Neuromatch 4

Norepinephrine (NE) is a neuromodulator that is released from projections of the locus coeruleus via extra-synaptic vesicle exocytosis. Tonic fluctuations in NE are involved in brain states, such as sleep, arousal, and attention. Previously, NE in the PFC was thought to be a homogenous field created by bulk release, but it remains unknown whether phasic (fast, short-term) fluctuations in NE can produce a spatially heterogeneous field, which could then structure cell firing at a fine spatial scale. To understand how spatiotemporal dynamics of norepinephrine (NE) release in the prefrontal cortex affect neuronal firing, we performed a novel in-vivo two-photon imaging experiment in layer ⅔ of the prefrontal cortex using a green fluorescent NE sensor and a red fluorescent Ca2+ sensor, which allowed us to simultaneously observe fine-scale neuronal and NE dynamics in the form of spatially localized fluorescence time series. Using generalized linear modeling, we found that the local NE field differs from the global NE field in transient periods of decorrelation, which are influenced by proximal NE release events. We used optical flow and pattern analysis to show that release and reuptake events can occur at the same location but at different times, and differential recruitment of release and reuptake sites over time is a potential mechanism for creating a heterogeneous NE field. Our generalized linear models predicting cellular dynamics show that the heterogeneous local NE field, and not the global field, drives cell firing dynamics. These results point to the importance of local, small-scale, phasic NE fluctuations for structuring cell firing. Prior research suggests that these phasic NE fluctuations in the PFC may play a role in attentional shifts, orienting to sensory stimuli in the environment, and in the selective gain of priority representations during stress (Mather, Clewett et al. 2016) (Aston-Jones and Bloom 1981).

Natural perception relies inherently on inferring causal structure in the environment. However, the neural mechanisms and functional circuits that are essential for representing and updating the hidden causal structure during multisensory processing are unknown. To address this, monkeys were trained to infer the probability of a potential common source from visual and proprioceptive signals on the basis of their spatial disparity in a virtual reality system. The proprioceptive drift reported by monkeys demonstrated that they combined historical information and current multisensory signals to estimate the hidden common source and subsequently updated both the causal structure and sensory representation. Single-unit recordings in premotor and parietal cortices revealed that neural activity in premotor cortex represents the core computation of causal inference, characterizing the estimation and update of the likelihood of integrating multiple sensory inputs at a trial-by-trial level. In response to signals from premotor cortex, neural activity in parietal cortex also represents the causal structure and further dynamically updates the sensory representation to maintain consistency with the causal inference structure. Thus, our results indicate how premotor cortex integrates historical information and sensory inputs to infer hidden variables and selectively updates sensory representations in parietal cortex to support behavior. This dynamic loop of frontal-parietal interactions in the causal inference framework may provide the neural mechanism to answer long-standing questions regarding how neural circuits represent hidden structures for body-awareness and agency.

Inhibitory neurons take on many forms and functions. How this diversity contributes to memory function is not completely known. Previous formal studies indicate inhibition differentiated by local and global connectivity in associative memory networks functions to rescale the level of retrieval of excitatory assemblies. However, such studies lack biological details such as a distinction between types of neurons (excitatory and inhibitory), unrealistic connection schemas, and non-sparse assemblies. In this study, we present a rate-based cortical model where neurons are distinguished (as excitatory, local inhibitory, or global inhibitory), connected more realistically, and where memory items correspond to sparse excitatory assemblies. We use this model to study how local-global inhibition balance can alter memory retrieval in associative memory structures, including naturalistic and artificial structures. Experimental studies have reported inhibitory neurons and their sub-types uniquely respond to specific stimuli and can form sophisticated, joint excitatory-inhibitory assemblies. Our model suggests such joint assemblies, as well as a distribution and rebalancing of overall inhibition between two inhibitory sub-populations – one connected to excitatory assemblies locally and the other connected globally – can quadruple the range of retrieval across related memories. We identify a possible functional role for local-global inhibitory balance to, in the context of choice or preference of relationships, permit and maintain a broader range of memory items when local inhibition is dominant and conversely consolidate and strengthen a smaller range of memory items when global inhibition is dominant. This model therefore highlights a biologically-plausible and behaviourally-useful function of inhibitory diversity in memory.

