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We discuss an approach to mathematically modelling systems made of objects that are coupled together, using generative models of the dependence relationships between states (or trajectories) of the things comprising such systems. This broad class includes open or non-equilibrium systems and is especially relevant to self-organising systems. The ensuing variational free energy principle (FEP) has certain advantages over using random dynamical systems explicitly, notably, by being more tractable and offering a parsimonious explanation of why the joint system evolves in the way that it does, based on the properties of the coupling between system components. Using the FEP allows us to model the dynamics of an object as if it were a process of variational inference, because variational free energy (or surprisal) is a Lyapunov function for its dynamics. In short, we argue that using generative models to represent and track relations among subsystems leads us to a particular statistical theory of interacting systems. Conversely, this theory enables us to construct nested models that respect the known relations among subsystems. We point out that the fact that a physical object conforms to the FEP does not necessarily imply that this object performs inference in the literal sense; rather, it is a useful explanatory fiction which replaces the 'explicit' dynamics of the object with an 'implicit' flow on free energy gradients - a fiction that may or may not be entertained by the object itself., Comment: 25+2 pages

Epilepsy is one of the most common neurological disorders, and many patients require surgical intervention when medication fails to control seizures. For effective surgical outcomes, precise localisation of the epileptogenic focus - often approximated through the Seizure Onset Zone (SOZ) - is critical yet remains a challenge. Active probing through electrical stimulation is already standard clinical practice for identifying epileptogenic areas. This paper advances the application of deep learning for SOZ localisation using Single Pulse Electrical Stimulation (SPES) responses. We achieve this by introducing Transformer models that incorporate cross-channel attention. We evaluate these models on held-out patient test sets to assess their generalisability to unseen patients and electrode placements. Our study makes three key contributions: Firstly, we implement an existing deep learning model to compare two SPES analysis paradigms - namely, divergent and convergent. These paradigms evaluate outward and inward effective connections, respectively. Our findings reveal a notable improvement in moving from a divergent (AUROC: 0.574) to a convergent approach (AUROC: 0.666), marking the first application of the latter in this context. Secondly, we demonstrate the efficacy of the Transformer models in handling heterogeneous electrode placements, increasing the AUROC to 0.730. Lastly, by incorporating inter-trial variability, we further refine the Transformer models, with an AUROC of 0.745, yielding more consistent predictions across patients. These advancements provide a deeper insight into SOZ localisation and represent a significant step in modelling patient-specific intracranial EEG electrode placements in SPES. Future work will explore integrating these models into clinical decision-making processes to bridge the gap between deep learning research and practical healthcare applications., Comment: 15 pages, 7 figures, submitted to CHIL 2024

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., Comment: 33 pages, 9 figures

This review motivates and synthesizes research efforts in neuroscience-inspired artificial intelligence and biomimetic computing in terms of mortal computation. Specifically, we characterize the notion of mortality by recasting ideas in biophysics, cybernetics, and cognitive science in terms of a theoretical foundation for sentient behavior. We frame the mortal computation thesis through the Markov blanket formalism and the circular causality entailed by inference, learning, and selection. The ensuing framework -- underwritten by the free energy principle -- could prove useful for guiding the construction of unconventional connectionist computational systems, neuromorphic intelligence, and chimeric agents, including sentient organoids, which stand to revolutionize the long-term future of embodied, enactive artificial intelligence and cognition research., Comment: Several revisions applied, corrected error in Jarzynski equality equation (w/ new citaion); references and citations now correctly aligned

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.

This paper considers neural representation through the lens of active inference, a normative framework for understanding brain function. It delves into how living organisms employ generative models to minimize the discrepancy between predictions and observations (as scored with variational free energy). The ensuing analysis suggests that the brain learns generative models to navigate the world adaptively, not (or not solely) to understand it. Different living organisms may possess an array of generative models, spanning from those that support action-perception cycles to those that underwrite planning and imagination; namely, from "explicit" models that entail variables for predicting concurrent sensations, like objects, faces, or people - to "action-oriented models" that predict action outcomes. It then elucidates how generative models and belief dynamics might link to neural representation and the implications of different types of generative models for understanding an agent's cognitive capabilities in relation to its ecological niche. The paper concludes with open questions regarding the evolution of generative models and the development of advanced cognitive abilities - and the gradual transition from "pragmatic" to "detached" neural representations. The analysis on offer foregrounds the diverse roles that generative models play in cognitive processes and the evolution of neural representation.

