A neuronal population measure of attention predicts behavioral performance on individual trials

Recent visual experience reshapes V4 neuronal activity and improves perceptual performance

Recent visual experience heavily influences our visual perception, but how this is mediated by the reshaping of neuronal activity to alter and improve perceptual discrimination remains unknown. We recorded from populations of neurons in visual cortical area V4 while monkeys performed a natural image change detection task under different experience conditions. We found that maximizing the recent experience with a particular image led to an improvement in the ability to detect a change in that image. This improvement was associated with decreased neural responses to the image, consistent with neuronal changes previously seen in studies of adaptation and expectation. We found that the magnitude of behavioral improvement was correlated with the magnitude of response suppression. Furthermore, this suppression of activity led to an increase in signal separation, providing evidence that a reduction in activity can improve stimulus encoding. Within populations of neurons, greater recent experience was associated with decreased trial-to-trial shared variability, indicating that a reduction in variability is a key means by which experience influences perception. Taken together, the results of our study contribute to an understanding of how recent visual experience can shape our perception and behavior through modulating activity patterns in mid-level visual cortex.

Dissociation of attentional state and behavioral outcome using local field potentials

Successful behavior depends on attentional state and other factors related to decision-making, which may modulate neuronal activity differently. Here, we investigated whether attentional state and behavioral outcome (i.e., whether a target is detected or missed) are distinguishable using the power and phase of local field potential (LFP) recorded bilaterally from area V4 of monkeys performing a cued visual attention task. To link each trial's outcome to pairwise measures of attention that are typically averaged across trials, we used several methods to obtain single-trial estimates of spike count correlation and phase consistency. Surprisingly, while attentional location was best discriminated using gamma and high-gamma power, behavioral outcome was best discriminated by alpha power and steady-state visually evoked potential. Power outperformed absolute phase in attentional/behavioral discriminability, although single-trial gamma phase consistency provided reasonably high attentional discriminability. Our results suggest a dissociation between the neuronal mechanisms that regulate attentional focus and behavioral outcome.

Interindividual Differences in Cognitive Variability Are Ubiquitous and Distinct From Mean Performance in a Battery of Eleven Tasks

Our performance on cognitive tasks fluctuates: the same individual completing the same task will differ in their response's moment-to-moment. For decades cognitive fluctuations have been implicitly ignored - treated as measurement error - with a focus instead on aggregates such as mean performance. Leveraging dense trial-by-trial data and novel time-series methods we explored variability as an intrinsically important phenotype. Across eleven cognitive tasks with over 7 million trials, we found highly reliable interindividual differences in cognitive variability in every task we examined. These differences are both qualitatively and quantitatively distinct from mean performance. Moreover, we found that a single dimension for variability across tasks was inadequate, demonstrating that previously posited global mechanisms for cognitive variability are at least partially incomplete. Our findings indicate that variability is a fundamental part of cognition - with the potential to offer novel insights into developmental processes.

Orthogonal neural encoding of targets and distractors supports multivariate cognitive control

The complex challenges of our mental life require us to coordinate multiple forms of neural information processing. Recent behavioural studies have found that people can coordinate multiple forms of attention, but the underlying neural control process remains obscure. We hypothesized that the brain implements multivariate control by independently monitoring feature-specific difficulty and independently prioritizing feature-specific processing. During functional MRI, participants performed a parametric conflict task that separately tags target and distractor processing. Consistent with feature-specific monitoring, univariate analyses revealed spatially segregated encoding of target and distractor difficulty in the dorsal anterior cingulate cortex. Consistent with feature-specific attentional priority, our encoding geometry analysis revealed overlapping but orthogonal representations of target and distractor coherence in the intraparietal sulcus. Coherence representations were mediated by control demands and aligned with both performance and frontoparietal activity, consistent with top-down attention. Together, these findings provide evidence for the neural geometry necessary to coordinate multivariate cognitive control.

The dynamics and geometry of choice in premotor cortex

The brain represents sensory variables in the coordinated activity of neural populations, in which tuning curves of single neurons define the geometry of the population code. Whether the same coding principle holds for dynamic cognitive variables remains unknown because internal cognitive processes unfold with a unique time course on single trials observed only in the irregular spiking of heterogeneous neural populations. Here we show the existence of such a population code for the dynamics of choice formation in the primate premotor cortex. We developed an approach to simultaneously infer population dynamics and tuning functions of single neurons to the population state. Applied to spike data recorded during decision-making, our model revealed that populations of neurons encoded the same dynamic variable predicting choices, and heterogeneous firing rates resulted from the diverse tuning of single neurons to this decision variable. The inferred dynamics indicated an attractor mechanism for decision computation. Our results reveal a common geometric principle for neural encoding of sensory and dynamic cognitive variables.

Pupil size predicts the onset of exploration in brain and behavior

In uncertain environments, intelligent decision-makers exploit actions that have been rewarding in the past, but also explore actions that could be even better. Several neuromodulatory systems are implicated in exploration, based, in part, on work linking exploration to pupil size-a peripheral correlate of neuromodulatory tone and index of arousal. However, pupil size could instead track variables that make exploration more likely, like volatility or reward, without directly predicting either exploration or its neural bases. Here, we simultaneously measured pupil size, exploration, and neural population activity in the prefrontal cortex while two rhesus macaques explored and exploited in a dynamic environment. We found that pupil size under constant luminance specifically predicted the onset of exploration, beyond what could be explained by reward history. Pupil size also predicted disorganized patterns of prefrontal neural activity at both the single neuron and population levels, even within periods of exploitation. Ultimately, our results support a model in which pupil-linked mechanisms promote the onset of exploration via driving the prefrontal cortex through a critical tipping point where prefrontal control dynamics become disorganized and exploratory decisions are possible.