Predictive coding represents a promising framework for understanding brain function, postulating that the brain continuously inhibits predictable sensory input, ensuring a preferential processing of surprising elements. A central aspect of this view on cortical computation is its hierarchical connectivity, involving recurrent message passing between excitatory bottom-up signals and inhibitory top-down feedback. Here we use computational modelling to demonstrate that such architectural hard-wiring is not necessary. Rather, predictive coding is shown to emerge as a consequence of energy efficiency, a fundamental requirement of neural processing. When training recurrent neural networks to minimise their energy consumption while operating in predictive environments, the networks self-organise into prediction and error units with appropriate inhibitory and excitatory interconnections and learn to inhibit predictable sensory input. We demonstrate that prediction units can reliably be identified through biases in their median preactivation, pointing towards a fundamental property of prediction units in the predictive coding framework. Moving beyond the view of purely top-down driven predictions, we demonstrate via virtual lesioning experiments that networks perform predictions on two timescales: fast lateral predictions among sensory units and slower prediction cycles that integrate evidence over time. Our results, which replicate across two separate data sets, suggest that predictive coding can be interpreted as a natural consequence of energy efficiency. More generally, they raise the question which other computational principles of brain function can be understood as a result of physical constraints posed by the brain, opening up a new area of bio-inspired, machine learning-powered neuroscience research.

We understand the brain in representational terms. E.g., we understand spatial navigation by appealing to the spatial properties that hippocampal cells represent, and the operations hippocampal circuits perform on those representations (Moser et al., 2008). Philosophers have been concerned with the nature of representation, and recently neuroscientists entered the debate, focusing specifically on neural representations. (Baker & Lansdell, n.d.; Egan, 2019; Piccinini & Shagrir, 2014; Poldrack, 2020; Shagrir, 2001). We want to know what representations are, how to discover them in the brain, and why they matter so much for our understanding of the brain. Those questions are framed in a traditional philosophical way: we start with explanations that use representational notions, and to more deeply understand those explanations we ask, what are representations — what is the definition of representation? What is it for some bit of neural activity to be a representation? I argue that there is an alternative, and much more fruitful, approach. Rather than asking what representations are, we should ask what the use of representational *notions* allows us to do in neuroscience — what thinking in representational terms helps scientists do or explain. I argue that this framing offers more fruitful ground for interdisciplinary collaboration by distinguishing the philosophical concerns that have a place in neuroscience from those that don’t (namely the definitional or metaphysical questions about representation). And I argue for a particular view of representational notions: they allow us to impose the structure of one domain onto another as a model of its causal structue. So, e.g., thinking about the hippocampus as representing spatial properties is a way of taking structures in those spatial properties, and projecting those structures (and algorithms that would implement them) them onto the brain as models of its causal structure.

Motor learning is typically assessed in the lab, affording a high degree of control over the task environment. However, this level of control often comes at the cost of smaller sample sizes and a homogenous pool of participants (e.g. college students). To address this, we have designed a web-based motor learning experiment, making it possible to reach a larger, more diverse set of participants. As a proof-of-concept, we collected 1,581 participants completing a visuomotor rotation task, where participants controlled a visual cursor on the screen with their mouse and trackpad. Motor learning was indexed by how fast participants were able to compensate for a 45° rotation imposed between the cursor and their actual movement. Using a cross-validated LASSO regression, we found that motor learning varied significantly with the participant’s age and sex, and also strongly correlated with the location of the target, visual acuity, and satisfaction with the experiment. In contrast, participants' mouse and browser type were features eliminated by the model, indicating that motor performance was not influenced by variations in computer hardware and software. Together, this proof-of-concept study demonstrates how large datasets can generate important insights into the factors underlying motor learning.

Panelists: - Surya Ganguli, Matteo Carandini, Anna Schapiro,Blake Richards. Moderator: Konrad Kording