Deep learning's immense capabilities are often constrained by the complexity of its models, leading to an increasing demand for effective sparsification techniques. Bayesian sparsification for deep learning emerges as a crucial approach, facilitating the design of models that are both computationally efficient and competitive in terms of performance across various deep learning applications. The state-of-the-art -- in Bayesian sparsification of deep neural networks -- combines structural shrinkage priors on model weights with an approximate inference scheme based on stochastic variational inference. However, model inversion of the full generative model is exceptionally computationally demanding, especially when compared to standard deep learning of point estimates. In this context, we advocate for the use of Bayesian model reduction (BMR) as a more efficient alternative for pruning of model weights. As a generalization of the Savage-Dickey ratio, BMR allows a post-hoc elimination of redundant model weights based on the posterior estimates under a straightforward (non-hierarchical) generative model. Our comparative study highlights the advantages of the BMR method relative to established approaches based on hierarchical horseshoe priors over model weights. We illustrate the potential of BMR across various deep learning architectures, from classical networks like LeNet to modern frameworks such as Vision Transformers and MLP-Mixers.

Building autonomous --- i.e., choosing goals based on one's needs -- and adaptive -- i.e., surviving in ever-changing environments -- agents has been a holy grail of artificial intelligence (AI). A living organism is a prime example of such an agent, offering important lessons about adaptive autonomy. Here, we focus on interoception, a process of monitoring one's internal environment to keep it within certain bounds, which underwrites the survival of an organism. To develop AI with interoception, we need to factorize the state variables representing internal environments from external environments and adopt life-inspired mathematical properties of internal environment states. This paper offers a new perspective on how interoception can help build autonomous and adaptive agents by integrating the legacy of cybernetics with recent advances in theories of life, reinforcement learning, and neuroscience., Comment: 28 pages, 4 figures, 3 boxes

We characterise the dynamics of neuronal activity, in terms of field theory, using neural units placed on a 2D-lattice modelling the cortical surface. The electrical activity of neuronal units was analysed with the aim of deriving a neural field model with a simple functional form that still able to predict or reproduce empirical findings. Each neural unit was modelled using a neural mass and the accompanying field theory was derived in the continuum limit. The field theory comprised coupled (real) Klein-Gordon fields, where predictions of the model fall within the range of experimental findings. These predictions included the frequency spectrum of electric activity measured from the cortex, which was derived using an equipartition of energy over eigenfunctions of the neural fields. Moreover, the neural field model was invariant, within a set of parameters, to the dynamical system used to model each neuronal mass. Specifically, topologically equivalent dynamical systems resulted in the same neural field model when connected in a lattice; indicating that the fields derived could be read as a canonical cortical field theory. We specifically investigated non-dispersive fields that provide a structure for the coding (or representation) of afferent information. Further elaboration of the ensuing neural field theory, including the effect of dispersive forces, could be of importance in the understanding of the cortical processing of information., Comment: 19 pages, 1 figure

A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable longer, more naturalistic neuronal recordings. The implicit opportunity for understanding the self-organised brain calls for new analysis methods that link temporal scales: from the order of milliseconds over which neuronal dynamics evolve, to the order of minutes, days or even years over which experimental observations unfold. This review article demonstrates how hierarchical generative models and Bayesian inference help to characterise neuronal activity across different time scales. Crucially, these methods go beyond describing statistical associations among observations and enable inference about underlying mechanisms. We offer an overview of fundamental concepts in state-space modeling and suggest a taxonomy for these methods. Additionally, we introduce key mathematical principles that underscore a separation of temporal scales, such as the slaving principle, and review Bayesian methods that are being used to test hypotheses about the brain with multi-scale data. We hope that this review will serve as a useful primer for experimental and computational neuroscientists on the state of the art and current directions of travel in the complex systems modelling literature., Comment: 20 pages, 5 figures

