arXiv subjects

Thomas Parr

Publications and source records attributed to Thomas Parr.

At least 19 recordsLinked to original sources

arXiv2026

Cycles of Discourse, Speech Dysfluency, and Active Inference

Speech is a complex motor and social act. We must not only produce and understand sequences of variable-length words formed of ordered syllables but also speak and listen in turn. This theoretical paper introduces a computational model of speech production and auditory segmentation based upon sequences of discrete phonemes. The purpose of this is to develop a vehicle to test (in silico) hypotheses about the mechanisms that govern loss of speech fluency, something that may happen transiently in people who stutter or progressively in various neurodegenerative conditions. The modelling here appeals to Partially Observable Markov Decision Processes that provide a useful generic formulation for specifying the internal model our brains might use to describe dynamic environments in which they can exert partial control and make partial observations. The core features of the specific model used here are: (1) a reciprocal mapping from words to sequences of varying numbers of phonemes (2) a common subset of states for both speech generation and speech perception. A further novel feature is a social component, in which one must infer who is speaking (self or other). We propose a series of hypotheses about the computational mechanisms that might underwrite speech breakdown. For example, we demonstrate that reducing the precision in the next word introduces pauses and start-of-word repetitions of the sort associated with stuttering. We examine the patterns of behaviour and belief-updating predicted by each of these hypotheses, with implications for both speaking and listening. Finally, we discuss plausible neural substrates for the underlying message passing that might be amenable to interrogation with functional imaging.

q-bio.NC↗

arXiv2025

Active inference and artificial reasoning

This technical note considers the sampling of outcomes that provide the greatest amount of information about the structure of underlying world models. This generalisation furnishes a principled approach to structure learning under a plausible set of generative models or hypotheses. In active inference, policies - i.e., combinations of actions - are selected based on their expected free energy, which comprises expected information gain and value. Information gain corresponds to the KL divergence between predictive posteriors with, and without, the consequences of action. Posteriors over models can be evaluated quickly and efficiently using Bayesian Model Reduction, based upon accumulated posterior beliefs about model parameters. The ensuing information gain can then be used to select actions that disambiguate among alternative models, in the spirit of optimal experimental design. We illustrate this kind of active selection or reasoning using partially observed discrete models; namely, a 'three-ball' paradigm used previously to describe artificial insight and 'aha moments' via (synthetic) introspection or sleep. We focus on the sample efficiency afforded by seeking outcomes that resolve the greatest uncertainty about the world model, under which outcomes are generated.

q-bio.NC↗

arXiv2025

SPM 25: open source neuroimaging analysis software

Statistical Parametric Mapping (SPM) is an integrated set of methods for testing hypotheses about the brain's structure and function, using data from imaging devices. These methods are implemented in an open source software package, SPM, which has been in continuous development for more than 30 years by an international community of developers. This paper reports the release of SPM 25.01, a major new version of the software that incorporates novel analysis methods, optimisations of existing methods, as well as improved practices for open science and software development.

q-bio.QM↗

arXiv2024

On the Minimal Theory of Consciousness Implicit in Active Inference

The multifaceted nature of subjective experience poses a challenge to the study of consciousness. Traditional neuroscientific approaches often concentrate on isolated facets, such as perceptual awareness or the global state of consciousness and construct a theory around the relevant empirical paradigms and findings. Theories of consciousness are, therefore, often difficult to compare; indeed, there might be little overlap in the phenomena such theories aim to explain. Here, we take a different approach: starting with active inference, a first principles framework for modelling behaviour as (approximate) Bayesian inference, and building up to a minimal theory of consciousness, which emerges from the shared features of computational models derived under active inference. We review a body of work applying active inference models to the study of consciousness and argue that there is implicit in all these models a small set of theoretical commitments that point to a minimal (and testable) theory of consciousness.

q-bio.NC↗

arXiv2024

A theory of generalised coordinates for stochastic differential equations

Stochastic differential equations are ubiquitous modelling tools in physics and the sciences. In most modelling scenarios, random fluctuations driving dynamics or motion have some non-trivial temporal correlation structure, which renders the SDE non-Markovian; a phenomenon commonly known as ``colored'' noise. Thus, an important objective is to develop effective tools for mathematically and numerically studying (possibly non-Markovian) SDEs. In this report, we formalise a mathematical theory for analysing and numerically studying SDEs based on so-called `generalised coordinates of motion'. Like the theory of rough paths, we analyse SDEs pathwise for any given realisation of the noise, not solely probabilistically. Like the established theory of Markovian realisation, we realise non-Markovian SDEs as a Markov process in an extended space. Unlike the established theory of Markovian realisation however, the Markovian realisations here are accurate on short timescales and may be exact globally in time, when flows and fluctuations are analytic. This theory is exact for SDEs with analytic flows and fluctuations, and is approximate when flows and fluctuations are differentiable. It provides useful analysis tools, which we employ to solve linear SDEs with analytic fluctuations. It may also be useful for studying rougher SDEs, as these may be identified as the limit of smoother ones. This theory supplies effective, computationally straightforward methods for simulation, filtering and control of SDEs; amongst others, we re-derive generalised Bayesian filtering, a state-of-the-art method for time-series analysis. Looking forward, this report suggests that generalised coordinates have far-reaching applications throughout stochastic differential equations.

