Neural implementations of Bayesian inference

Representation of a perceptual bias in the prefrontal cortex

Perception is influenced by sensory stimulation, prior knowledge, and contextual cues, which collectively contribute to the emergence of perceptual biases. However, the precise neural mechanisms underlying these biases remain poorly understood. This study aims to address this gap by analyzing neural recordings from the prefrontal cortex (PFC) of monkeys performing a vibrotactile frequency discrimination task. Our findings provide empirical evidence supporting the hypothesis that perceptual biases can be reflected in the neural activity of the PFC. We found that the state-space trajectories of PFC neuronal activity encoded a warped representation of the first frequency presented during the task. Remarkably, this distorted representation of the frequency aligned with the predictions of its Bayesian estimator. The identification of these neural correlates expands our understanding of the neural basis of perceptual biases and highlights the involvement of the PFC in shaping perceptual experiences. Similar analyses could be employed in other delayed comparison tasks and in various brain regions to explore where and how neural activity reflects perceptual biases during different stages of the trial.

Emergent perceptual biases from state-space geometry in trained spiking recurrent neural networks

A stimulus held in working memory is perceived as contracted toward the average stimulus. This contraction bias has been extensively studied in psychophysics, but little is known about its origin from neural activity. By training recurrent networks of spiking neurons to discriminate temporal intervals, we explored the causes of this bias and how behavior relates to population firing activity. We found that the trained networks exhibited animal-like behavior. Various geometric features of neural trajectories in state space encoded warped representations of the durations of the first interval modulated by sensory history. Formulating a normative model, we showed that these representations conveyed a Bayesian estimate of the interval durations, thus relating activity and behavior. Importantly, our findings demonstrate that Bayesian computations already occur during the sensory phase of the first stimulus and persist throughout its maintenance in working memory, until the time of stimulus comparison.

Erroneous predictive coding across brain hierarchies in a non-human primate model of autism spectrum disorder

In autism spectrum disorder (ASD), atypical sensory experiences are often associated with irregularities in predictive coding, which proposes that the brain creates hierarchical sensory models via a bidirectional process of predictions and prediction errors. However, it remains unclear how these irregularities manifest across different functional hierarchies in the brain. To address this, we study a marmoset model of ASD induced by valproic acid (VPA) treatment. We record high-density electrocorticography (ECoG) during an auditory task with two layers of temporal control, and applied a quantitative model to quantify the integrity of predictive coding across two distinct hierarchies. Our results demonstrate a persistent pattern of sensory hypersensitivity and unstable predictions across two brain hierarchies in VPA-treated animals, and reveal the associated spatio-spectro-temporal neural signatures. Despite the regular occurrence of imprecise predictions in VPA-treated animals, we observe diverse configurations of underestimation or overestimation of sensory regularities within the hierarchies. Our results demonstrate the coexistence of the two primary Bayesian accounts of ASD: overly-precise sensory observations and weak prior beliefs, and offer a potential multi-layered biomarker for ASD, which could enhance our understanding of its diverse symptoms.

Exploring the Architectural Biases of the Canonical Cortical Microcircuit

The cortex plays a crucial role in various perceptual and cognitive functions, driven by its basic unit, the canonical cortical microcircuit. Yet, we remain short of a framework that definitively explains the structure-function relationships of this fundamental neuroanatomical motif. To better understand how physical substrates of cortical circuitry facilitate their neuronal dynamics, we employ a computational approach using recurrent neural networks and representational analyses. We examine the differences manifested by the inclusion and exclusion of biologically-motivated inter-areal laminar connections on the computational roles of different neuronal populations in the microcircuit of two hierarchically-related areas, throughout learning. Our findings show that the presence of feedback connections correlates with the functional modularization of cortical populations in different layers, and provides the microcircuit with a natural inductive bias to differentiate expected and unexpected inputs at initialization. Furthermore, when testing the effects of training the microcircuit and its variants with a predictive-coding inspired strategy, we find that doing so helps better encode noisy stimuli in areas of the cortex that receive feedback, all of which combine to suggest evidence for a predictive-coding mechanism serving as an intrinsic operative logic in the cortex.

Single trial Bayesian inference by population vector readout in the barn owl's sound localization system

Bayesian models have proven effective in characterizing perception, behavior, and neural encoding across diverse species and systems. The neural implementation of Bayesian inference in the barn owl's sound localization system and behavior has been previously explained by a non-uniform population code model. This model specifies the neural population activity pattern required for a population vector readout to match the optimal Bayesian estimate. While prior analyses focused on trial-averaged comparisons of model predictions with behavior and single-neuron responses, it remains unknown whether this model can accurately approximate Bayesian inference on single trials under varying sensory reliability, a fundamental condition for natural perception and behavior. In this study, we utilized mathematical analysis and simulations to demonstrate that decoding a non-uniform population code via a population vector readout approximates the Bayesian estimate on single trials for varying sensory reliabilities. Our findings provide additional support for the non-uniform population code model as a viable explanation for the barn owl's sound localization pathway and behavior.

