, for the member, by the members. -/- • The paper provides the structure, operation method, and conceptual framework of the SM3D Portal's community coaching method, which is built to help Early Career Researchers (ECRs) and researchers in low-resource settings overcome the obstacle of inequality and start their career progress. • The paper presents three major science philosophies envisioning the establishment and operation of scholarly community coaching. • The paper employs the mindsponge theory and BMF analytics to construct a conceptual framework explaining how an environment is created to help shift members’ mindsets from “I can't do it” to “I can do it.”. (shrink)

This article investigates religious ideals persistent in the datafication of information society. Its nodal point is Thomas Bayes, after whom Laplace names the primal probability algorithm. It reconsiders their mathematical innovations with Laplace's providential deism and Bayes' singular theological treatise. Conceptions of divine justice one finds among probability theorists play no small part in the algorithmic data-mining and microtargeting of Cambridge Analytica. Theological traces within mathematical computation are emphasized as the vantage over large numbers shifts to weights beyond enumeration (...) in probability theory. Collateral secularizations of predestination and theodicy emerge as probability optimizes into Bayesian prediction and machine learning. The paper revisits the semiotics and theism of Peirce and a given beyond the probable in Whitehead to recontextualize the critiques of providence by Agamben and Foucault. It reconsiders datafication problems alongside Nietzschean valuations. Religiosity likely remains encoded within the very algorithms presumed purified by technoscientific secularity or mathematical dispassion. (shrink)

General Morphological Analysis (GMA) is a method for structuring a conceptual problem space – called a morphospace – and, through a process of existential combinatorics, synthesizing a solution space. As such, it is a basic modelling method, on a par with other scientific modelling methods including System Dynamics Modelling, Bayesian Networks and various types graph-based “influence diagrams”. The purpose of this article is 1) to present the theoretical and methodological basics of morphological modelling; 2) to situate GMA within a (...) broader modelling theoretical framework by developing a (morphological) model representing different modelling methods, and 3) to demonstrate some of the basic modelling techniques that can be carried out with GMA using dedicated computer support. (shrink)

Science urges philosophy to be more empirical and philosophy urges science to be more reflective. This markedly occurred along the “discovery of the artificial” (CORDESCHI 2002): in the early days of Cybernetics and Artificial Intelligence (AI) researchers aimed at making machines more cognizant while setting up a framework to better understand human intelligence. By and large, those genuine goals still hold today, whereas AI has become more concerned with specific aspects of intelligence, such as (machine) learning, reasoning, vision, and action. (...) As a matter of fact, the field suffers from a chasm between two formerly integrated aspects. One is the engineering endeavour involving the development of tools, e.g., autonomous systems for driving cars as well as software for semantic information retrieval. The other is the philosophical debate that tries to answer questions concerning the nature of intelligence. Bridging these two levels can indeed be crucial in developing a deeper understanding of minds. An opportunity might be offered by the cogent theme of emotions. Traditionally, computer science, psychological and philosophical research have been compelled to investigate mental processes that do not involve mood, emotions and feelings, in spite of Simon’s early caveat (SIMON 1967) that a general theory of cognition must incorporate the influences of emotion. Given recent neurobiological findings and technological advances, the time is ripe to seriously weigh this promising, albeit controversial, opportunity. (shrink)

In this chapter I analyse an objection to phenomenal conservatism to the effect that phenomenal conservatism is unacceptable because it is incompatible with Bayesianism. I consider a few responses to it and dismiss them as misled or problematic. Then, I argue that this objection doesn’t go through because it rests on an implausible formalization of the notion of seeming-based justification. In the final part of the chapter, I investigate how seeming-based justification and justification based on one’s reflective belief that one (...) has a seeming interact with one another. (shrink)

This paper argues that the idea of a computer is unique. Calculators and analog computers are not different ideas about computers, and nature does not compute by itself. Computers, once clearly defined in all their terms and mechanisms, rather than enumerated by behavioral examples, can be more than instrumental tools in science, and more than source of analogies and taxonomies in philosophy. They can help us understand semantic content and its relation to form. This can be achieved because they have (...) the potential to do more than calculators, which are computers that are designed not to learn. Today’s computers are not designed to learn; rather, they are designed to support learning; therefore, any theory of content tested by computers that currently exist must be of an empirical, rather than a formal nature. If they are designed someday to learn, we will see a change in roles, requiring an empirical theory about the Turing architecture’s content, using the primitives of learning machines. This way of thinking, which I call the intensional view of computers, avoids the problems of analogies between minds and computers. It focuses on the constitutive properties of computers, such as showing clearly how they can help us avoid the infinite regress in interpretation, and how we can clarify the terms of the suggested mechanisms to facilitate a useful debate. Within the intensional view, syntax and content in the context of computers become two ends of physically realizing correspondence problems in various domains. (shrink)

Dogmatism is sometimes thought to be incompatible with Bayesian models of rational learning. I show that the best model for updating imprecise credences is compatible with dogmatism.

As stochastic independence is essential to the mathematical development of probability theory, it seems that any foundational work on probability should be able to account for this property. Bayesian decision theory appears to be wanting in this respect. Savage’s postulates on preferences under uncertainty entail a subjective expected utility representation, and this asserts only the existence and uniqueness of a subjective probability measure, regardless of its properties. What is missing is a preference condition corresponding to stochastic independence. To fill (...) this significant gap, the article axiomatizes Bayesian decision theory afresh and proves several representation theorems in this novel framework. (shrink)