math.PR↗

arXiv2024

From pixels to planning: scale-free active inference

This paper describes a discrete state-space model -- and accompanying methods -- for generative modelling. This model generalises partially observed Markov decision processes to include paths as latent variables, rendering it suitable for active inference and learning in a dynamic setting. Specifically, we consider deep or hierarchical forms using the renormalisation group. The ensuing renormalising generative models (RGM) can be regarded as discrete homologues of deep convolutional neural networks or continuous state-space models in generalised coordinates of motion. By construction, these scale-invariant models can be used to learn compositionality over space and time, furnishing models of paths or orbits; i.e., events of increasing temporal depth and itinerancy. This technical note illustrates the automatic discovery, learning and deployment of RGMs using a series of applications. We start with image classification and then consider the compression and generation of movies and music. Finally, we apply the same variational principles to the learning of Atari-like games.

cs.LG↗

arXiv2023

Active Inference and Intentional Behaviour

Recent advances in theoretical biology suggest that basal cognition and sentient behaviour are emergent properties of in vitro cell cultures and neuronal networks, respectively. Such neuronal networks spontaneously learn structured behaviours in the absence of reward or reinforcement. In this paper, we characterise this kind of self-organisation through the lens of the free energy principle, i.e., as self-evidencing. We do this by first discussing the definitions of reactive and sentient behaviour in the setting of active inference, which describes the behaviour of agents that model the consequences of their actions. We then introduce a formal account of intentional behaviour, that describes agents as driven by a preferred endpoint or goal in latent state-spaces. We then investigate these forms of (reactive, sentient, and intentional) behaviour using simulations. First, we simulate the aforementioned in vitro experiments, in which neuronal cultures spontaneously learn to play Pong, by implementing nested, free energy minimising processes. The simulations are then used to deconstruct the ensuing predictive behaviour, leading to the distinction between merely reactive, sentient, and intentional behaviour, with the latter formalised in terms of inductive planning. This distinction is further studied using simple machine learning benchmarks (navigation in a grid world and the Tower of Hanoi problem), that show how quickly and efficiently adaptive behaviour emerges under an inductive form of active inference.

q-bio.NC↗

arXiv2023

Supervised structure learning

This paper concerns structure learning or discovery of discrete generative models. It focuses on Bayesian model selection and the assimilation of training data or content, with a special emphasis on the order in which data are ingested. A key move - in the ensuing schemes - is to place priors on the selection of models, based upon expected free energy. In this setting, expected free energy reduces to a constrained mutual information, where the constraints inherit from priors over outcomes (i.e., preferred outcomes). The resulting scheme is first used to perform image classification on the MNIST dataset to illustrate the basic idea, and then tested on a more challenging problem of discovering models with dynamics, using a simple sprite-based visual disentanglement paradigm and the Tower of Hanoi (cf., blocks world) problem. In these examples, generative models are constructed autodidactically to recover (i.e., disentangle) the factorial structure of latent states - and their characteristic paths or dynamics.

cs.LG↗

arXiv2023

A variational synthesis of evolutionary and developmental dynamics

This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian mechanics of particular partitions to understand how slow phylogenetic processes constrain - and are constrained by - fast, phenotypic processes. The main result is a formulation of adaptive fitness as a path integral of phenotypic fitness. Paths of least action, at the phenotypic and phylogenetic scales, can then be read as inference and learning processes, respectively. In this view, a phenotype actively infers the state of its econiche under a generative model, whose parameters are learned via natural (bayesian model selection). The ensuing variational synthesis features some unexpected aspects. Perhaps the most notable is that it is not possible to describe or model a population of conspecifics per se. Rather, it is necessary to consider populations - and nested meta-populations - of different natural kinds that influence each other. This paper is limited to a description of the mathematical apparatus and accompanying ideas. Subsequent work will use these methods for simulations and numerical analyses - and identify points of contact with related mathematical formulations of evolution.