Hippocampal pyramidal cells have been widely studied during locomotion, when theta oscillations are present, and during short wave ripples at rest, when replay takes place. However, we find a subset of pyramidal cells that are preferably active during rest, in the absence of theta oscillations and short wave ripples. We recorded these cells using two-photon imaging in dorsal CA1 of the hippocampus of mice, during a virtual reality object location recognition task. During locomotion, the cells show a similar level of activity as control cells, but their activity increases during rest, when this population of cells shows highly synchronous, oscillatory activity at a low frequency (0.1-0.4 Hz). In addition, during both locomotion and rest these cells show place coding, suggesting they may play a role in maintaining a representation of the current location, even when the animal is not moving. We performed simultaneous electrophysiological and calcium recordings, which showed a higher correlation of activity between the LFO and the hippocampal cells in the 0.1-0.4 Hz low frequency band during rest than during locomotion. However, the relationship between the LFO and calcium signals varied between electrodes, suggesting a localized effect. We used the Allen Brain Observatory Neuropixels Visual Coding dataset to further explore this. These data revealed localised low frequency oscillations in CA1 and DG during rest. Overall, we show a novel population of hippocampal cells, and a novel oscillatory band of activity in hippocampus during rest.

Real world datasets commonly contain nonlinearly separable classes, requiring nonlinear classifiers. However, these classifiers are less computationally efficient than their linear counterparts. This inefficiency wastes energy, resources and time. We were inspired by the efficiency of the brain to create a novel type of computationally efficient Artificial Neural Network (ANN) called Rank Similarity Filters. They can be used to both transform and classify nonlinearly separable datasets with many datapoints and dimensions. The weights of the filters are set using the rank orders of features in a datapoint, or optionally the 'confusion' adjusted ranks between features (determined from their distributions in the dataset). The activation strength of a filter determines its similarity to other points in the dataset, a measure based on cosine similarity. The activation of many Rank Similarity Filters transforms samples into a new nonlinear space suitable for linear classification (Rank Similarity Transform (RST)). We additionally used this method to create the nonlinear Rank Similarity Classifier (RSC), which is a fast and accurate multiclass classifier, and the nonlinear Rank Similarity Probabilistic Classifier (RSPC), which is an extension to the multilabel case. We evaluated the classifiers on multiple datasets and RSC is competitive with existing classifiers but with superior computational efficiency. Code for RST, RSC and RSPC is open source and was written in Python using the popular scikit-learn framework to make it easily accessible (https://github.com/KatharineShapcott/rank-similarity). In future extensions the algorithm can be applied to hardware suitable for the parallelization of an ANN (GPU) and a Spiking Neural Network (neuromorphic computing) with corresponding performance gains. This makes Rank Similarity Filters a promising biologically inspired solution to the problem of efficient analysis of nonlinearly separable data.

Recently, the field of computational neuroscience has seen an explosion of the use of trained recurrent network models (RNNs) to model patterns of neural activity. These RNN models are typically characterized by tuned recurrent interactions between rate 'units' whose dynamics are governed by smooth, continuous differential equations. However, the response of biological single neurons is better described by all-or-none events - spikes - that are triggered in response to the processing of their synaptic input by the complex dynamics of their membrane. One line of research has attempted to resolve this discrepancy by linking the average firing probability of a population of simplified spiking neuron models to rate dynamics similar to those used for RNN units. However, challenges remain to account for complex temporal dependencies in the biological single neuron response and for the heterogeneity of synaptic input across the population. Here, we make progress by showing how to derive dynamic rate equations for a population of spiking neurons with multi-timescale adaptation properties - as this was shown to accurately model the response of biological neurons - while they receive independent time-varying inputs, leading to plausible asynchronous activity in the network. The resulting rate equations yield an insightful segregation of the population's response into dynamics that are driven by the mean signal received by the neural population, and dynamics driven by the variance of the input across neurons, with respective timescales that are in agreement with slice experiments. Further, these equations explain how input variability can shape log-normal instantaneous rate distributions across neurons, as observed in vivo. Our results help interpret properties of the neural population response and open the way to investigating whether the more biologically plausible and dynamically complex rate model we derive could provide useful inductive biases if used in an RNN to solve specific tasks.