Humans can produce complex whole-body motions when interacting with their surroundings, by planning, executing and combining individual limb movements. We investigated this fundamental aspect of motor control in the setting of autonomous robotic operations. We approach this problem by hierarchical generative modelling equipped with multi-level planning-for autonomous task completion-that mimics the deep temporal architecture of human motor control. Here, temporal depth refers to the nested time scales at which successive levels of a forward or generative model unfold, for example, delivering an object requires a global plan to contextualise the fast coordination of multiple local movements of limbs. This separation of temporal scales also motivates robotics and control. Specifically, to achieve versatile sensorimotor control, it is advantageous to hierarchically structure the planning and low-level motor control of individual limbs. We use numerical and physical simulation to conduct experiments and to establish the efficacy of this formulation. Using a hierarchical generative model, we show how a humanoid robot can autonomously complete a complex task that necessitates a holistic use of locomotion, manipulation, and grasping. Specifically, we demonstrate the ability of a humanoid robot that can retrieve and transport a box, open and walk through a door to reach the destination, approach and kick a football, while showing robust performance in presence of body damage and ground irregularities. Our findings demonstrated the effectiveness of using human-inspired motor control algorithms, and our method provides a viable hierarchical architecture for the autonomous completion of challenging goal-directed tasks.

Artificial intelligence (AI) is rapidly becoming one of the key technologies of this century. The majority of results in AI thus far have been achieved using deep neural networks trained with the error backpropagation learning algorithm. However, the ubiquitous adoption of this approach has highlighted some important limitations such as substantial computational cost, difficulty in quantifying uncertainty, lack of robustness, unreliability, and biological implausibility. It is possible that addressing these limitations may require schemes that are inspired and guided by neuroscience theories. One such theory, called predictive coding (PC), has shown promising performance in machine intelligence tasks, exhibiting exciting properties that make it potentially valuable for the machine learning community: PC can model information processing in different brain areas, can be used in cognitive control and robotics, and has a solid mathematical grounding in variational inference, offering a powerful inversion scheme for a specific class of continuous-state generative models. With the hope of foregrounding research in this direction, we survey the literature that has contributed to this perspective, highlighting the many ways that PC might play a role in the future of machine learning and computational intelligence at large., Comment: 37 Pages, 9 Figures

Collective motion is ubiquitous in nature; groups of animals, such as fish, birds, and ungulates appear to move as a whole, exhibiting a rich behavioral repertoire that ranges from directed movement to milling to disordered swarming. Typically, such macroscopic patterns arise from decentralized, local interactions among constituent components (e.g., individual fish in a school). Preeminent models of this process describe individuals as self-propelled particles, subject to self-generated motion and 'social forces' such as short-range repulsion and long-range attraction or alignment. However, organisms are not particles; they are probabilistic decision-makers. Here, we introduce an approach to modelling collective behavior based on active inference. This cognitive framework casts behavior as the consequence of a single imperative: to minimize surprise. We demonstrate that many empirically-observed collective phenomena, including cohesion, milling and directed motion, emerge naturally when considering behavior as driven by active Bayesian inference -- without explicitly building behavioral rules or goals into individual agents. Furthermore, we show that active inference can recover and generalize the classical notion of social forces as agents attempt to suppress prediction errors that conflict with their expectations. By exploring the parameter space of the belief-based model, we reveal non-trivial relationships between the individual beliefs and group properties like polarization and the tendency to visit different collective states. We also explore how individual beliefs about uncertainty determine collective decision-making accuracy. Finally, we show how agents can update their generative model over time, resulting in groups that are collectively more sensitive to external fluctuations and encode information more robustly., Comment: 29 pages (main text), 29 pages (supplemental appendices), 4 figures, 1 supplemental figure, 5 movies