Mesoscale simulations predict the role of synergistic cerebellar plasticity during classical eyeblink conditioning

According to the motor learning theory by Albus and Ito, synaptic depression at the parallel fibre to Purkinje cells synapse (pf-PC) is the main substrate responsible for learning sensorimotor contingencies under climbing fibre control. However, recent experimental evidence challenges this relatively monopolistic view of cerebellar learning. Bidirectional plasticity appears crucial for learning, in which different microzones can undergo opposite changes of synaptic strength (e.g. downbound microzones-more likely depression, upbound microzones-more likely potentiation), and multiple forms of plasticity have been identified, distributed over different cerebellar circuit synapses. Here, we have simulated classical eyeblink conditioning (CEBC) using an advanced spiking cerebellar model embedding downbound and upbound modules that are subject to multiple plasticity rules. Simulations indicate that synaptic plasticity regulates the cascade of precise spiking patterns spreading throughout the cerebellar cortex and cerebellar nuclei. CEBC was supported by plasticity at the pf-PC synapses as well as at the synapses of the molecular layer interneurons (MLIs), but only the combined switch-off of both sites of plasticity compromised learning significantly. By differentially engaging climbing fibre information and related forms of synaptic plasticity, both microzones contributed to generate a well-timed conditioned response, but it was the downbound module that played the major role in this process. The outcomes of our simulations closely align with the behavioural and electrophysiological phenotypes of mutant mice suffering from cell-specific mutations that affect processing of their PC and/or MLI synapses. Our data highlight that a synergy of bidirectional plasticity rules distributed across the cerebellum can facilitate finetuning of adaptive associative behaviours at a high spatiotemporal resolution.

Studying the neural representations of uncertainty

The study of the brain's representations of uncertainty is a central topic in neuroscience. Unlike most quantities of which the neural representation is studied, uncertainty is a property of an observer's beliefs about the world, which poses specific methodological challenges. We analyze how the literature on the neural representations of uncertainty addresses those challenges and distinguish between 'code-driven' and 'correlational' approaches. Code-driven approaches make assumptions about the neural code for representing world states and the associated uncertainty. By contrast, correlational approaches search for relationships between uncertainty and neural activity without constraints on the neural representation of the world state that this uncertainty accompanies. To compare these two approaches, we apply several criteria for neural representations: sensitivity, specificity, invariance and functionality. Our analysis reveals that the two approaches lead to different but complementary findings, shaping new research questions and guiding future experiments.

Visual perspective, distance, and felt presence of others in dreams

The peripersonal space, that is, the limited space surrounding the body, involves multisensory coding and representation of the self in space. Previous studies have shown that peripersonal space representation and the visual perspective on the environment can be dramatically altered when neurotypical individuals self-identify with a distant avatar (i.e., in virtual reality) or during clinical conditions (i.e., out-of-body experience, heautoscopy, depersonalization). Despite its role in many cognitive/social functions, the perception of peripersonal space in dreams, and its relationship with the perception of other characters (interpersonal distance in dreams), remain largely uncharted. The present study aimed to explore the visuospatial properties of this space, which is likely to underlie self-location as well as self/other distinction in dreams. 530 healthy volunteers answered a web-based questionnaire to measure their dominant visuo-spatial perspective in dreams, the frequency of recall for felt distances between their dream self and other dream characters, and the dreamers' viewing angle of other dream characters. Most participants reported dream experiences from a first-person perspective (1PP) (82%) compared to a third-person perspective (3PP) (18%). Independent of their dream perspective, participants reported that they generally perceived other dream characters in their close space, that is, at distance of either between 0 and 90 cm, or 90-180 cm, than in further spaces (180-270 cm). Regardless of the perspective (1PP or 3PP), both groups also reported more frequently seeing other dream characters from eye level (0° angle of viewing) than from above (30° and 60°) or below eye level (-30° and -60°). Moreover, the intensity of sensory experiences in dreams, as measured by the Bodily Self-Consciousness in Dreams Questionnaire, was higher in individuals who habitually see other dream characters closer to their personal dream self (i.e., within 0-90 cm and 90-180 cm). These preliminary findings offer a new, phenomenological account of space representation in dreams with regards to the felt presence of others. They might provide insights not only to our understanding of how dreams are formed, but also to the type of neurocomputations involved in self/other distinction.