Low-dimensional population dynamics can be observed in neural activity recorded from the prefrontal cortex (PFC) of subjects performing simple cognitive tasks. Many studies have shown that recurrent neural networks (RNNs) trained on the same tasks can reproduce qualitatively these state space trajectories, and have used them as models of how neuronal dynamics implement task computations. The PFC is also viewed as a conductor that organizes the communication between cortical areas and provides contextual information. It is then not clear what is its role in solving simple cognitive tasks. Do the low-dimensional trajectories observed in the PFC really correspond to the computations that it performs? Or do they indirectly reflect the computations occurring within the cortical areas projecting to the PFC? To address these questions, we modelled cortical areas with a modular RNN and equipped it with a PFC-like cognitive system. When trained on cognitive tasks, this multi-system brain model can reproduce the low-dimensional population responses observed in neuronal activity as well as classical RNNs. Qualitatively different mechanisms can emerge from the training process when varying some details of the architecture such as the time constants. In particular, there is one class of models where it is the dynamics of the cognitive system that is implementing the task computations, and another where the cognitive system is only necessary to provide contextual information about the task rule as task performance is not impaired when preventing the system from accessing the task inputs. These constitute two different hypotheses about the causal role of the PFC in solving simple cognitive tasks, which could motivate further experiments on the brain.

Spike Timing Dependent Plasticity (STDP) is argued to modulate synaptic strength depending on the timing of pre- and postsynaptic spikes. Physiological experiments identified a variety of temporal kernels: Hebbian, anti-Hebbian and symmetrical LTP/LTD. In this work we present a novel plasticity model, the Voltage-Dependent Pathway Model (VDP), which is able to replicate those distinct kernel types and intermediate versions with varying LTP/LTD ratios and symmetry features. In addition, unlike previous models it retains these characteristics for different neuron models, which allows for comparison of plasticity in different neuron types. The plastic updates depend on the relative strength and activation of separately modeled LTP and LTD pathways, which are modulated by glutamate release and postsynaptic voltage. We used the 15 neuron type parametrizations in the GLIF5 model presented by Teeter et al. (2018) in combination with the VDP to simulate a range of standard plasticity protocols including standard STDP experiments, frequency dependency experiments and low frequency stimulation protocols. Slight variation in kernel stability and frequency effects can be identified between the neuron types, suggesting that the neuron type may have an effect on the effective learning rule. This plasticity model builds a middle ground between biophysical and phenomenological models allowing not just for the combination with more complex and biophysical neuron models, but is also computationally efficient so can be used in network simulations. Therefore it offers the possibility to explore the functional role of the different kernel types and electrophysiological differences in heterogeneous networks in future work.

Decision-making in noisy environments with constant sensory evidence involves integrating sequentially-sampled evidence, a strategy formalized by diffusion models which is supported by decades behavioral and neural findings. By contrast, it is unknown whether this strategy is also used during decision-making when the underlying sensory evidence is expected to change. Here, we trained monkeys to identify the dominant color of a dynamically refreshed checkerboard pattern that doesn't become informative until after a variable delay. Animals' behavioral responses were briefly suppressed after an abrupt change in evidence, and many neurons in the frontal eye field displayed a corresponding dip in activity at this time, similar to the dip frequently observed after stimulus onset. Generalized drift-diffusion models revealed that behavior and neural activity were consistent with a brief suppression of motor output without a change in evidence accumulation itself, in contrast to the popular belief that evidence accumulation is paused or reset. These results suggest that a brief interruption in motor preparation is an important strategy for dealing with changing evidence during perceptual decision making.

The world around us is complex, but at the same time full of meaningful regularities. We can detect, learn and exploit these regularities automatically in an unsupervised manner i.e. without any direct instruction or explicit reward. For example, we effortlessly estimate the average tallness of people in a room, or the boundaries between words in a language. These regularities and prior knowledge, once learned, can affect the way we acquire and interpret new information to build and update our internal model of the world for future decision-making processes. Despite the ubiquity of passively learning from the structured information in the environment, the mechanisms that support learning from real-world experience are largely unknown. By combing sophisticated cognitive tasks in human and rats, neuronal measurements and perturbations in rat and network modelling, we aim to build a multi-level description of how sensory history is utilised in inferring regularities in temporally extended tasks. In this talk, I will specifically focus on a comparative rat and human model, in combination with neural network models to study how past sensory experiences are utilized to impact working memory and decision making behaviours.

It is common for animals to use self-generated movements to actively sense the surrounding environment. For instance, rodents rhythmically move their whiskers to explore the space close to their body. The mouse whisker system has become a standard model to study active sensing and sensorimotor integration through feedback loops. In this work, we developed a bioinspired spiking neural network model of the sensorimotor peripheral whisker system, modelling trigeminal ganglion, trigeminal nuclei, facial nuclei, and central pattern generator neuronal populations. This network was embedded in a virtual mouse robot, exploiting the Neurorobotics Platform, a simulation platform offering a virtual environment to develop and test robots driven by brain-inspired controllers. Eventually, the peripheral whisker system was properly connected to an adaptive cerebellar network controller. The whole system was able to drive active whisking with learning capability, matching neural correlates of behaviour experimentally recorded in mice.