q-bio.PE↗

arXiv2022

Bistable perception, precision and neuromodulation

Bistable perception follows from observing a static, ambiguous, (visual) stimulus with two possible interpretations. Here, we present an active (Bayesian) inference account of bistable perception and posit that perceptual transitions between different interpretations (i.e., inferences) of the same stimulus ensue from specific eye movements that shift the focus to a different visual feature. Formally, these inferences are a consequence of precision control that determines how confident beliefs are and change the frequency with which one can perceive - and alternate between - two distinct percepts. We hypothesised that there are multiple, but distinct, ways in which precision modulation can interact to give rise to a similar frequency of bistable perception. We validated this using numerical simulations of the Necker's cube paradigm and demonstrate the multiple routes that underwrite the frequency of perceptual alternation. Our results provide an (enactive) computational account of the intricate precision balance underwriting bistable perception. Importantly, these precision parameters can be considered the computational homologues of particular neurotransmitters - i.e., acetylcholine, noradrenaline, dopamine - that have been previously implicated in controlling bistable perception, providing a computational link between the neurochemistry and perception.

q-bio.NC↗

arXiv2022

Path integrals, particular kinds, and strange things

This paper describes a path integral formulation of the free energy principle. The ensuing account expresses the paths or trajectories that a particle takes as it evolves over time. The main results are a method or principle of least action that can be used to emulate the behaviour of particles in open exchange with their external milieu. Particles are defined by a particular partition, in which internal states are individuated from external states by active and sensory blanket states. The variational principle at hand allows one to interpret internal dynamics - of certain kinds of particles - as inferring external states that are hidden behind blanket states. We consider different kinds of particles, and to what extent they can be imbued with an elementary form of inference or sentience. Specifically, we consider the distinction between dissipative and conservative particles, inert and active particles and, finally, ordinary and strange particles. Strange particles can be described as inferring their own actions, endowing them with apparent autonomy or agency. In short - of the kinds of particles afforded by a particular partition - strange kinds may be apt for describing sentient behaviour.

nlin.AO↗

arXiv2022

Reclaiming saliency: rhythmic precision-modulated action and perception

Computational models of visual attention in artificial intelligence and robotics have been inspired by the concept of a saliency map. These models account for the mutual information between the (current) visual information and its estimated causes. However, they fail to consider the circular causality between perception and action. In other words, they do not consider where to sample next, given current beliefs. Here, we reclaim salience as an active inference process that relies on two basic principles: uncertainty minimisation and rhythmic scheduling. For this, we make a distinction between attention and salience. Briefly, we associate attention with precision control, i.e., the confidence with which beliefs can be updated given sampled sensory data, and salience with uncertainty minimisation that underwrites the selection of future sensory data. Using this, we propose a new account of attention based on rhythmic precision-modulation and discuss its potential in robotics, providing numerical experiments that showcase advantages of precision-modulation for state and noise estimation, system identification and action selection for informative path planning.

cs.RO↗

arXiv2022

The free energy principle made simpler but not too simple

This paper provides a concise description of the free energy principle, starting from a formulation of random dynamical systems in terms of a Langevin equation and ending with a Bayesian mechanics that can be read as a physics of sentience. It rehearses the key steps using standard results from statistical physics. These steps entail (i) establishing a particular partition of states based upon conditional independencies that inherit from sparsely coupled dynamics, (ii) unpacking the implications of this partition in terms of Bayesian inference and (iii) describing the paths of particular states with a variational principle of least action. Teleologically, the free energy principle offers a normative account of self-organisation in terms of optimal Bayesian design and decision-making, in the sense of maximising marginal likelihood or Bayesian model evidence. In summary, starting from a description of the world in terms of random dynamical systems, we end up with a description of self-organisation as sentient behaviour that can be interpreted as self-evidencing; namely, self-assembly, autopoiesis or active inference.

cond-mat.stat-mech↗

arXiv2021

Active inference, Bayesian optimal design, and expected utility

Active inference, a corollary of the free energy principle, is a formal way of describing the behavior of certain kinds of random dynamical systems that have the appearance of sentience. In this chapter, we describe how active inference combines Bayesian decision theory and optimal Bayesian design principles under a single imperative to minimize expected free energy. It is this aspect of active inference that allows for the natural emergence of information-seeking behavior. When removing prior outcomes preferences from expected free energy, active inference reduces to optimal Bayesian design, i.e., information gain maximization. Conversely, active inference reduces to Bayesian decision theory in the absence of ambiguity and relative risk, i.e., expected utility maximization. Using these limiting cases, we illustrate how behaviors differ when agents select actions that optimize expected utility, expected information gain, and expected free energy. Our T-maze simulations show optimizing expected free energy produces goal-directed information-seeking behavior while optimizing expected utility induces purely exploitive behavior and maximizing information gain engenders intrinsically motivated behavior.