Post-injury pain and behaviour: a control theory perspective

Injuries of various types occur commonly in the lives of humans and other animals and lead to a pattern of persistent pain and recuperative behaviour that allows safe and effective recovery. In this Perspective, we propose a control-theoretic framework to explain the adaptive processes in the brain that drive physiological post-injury behaviour. We set out an evolutionary and ethological view on how animals respond to injury, illustrating how the behavioural state associated with persistent pain and recuperation may be just as important as phasic pain in ensuring survival. Adopting a normative approach, we suggest that the brain implements a continuous optimal inference of the current state of injury from diverse sensory and physiological signals. This drives the various effector control mechanisms of behavioural homeostasis, which span the modulation of ongoing motivation and perception to drive rest and hyper-protective behaviours. However, an inherent problem with this is that these protective behaviours may partially obscure information about whether injury has resolved. Such information restriction may seed a tendency to aberrantly or persistently infer injury, and may thus promote the transition to pathological chronic pain states.

Bayesian logical neural networks for human-centered applications in medicine

Background: Medicine is characterized by its inherent uncertainty, i.e., the difficulty of identifying and obtaining exact outcomes from available data. Electronic Health Records aim to improve the exactitude of health management, for instance using automatic data recording techniques or the integration of structured as well as unstructured data. However, this data is far from perfect and is usually noisy, implying that epistemic uncertainty is almost always present in all biomedical research fields. This impairs the correct use and interpretation of the data not only by health professionals but also in modeling techniques and AI models incorporated in professional recommender systems. Method: In this work, we report a novel modeling methodology combining structural explainable models, defined on Logic Neural Networks which replace conventional deep-learning methods with logical gates embedded in neural networks, and Bayesian Networks to model data uncertainties. This means, we do not account for the variability of the input data, but we train single models according to the data and deliver different Logic-Operator neural network models that could adapt to the input data, for instance, medical procedures (Therapy Keys depending on the inherent uncertainty of the observed data. Result: Thus, our model does not only aim to assist physicians in their decisions by providing accurate recommendations; it is above all a user-centered solution that informs the physician when a given recommendation, in this case, a therapy, is uncertain and must be carefully evaluated. As a result, the physician must be a professional who does not solely rely on automatic recommendations. This novel methodology was tested on a database for patients with heart insufficiency and can be the basis for future applications of recommender systems in medicine.

Attractive and repulsive effects of sensory history concurrently shape visual perception

BACKGROUND

Sequential effects of environmental stimuli are ubiquitous in most behavioral tasks involving magnitude estimation, memory, decision making, and emotion. The human visual system exploits continuity in the visual environment, which induces two contrasting perceptual phenomena shaping visual perception. Previous work reported that perceptual estimation of a stimulus may be influenced either by attractive serial dependencies or repulsive aftereffects, with a number of experimental variables suggested as factors determining the direction and magnitude of sequential effects. Recent studies have theorized that these two effects concurrently arise in perceptual processing, but empirical evidence that directly supports this hypothesis is lacking, and it remains unclear whether and how attractive and repulsive sequential effects interact in a trial. Here we show that the two effects concurrently modulate estimation behavior in a typical sequence of perceptual tasks.

RESULTS

We first demonstrate that observers' estimation error as a function of both the previous stimulus and response cannot be fully described by either attractive or repulsive bias but is instead well captured by a summation of repulsion from the previous stimulus and attraction toward the previous response. We then reveal that the repulsive bias is centered on the observer's sensory encoding of the previous stimulus, which is again repelled away from its own preceding trial, whereas the attractive bias is centered precisely on the previous response, which is the observer's best prediction about the incoming stimuli.

CONCLUSIONS

Our findings provide strong evidence that sensory encoding is shaped by dynamic tuning of the system to the past stimuli, inducing repulsive aftereffects, and followed by inference incorporating the prediction from the past estimation, leading to attractive serial dependence.

A virtual reality time reproduction task for rodents

Estimates of the duration of time intervals and other magnitudes exhibit characteristic biases that likely result from error minimization strategies. To investigate such phenomena, magnitude reproduction tasks are used with humans and other primates. However, such behavioral tasks do not exist for rodents, one of the most important animal orders for neuroscience. We, therefore, developed a time reproduction task that can be used with rodents. It involves an animal reproducing the duration of a timed visual stimulus by walking along a corridor. The task was implemented in virtual reality, which allowed us to ensure that the animals were actually estimating time. The hallway did not contain prominent spatial cues and movement could be de-correlated from optic flow, such that the animals could not learn a mapping between stimulus duration and covered distance. We tested the reproduction of durations of several seconds in three different stimulus ranges. The gerbils reproduced the durations with a precision similar to experiments on humans. Their time reproductions also exhibited the characteristic biases of magnitude estimation experiments. These results demonstrate that our behavioral paradigm provides a means to study time reproduction in rodents.