Several lines of research have demonstrated that internally generated sensory experience - such as during memory, dreaming and mental imagery - activates similar neural representations as externally triggered perception. This overlap raises a fundamental challenge: how is the brain able to keep apart signals reflecting imagination and reality? In a series of online psychophysics experiments combined with computational modelling, we investigated to what extent imagination and perception are confused when the same content is simultaneously imagined and perceived. We found that simultaneous congruent mental imagery consistently led to an increase in perceptual presence responses, and that congruent perceptual presence responses were in turn associated with a more vivid imagery experience. Our findings can be best explained by a simple signal detection model in which imagined and perceived signals are added together. Perceptual reality monitoring can then easily be implemented by evaluating whether this intermixed signal is strong or vivid enough to pass a ‘reality threshold’. Our model suggests that, in contrast to self-generated sensory changes during movement, our brain does not discount self-generated sensory signals during mental imagery. This has profound implications for our understanding of reality monitoring and perception in general.

Brains must integrate complex sensory information and compare to past events to generate appropriate behavioral responses. The neural circuit basis of these computations is unclear and the underlying structure unknown. Here, we mapped the comprehensive synaptic wiring diagram of the fruit fly larva brain, which contains 3,013 neurons and 544K synaptic sites. It is the most complete insect connectome to date: 1) Both brain hemispheres are reconstructed, allowing investigation of neural pathways that include contralateral axons, which we found in 37% of brain neurons. 2) All sensory neurons and descending neurons are reconstructed, allowing one to follow signals in an uninterrupted chain—from the sensory periphery, through the brain, to motor neurons in the nerve cord. We developed novel computational tools, allowing us to cluster the brain and investigate how information flows through it. We discovered that feedforward pathways from sensory to descending neurons are multilayered and highly multimodal. Robust feedback was observed at almost all levels of the brain, including descending neurons. We investigated how the brain hemispheres communicate with each other and the nerve cord, leading to identification of novel circuit motifs. This work provides the complete blueprint of a brain and a strong foundation to study the structure-function relationship of neural circuits.

The brain represents the external world through the bottleneck of sensory organs. The network of hierarchically organized neurons is thought to recover the causes of sensory inputs to reconstruct the reality in the brain in idiosyncratic ways depending on individuals and their internal states. How can we understand the world model represented in an individual’s brain, or the neuroverse? My lab has been working on brain decoding of visual perception and subjective experiences such as imagery and dreaming using machine learning and deep neural network representations. In this talk, I will outline the progress of brain decoding methods and present how subjective experiences are externalized as images and how they could be shared across individuals via neural code conversion. The prospects of these approaches in basic science and neurotechnology will be discussed.

How psychedelic drugs change the activity of cortical neuronal populations is not well understood. It is also not clear which changes are specific to transition into the psychedelic brain state and which are shared with other brain state transitions. Here, we used Neuropixels probes to record from large populations of neurons in prefrontal cortex of mice given the psychedelic drug TCB-2. The primary effect of drug ingestion was stretching of the distribution of log firing rates of the recorded population. This phenomenon was previously observed across transitions between sleep and wakefulness, which prompted us to examine how common it is. We found that modulation of the width of the log-rate distribution of a neuronal population occurred in multiple areas of the cortex and in the hippocampus even in awake drug-free mice, driven by intrinsic fluctuations in their arousal level. Arousal, however, did not explain the stretching of the log-rate distribution by TCB-2. In both psychedelic and intrinsically occurring brain state transitions, the stretching or squeezing of the log-rate distribution of an entire neuronal population were the result of a more close overlap between log-rate distributions of the upregulated and downregulated subpopulations in one brain state compared to the other brain state. Often, we also observed that the log-rate distribution of the downregulated subpopulation was stretched, whereas the log-rate distribution of the upregulated subpopulation was squeezed. In both subpopulations, the stretching and squeezing were a signature of a greater relative impact of the brain state transition on the rates of the slow-firing neurons. These findings reveal a generic pattern of reorganisation of neuronal firing rates by different kinds of brain state transitions.