Even though the brain operates in pure darkness, within the skull, it can infer the most likely causes of its sensory input. An approach to modelling this inference is to assume that the brain has a generative model of the world, which it can invert to infer the hidden causes behind its sensory stimuli, that is, perception. This assumption raises key questions: how to formulate the problem of designing brain-inspired generative models, how to invert them for the tasks of inference and learning, what is the appropriate loss function to be optimised, and, most importantly, what are the different choices of mean field approximation (MFA) and their implications for variational inference (VI)., Comment: 7 pages, 2 figures

We present a didactic introduction to spectral Dynamic Causal Modelling (DCM), a Bayesian state-space modelling approach used to infer effective connectivity from non-invasive neuroimaging data. Spectral DCM is currently the most widely applied DCM variant for resting-state functional MRI analysis. Our aim is to explain its technical foundations to an audience with limited expertise in state-space modelling and spectral data analysis. Particular attention will be paid to cross-spectral density, which is the most distinctive feature of spectral DCM and is closely related to functional connectivity, as measured by (zero-lag) Pearson correlations. In fact, the model parameters estimated by spectral DCM are those that best reproduce the cross-correlations between all measurements--at all time lags--including the zero-lag correlations that are usually interpreted as functional connectivity. We derive the functional connectivity matrix from the model equations and show how changing a single effective connectivity parameter can affect all pairwise correlations. To complicate matters, the pairs of brain regions showing the largest changes in functional connectivity do not necessarily coincide with those presenting the largest changes in effective connectivity. We discuss the implications and conclude with a comprehensive summary of the assumptions and limitations of spectral DCM.

This paper investigates the prospect of developing human-interpretable, explainable artificial intelligence (AI) systems based on active inference and the free energy principle. We first provide a brief overview of active inference, and in particular, of how it applies to the modeling of decision-making, introspection, as well as the generation of overt and covert actions. We then discuss how active inference can be leveraged to design explainable AI systems, namely, by allowing us to model core features of ``introspective'' processes and by generating useful, human-interpretable models of the processes involved in decision-making. We propose an architecture for explainable AI systems using active inference. This architecture foregrounds the role of an explicit hierarchical generative model, the operation of which enables the AI system to track and explain the factors that contribute to its own decisions, and whose structure is designed to be interpretable and auditable by human users. We outline how this architecture can integrate diverse sources of information to make informed decisions in an auditable manner, mimicking or reproducing aspects of human-like consciousness and introspection. Finally, we discuss the implications of our findings for future research in AI, and the potential ethical considerations of developing AI systems with (the appearance of) introspective capabilities.

This paper presents a model of consciousness that follows directly from the free-energy principle (FEP). We first rehearse the classical and quantum formulations of the FEP. In particular, we consider the inner screen hypothesis that follows from the quantum information theoretic version of the FEP. We then review applications of the FEP to the known sparse (nested and hierarchical) neuro-anatomy of the brain. We focus on the holographic structure of the brain, and how this structure supports (overt and covert) action., Comment: This is the right version of the paper, with the references showing

Predictive coding (PC) accounts of perception now form one of the dominant computational theories of the brain, where they prescribe a general algorithm for inference and learning over hierarchical latent probabilistic models. Despite this, they have enjoyed little export to the broader field of machine learning, where comparative generative modelling techniques have flourished. In part, this has been due to the poor performance of models trained with PC when evaluated by both sample quality and marginal likelihood. By adopting the perspective of PC as a variational Bayes algorithm under the Laplace approximation, we identify the source of these deficits to lie in the exclusion of an associated Hessian term in the PC objective function, which would otherwise regularise the sharpness of the probability landscape and prevent over-certainty in the approximate posterior. To remedy this, we make three primary contributions: we begin by suggesting a simple Monte Carlo estimated evidence lower bound which relies on sampling from the Hessian-parameterised variational posterior. We then derive a novel block diagonal approximation to the full Hessian matrix that has lower memory requirements and favourable mathematical properties. Lastly, we present an algorithm that combines our method with standard PC to reduce memory complexity further. We evaluate models trained with our approach against the standard PC framework on image benchmark datasets. Our approach produces higher log-likelihoods and qualitatively better samples that more closely capture the diversity of the data-generating distribution.