stat.ML↗

arXiv2021

Bayesian brains and the R\'enyi divergence

Under the Bayesian brain hypothesis, behavioural variations can be attributed to different priors over generative model parameters. This provides a formal explanation for why individuals exhibit inconsistent behavioural preferences when confronted with similar choices. For example, greedy preferences are a consequence of confident (or precise) beliefs over certain outcomes. Here, we offer an alternative account of behavioural variability using R\'enyi divergences and their associated variational bounds. R\'enyi bounds are analogous to the variational free energy (or evidence lower bound) and can be derived under the same assumptions. Importantly, these bounds provide a formal way to establish behavioural differences through an $\alpha$ parameter, given fixed priors. This rests on changes in $\alpha$ that alter the bound (on a continuous scale), inducing different posterior estimates and consequent variations in behaviour. Thus, it looks as if individuals have different priors, and have reached different conclusions. More specifically, $\alpha \to 0^{+}$ optimisation leads to mass-covering variational estimates and increased variability in choice behaviour. Furthermore, $\alpha \to + \infty$ optimisation leads to mass-seeking variational posteriors and greedy preferences. We exemplify this formulation through simulations of the multi-armed bandit task. We note that these $\alpha$ parameterisations may be especially relevant, i.e., shape preferences, when the true posterior is not in the same family of distributions as the assumed (simpler) approximate density, which may be the case in many real-world scenarios. The ensuing departure from vanilla variational inference provides a potentially useful explanation for differences in behavioural preferences of biological (or artificial) agents under the assumption that the brain performs variational Bayesian inference.

q-bio.NC↗

arXiv2020

Anticipation in architectural experience: a computational neurophenomenology for architecture?

The perceptual experience of architecture is enacted by the sensory and motor system. When we act, we change the perceived environment according to a set of expectations that depend on our body and the built environment. The continuous process of collecting sensory information is thus based on bodily affordances. Affordances characterize the fit between the physical structure of the body and capacities for movement in the built environment. Since little has been done regarding the role of architectural design in the emergence of perceptual experience on a neuronal level, this paper offers a first step towards the role of architectural design in perceptual experience. An approach to synthesize concepts from computational neuroscience with architectural phenomenology into a computational neurophenomenology is considered. The outcome is a framework under which studies of architecture and cognitive neuroscience can be cast.

q-bio.NC↗

arXiv2020

Reward Maximisation through Discrete Active Inference

Active inference is a probabilistic framework for modelling the behaviour of biological and artificial agents, which derives from the principle of minimising free energy. In recent years, this framework has successfully been applied to a variety of situations where the goal was to maximise reward, offering comparable and sometimes superior performance to alternative approaches. In this paper, we clarify the connection between reward maximisation and active inference by demonstrating how and when active inference agents perform actions that are optimal for maximising reward. Precisely, we show the conditions under which active inference produces the optimal solution to the Bellman equation--a formulation that underlies several approaches to model-based reinforcement learning and control. On partially observed Markov decision processes, the standard active inference scheme can produce Bellman optimal actions for planning horizons of 1, but not beyond. In contrast, a recently developed recursive active inference scheme (sophisticated inference) can produce Bellman optimal actions on any finite temporal horizon. We append the analysis with a discussion of the broader relationship between active inference and reinforcement learning.

cs.AI↗

arXiv2020

Dynamic causal modelling of immune heterogeneity

An interesting inference drawn by some Covid-19 epidemiological models is that there exists a proportion of the population who are not susceptible to infection -- even at the start of the current pandemic. This paper introduces a model of the immune response to a virus. This is based upon the same sort of mean-field dynamics as used in epidemiology. However, in place of the location, clinical status, and other attributes of people in an epidemiological model, we consider the state of a virus, B and T-lymphocytes, and the antibodies they generate. Our aim is to formalise some key hypotheses as to the mechanism of resistance. We present a series of simple simulations illustrating changes to the dynamics of the immune response under these hypotheses. These include attenuated viral cell entry, pre-existing cross-reactive humoral (antibody-mediated) immunity, and enhanced T-cell dependent immunity. Finally, we illustrate the potential application of this sort of model by illustrating variational inversion (using simulated data) of this model to illustrate its use in testing hypotheses. In principle, this furnishes a fast and efficient immunological assay--based on sequential serology--that provides a (i) quantitative measure of latent immunological responses and (ii) a Bayes optimal classification of the different kinds of immunological response (c.f., glucose tolerance tests used to test for insulin resistance). This may be especially useful in assessing SARS-CoV-2 vaccines.

q-bio.QM↗