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.

Living systems face both environmental complexity and limited access to free-energy resources. Survival under these conditions requires a control system that can activate, or deploy, available perception and action resources in a context specific way. We show here that when systems are described as executing active inference driven by the free-energy principle (and hence can be considered Bayesian prediction-error minimizers), their control flow systems can always be represented as tensor networks (TNs). We show how TNs as control systems can be implmented within the general framework of quantum topological neural networks, and discuss the implications of these results for modeling biological systems at multiple scales., Comment: 44 pgs

We consider the theoretical constraints on interactions between coupled cortical columns. Each column comprises a set of neural populations, where each population is modelled as a neural mass. The existence of semi-stable states within a cortical column has been shown to be dependent on the type of interaction between the constituent neuronal subpopulations, i.e., the form of the implicit synaptic convolution kernels. Current-to-current coupling has been shown, in contrast to potential-to-current coupling, to create semi-stable states within a cortical column. In this analytic and numerical study, the interaction between semi-stable states is characterized by equations of motion for ensemble activity. We show that for small excitations, the dynamics follow the Kuramoto model. However, in contrast to previous work, we derive coupled equations between phase and amplitude dynamics. This affords the possibility of defining connectivity as a dynamic variable. The turbulent flow of phase dynamics found in networks of Kuramoto oscillators indicate turbulent changes in dynamic connectivity for coupled cortical columns. Crucially, this is something that has been recorded in epileptic seizures. We used the results we derived to estimate a seizure propagation model, which allowed for relatively straightforward inversions using variational Laplace (a.k.a., Dynamic Causal Modelling). The face validity of the ensuing seizure propagation model was established using simulated data as a prelude to future work; which will investigate dynamic connectivity from empirical data. This model also allows predictions of seizure evolution, induced by virtual lesions to synaptic connectivity: something that could be of clinical use, when applied to epilepsy surgical cases.

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.

This white paper lays out a vision of research and development in the field of artificial intelligence for the next decade (and beyond). Its denouement is a cyber-physical ecosystem of natural and synthetic sense-making, in which humans are integral participants -- what we call ''shared intelligence''. This vision is premised on active inference, a formulation of adaptive behavior that can be read as a physics of intelligence, and which inherits from the physics of self-organization. In this context, we understand intelligence as the capacity to accumulate evidence for a generative model of one's sensed world -- also known as self-evidencing. Formally, this corresponds to maximizing (Bayesian) model evidence, via belief updating over several scales: i.e., inference, learning, and model selection. Operationally, this self-evidencing can be realized via (variational) message passing or belief propagation on a factor graph. Crucially, active inference foregrounds an existential imperative of intelligent systems; namely, curiosity or the resolution of uncertainty. This same imperative underwrites belief sharing in ensembles of agents, in which certain aspects (i.e., factors) of each agent's generative world model provide a common ground or frame of reference. Active inference plays a foundational role in this ecology of belief sharing -- leading to a formal account of collective intelligence that rests on shared narratives and goals. We also consider the kinds of communication protocols that must be developed to enable such an ecosystem of intelligences and motivate the development of a shared hyper-spatial modeling language and transaction protocol, as a first -- and key -- step towards such an ecology., Comment: 23+18 pages, one figure, one six page appendix

Natural language syntax yields an unbounded array of hierarchically structured expressions. We claim that these are used in the service of active inference in accord with the free-energy principle (FEP). While conceptual advances alongside modelling and simulation work have attempted to connect speech segmentation and linguistic communication with the FEP, we extend this program to the underlying computations responsible for generating syntactic objects. We argue that recently proposed principles of economy in language design - such as "minimal search" criteria from theoretical syntax - adhere to the FEP. This affords a greater degree of explanatory power to the FEP - with respect to higher language functions - and offers linguistics a grounding in first principles with respect to computability. We show how both tree-geometric depth and a Kolmogorov complexity estimate (recruiting a Lempel-Ziv compression algorithm) can be used to accurately predict legal operations on syntactic workspaces, directly in line with formulations of variational free energy minimization. This is used to motivate a general principle of language design that we term Turing-Chomsky Compression (TCC). We use TCC to align concerns of linguists with the normative account of self-organization furnished by the FEP, by marshalling evidence from theoretical linguistics and psycholinguistics to ground core principles of efficient syntactic computation within active inference.

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., Comment: 33 pages (excluding references), 6 figures

This paper presents a meta-theory of the usage of the free energy principle (FEP) and examines its scope in the modelling of physical systems. We consider the so-called `map-territory fallacy' and the fallacious reification of model properties. By showing that the FEP is a consistent, physics-inspired theory of inferences of inferences, we disprove the assertion that the map-territory fallacy contradicts the principled usage of the FEP. As such, we argue that deploying the map-territory fallacy to criticise the use of the FEP and Bayesian mechanics itself constitutes a fallacy: what we call the {\it map-territory fallacy fallacy}. In so doing, we emphasise a few key points: the uniqueness of the FEP as a model of particles or agents that model their environments; the restoration of convention to the FEP via its relation to the principle of constrained maximum entropy; the `Jaynes optimality' of the FEP under this relation; and finally, the way that this meta-theoretical approach to the FEP clarifies its utility and scope as a formal modelling tool. Taken together, these features make the FEP, uniquely, {\it the} ideal model of generic systems in statistical physics., Comment: 23 pages

We show how any system with morphological degrees of freedom and locally limited free energy will, under the constraints of the free energy principle, evolve toward a neuromorphic morphology that supports hierarchical computations in which each level of the hierarchy enacts a coarse-graining of its inputs, and dually a fine-graining of its outputs. Such hierarchies occur throughout biology, from the architectures of intracellular signal transduction pathways to the large-scale organization of perception and action cycles in the mammalian brain. Formally, the close formal connections between cone-cocone diagrams (CCCD) as models of quantum reference frames on the one hand, and between CCCDs and topological quantum field theories on the other, allow the representation of such computations in the fully-general quantum-computational framework of topological quantum neural networks.

Neural mass models are used to simulate cortical dynamics and to explain the electrical and magnetic fields measured using electro- and magnetoencephalography. Simulations evince a complex phase-space structure for these kinds of models; including stationary points and limit cycles and the possibility for bifurcations and transitions among different modes of activity. This complexity allows neural mass models to describe the itinerant features of brain dynamics. However, expressive, nonlinear neural mass models are often difficult to fit to empirical data without additional simplifying assumptions: e.g., that the system can be modelled as linear perturbations around a fixed point. In this study we offer a mathematical analysis of neural mass models, specifically the canonical microcircuit model, providing analytical solutions describing dynamical itinerancy. We derive a perturbation analysis up to second order of the phase flow, together with adiabatic approximations. This allows us to describe amplitude modulations as gradient flows on a potential function of intrinsic connectivity. These results provide analytic proof-of-principle for the existence of semi-stable states of cortical dynamics at the scale of a cortical column. Crucially, this work allows for model inversion of neural mass models, not only around fixed points, but over regions of phase space that encompass transitions among semi or multi-stable states of oscillatory activity. In principle, this formulation of cortical dynamics may improve our understanding of the itinerancy that underwrites measures of cortical activity (through EEG or MEG). Crucially, these theoretical results speak to model inversion in the context of multiple semi-stable brain states, such as onset of seizure activity in epilepsy or beta bursts in Parkinsons disease., Comment: 40 pages, 8 figures

The aim of this paper is to introduce a field of study that has emerged over the last decade called Bayesian mechanics. Bayesian mechanics is a probabilistic mechanics, comprising tools that enable us to model systems endowed with a particular partition (i.e., into particles), where the internal states (or the trajectories of internal states) of a particular system encode the parameters of beliefs about external states (or their trajectories). These tools allow us to write down mechanical theories for systems that look as if they are estimating posterior probability distributions over the causes of their sensory states. This provides a formal language for modelling the constraints, forces, potentials, and other quantities determining the dynamics of such systems, especially as they entail dynamics on a space of beliefs (i.e., on a statistical manifold). Here, we will review the state of the art in the literature on the free energy principle, distinguishing between three ways in which Bayesian mechanics has been applied to particular systems (i.e., path-tracking, mode-tracking, and mode-matching). We go on to examine a duality between the free energy principle and the constrained maximum entropy principle, both of which lie at the heart of Bayesian mechanics, and discuss its implications., Comment: 50+7 pages, six figures. Invited contribution to "Making and Breaking Symmetries in Mind and Life," a special issue of the journal Royal Society Interface. First two authors have contributed equally

How is information processed in the brain during perception? Mechanistic insight is achieved only when experiments are employed to test formal or computational models. In analogy to lesion studies, phantom perception may serve as a vehicle to understand the fundamental processing principles underlying auditory perception. With a special focus on tinnitus -- as the prime example of auditory phantom perception -- we review recent work at the intersection of artificial intelligence, psychology, and neuroscience. In particular, we discuss why everyone with tinnitus suffers from hearing loss, but not everyone with hearing loss suffers from tinnitus. We argue that the increase of sensory precision due to Bayesian inference could be caused by intrinsic neural noise and lead to a prediction error in the cerebral cortex. Hence, two fundamental processing principles - being ubiquitous in the brain - provide the most explanatory power for the emergence of tinnitus: predictive coding as a top-down, and stochastic resonance as a complementary bottom-up mechanism. We conclude that both principles play a crucial role in healthy auditory perception., Comment: arXiv admin note: substantial text overlap with arXiv:2010.01914

The characteristics and determinants of health and disease are often organised in space, reflecting our spatially extended nature. Understanding the influence of such factors requires models capable of capturing spatial relations. Though a mature discipline, spatial analysis is comparatively rare in medicine, arguably a consequence of the complexity of the domain and the inclemency of the data regimes that govern it. Drawing on statistical parametric mapping, a framework for topological inference well-established in the realm of neuroimaging, we propose and validate a novel approach to the spatial analysis of diverse clinical data - GeoSPM - based on differential geometry and random field theory. We evaluate GeoSPM across an extensive array of synthetic simulations encompassing diverse spatial relationships, sampling, and corruption by noise, and demonstrate its application on large-scale data from UK Biobank. GeoSPM is transparently interpretable, can be implemented with ease by non-specialists, enables flexible modelling of complex spatial relations, exhibits robustness to noise and under-sampling, offers well-founded criteria of statistical significance, and is through computational efficiency readily scalable to large datasets. We provide a complete, open-source software implementation of GeoSPM, and suggest that its adoption could catalyse the wider use of spatial analysis across the many aspects of medicine that urgently demand it., Comment: 29 pages, 22 figures

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.

In this chapter, we identify fundamental geometric structures that underlie the problems of sampling, optimisation, inference and adaptive decision-making. Based on this identification, we derive algorithms that exploit these geometric structures to solve these problems efficiently. We show that a wide range of geometric theories emerge naturally in these fields, ranging from measure-preserving processes, information divergences, Poisson geometry, and geometric integration. Specifically, we explain how (i) leveraging the symplectic geometry of Hamiltonian systems enable us to construct (accelerated) sampling and optimisation methods, (ii) the theory of Hilbertian subspaces and Stein operators provides a general methodology to obtain robust estimators, (iii) preserving the information geometry of decision-making yields adaptive agents that perform active inference. Throughout, we emphasise the rich connections between these fields; e.g., inference draws on sampling and optimisation, and adaptive decision-making assesses decisions by inferring their counterfactual consequences. Our exposition provides a conceptual overview of underlying ideas, rather than a technical discussion, which can be found in the references herein., Comment: 30 pages, 4 figures; 42 pages including table of contents and references

We apply Dynamic Causal Models to electrocorticogram recordings from two macaque monkeys performing a problem-solving task that engages working memory, and induces time-on-task effects. We thus provide a computational account of changes in effective connectivity within two regions of the fronto-parietal network, the dorsolateral prefrontal cortex and the pre-supplementary motor area. We find that forward connections between the two regions increased in strength when task demands increased, and as the experimental session progressed. Similarities in the effects of task demands and time on task allow us to interpret changes in frontal connectivity in terms of increased attentional effort allocation that compensates cognitive fatigue.

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., Comment: 44 pages, 9 Figures; 64 pages including graphical abstract, highlights and references

Active inference is an account of cognition and behavior in complex systems which brings together action, perception, and learning under the theoretical mantle of Bayesian inference. Active inference has seen growing applications in academic research, especially in fields that seek to model human or animal behavior. While in recent years, some of the code arising from the active inference literature has been written in open source languages like Python and Julia, to-date, the most popular software for simulating active inference agents is the DEM toolbox of SPM, a MATLAB library originally developed for the statistical analysis and modelling of neuroimaging data. Increasing interest in active inference, manifested both in terms of sheer number as well as diversifying applications across scientific disciplines, has thus created a need for generic, widely-available, and user-friendly code for simulating active inference in open-source scientific computing languages like Python. The Python package we present here, pymdp (see https://github.com/infer-actively/pymdp), represents a significant step in this direction: namely, we provide the first open-source package for simulating active inference with partially-observable Markov Decision Processes or POMDPs. We review the package's structure and explain its advantages like modular design and customizability, while providing in-text code blocks along the way to demonstrate how it can be used to build and run active inference processes with ease. We developed pymdp to increase the accessibility and exposure of the active inference framework to researchers, engineers, and developers with diverse disciplinary backgrounds. In the spirit of open-source software, we also hope that it spurs new innovation, development, and collaboration in the growing active inference community.

The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on surprisal (a.k.a., self-information). This upper bound can be read as a Bayesian prediction error. Equivalently, its negative is a lower bound on Bayesian model evidence (a.k.a., marginal likelihood). In short, certain random dynamical systems evince a kind of self-evidencing. Here, we reformulate the FEP in the formal setting of spacetime-background free, scale-free quantum information theory. We show how generic quantum systems can be regarded as observers, which with the standard freedom of choice assumption become agents capable of assigning semantics to observational outcomes. We show how such agents minimize Bayesian prediction error in environments characterized by uncertainty, insufficient learning, and quantum contextuality. We show that in its quantum-theoretic formulation, the FEP is asymptotically equivalent to the Principle of Unitarity. Based on these results, we suggest that biological systems employ quantum coherence as a computational resource and - implicitly - as a communication resource. We summarize a number of problems for future research, particularly involving the resources required for classical communication and for detecting and responding to quantum context switches., Comment: 57 pgs, 6 figs

The body sends interoceptive visceral information through deep brain structures to the cerebral cortex. The insula cortex, organized in hierarchical modules, is the major cortical region receiving interoceptive afferents and contains visceral topographic maps. Yet, the biological significance of the insula's modular architecture in relation to deep brain regions remains unsolved. In this opinion, we propose the Insula Hierarchical Modular Adaptive Interoception Control (IMAC) model to suggest that insula modules (granular, dysgranular and agranular subregions), forming networks with prefrontal (supplementary motor area, dorsolateral and ventromedial cortices) and striatum (posterior, dorsomedial and ventromedial) subregions, are specialized for higher-order interoceptive representations, recruited in a context-dependent manner to support habitual, model-based and exploratory adaptive behavior. We then discuss how insula interoceptive representations, or metaceptions, could give rise to conscious interoceptive feelings built up from low-order visceral representations and associated basic emotions located in deep interoceptive brain structures., Comment: 22 pages, 3 figures, opinion