Arousal and Locomotion Differently Modulate Activity of Somatostatin Neurons across Cortex

Arousal powerfully influences cortical activity, in part by modulating local inhibitory circuits. Somatostatin (SOM)-expressing inhibitory interneurons are particularly well situated to shape local population activity in response to shifts in arousal, yet the relationship between arousal state and SOM activity has not been characterized outside of sensory cortex. To determine whether SOM activity is similarly modulated by behavioral state across different levels of the cortical processing hierarchy, we compared the behavioral modulation of SOM-expressing neurons in auditory cortex (AC), a primary sensory region, and posterior parietal cortex (PPC), an association-level region of cortex, in mice. Behavioral state modulated activity differently in AC and PPC. In PPC, transitions to high arousal were accompanied by large increases in activity across the full PPC neural population, especially in SOM neurons. In AC, arousal transitions led to more subtle changes in overall activity, as individual SOM and Non-SOM neurons could be either positively or negatively modulated during transitions to high arousal states. The coding of sensory information in population activity was enhanced during periods of high arousal in AC, but not in PPC. Our findings suggest unique relationships between activity in local circuits and arousal across cortex, which may be tailored to the roles of specific cortical regions in sensory processing or the control of behavior.

Neural manifold analysis of brain circuit dynamics in health and disease

Recent developments in experimental neuroscience make it possible to simultaneously record the activity of thousands of neurons. However, the development of analysis approaches for such large-scale neural recordings have been slower than those applicable to single-cell experiments. One approach that has gained recent popularity is neural manifold learning. This approach takes advantage of the fact that often, even though neural datasets may be very high dimensional, the dynamics of neural activity tends to traverse a much lower-dimensional space. The topological structures formed by these low-dimensional neural subspaces are referred to as "neural manifolds", and may potentially provide insight linking neural circuit dynamics with cognitive function and behavioral performance. In this paper we review a number of linear and non-linear approaches to neural manifold learning, including principal component analysis (PCA), multi-dimensional scaling (MDS), Isomap, locally linear embedding (LLE), Laplacian eigenmaps (LEM), t-SNE, and uniform manifold approximation and projection (UMAP). We outline these methods under a common mathematical nomenclature, and compare their advantages and disadvantages with respect to their use for neural data analysis. We apply them to a number of datasets from published literature, comparing the manifolds that result from their application to hippocampal place cells, motor cortical neurons during a reaching task, and prefrontal cortical neurons during a multi-behavior task. We find that in many circumstances linear algorithms produce similar results to non-linear methods, although in particular cases where the behavioral complexity is greater, non-linear methods tend to find lower-dimensional manifolds, at the possible expense of interpretability. We demonstrate that these methods are applicable to the study of neurological disorders through simulation of a mouse model of Alzheimer's Disease, and speculate that neural manifold analysis may help us to understand the circuit-level consequences of molecular and cellular neuropathology.

Dimensionality reduction of calcium-imaged neuronal population activity

Calcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear if the dimensionality reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality reduction methods. We also developed a method to perform deconvolution and dimensionality reduction simultaneously (Calcium Imaging Linear Dynamical System, CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from simulated calcium imaging data. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.

Tracking momentary fluctuations in human attention with a cognitive brain-machine interface

Selective attention produces systematic effects on neural states. It is unclear whether, conversely, momentary fluctuations in neural states have behavioral significance for attention. We investigated this question in the human brain with a cognitive brain-machine interface (cBMI) for tracking electrophysiological steady-state visually evoked potentials (SSVEPs) in real-time. Discrimination accuracy (d') was significantly higher when target stimuli were triggered at high, versus low, SSVEP power states. Target and distractor SSVEP power was uncorrelated across the hemifields, and target d' was unaffected by distractor SSVEP power states. Next, we trained participants on an auditory neurofeedback paradigm to generate biased, cross-hemispheric competitive interactions between target and distractor SSVEPs. The strongest behavioral effects emerged when competitive SSVEP dynamics unfolded at a timescale corresponding to the deployment of endogenous attention. In sum, SSVEP power dynamics provide a reliable readout of attentional state, a result with critical implications for tracking and training human attention.

Neural signature of the perceptual decision in the neural population responses of the inferior temporal cortex

Rapid categorization of visual objects is critical for comprehending our complex visual world. The role of individual cortical neurons and neural populations in categorizing visual objects during passive vision has previously been studied. However, it is unclear whether and how perceptually guided behaviors affect the encoding of stimulus categories by neural population activity in the higher visual cortex. Here we studied the activity of the inferior temporal (IT) cortical neurons in macaque monkeys during both passive viewing and categorization of ambiguous body and object images. We found enhanced category information in the IT neural population activity during the correct, but not wrong, trials of the categorization task compared to the passive task. This encoding enhancement was task difficulty dependent with progressively larger values in trials with more ambiguous stimuli. Enhancement of IT neural population information for behaviorally relevant stimulus features suggests IT neural networks' involvement in perceptual decision-making behavior.

Altered Response Dynamics and Increased Population Correlation to Tonal Stimuli Embedded in Noise in Aging Auditory Cortex

Age-related hearing loss (presbycusis) is a chronic health condition that affects one-third of the world population. One hallmark of presbycusis is a difficulty hearing in noisy environments. Presbycusis can be separated into two components: alterations of peripheral mechanotransduction of sound in the cochlea and central alterations of auditory processing areas of the brain. Although the effects of the aging cochlea in hearing loss have been well studied, the role of the aging brain in hearing loss is less well understood. Therefore, to examine how age-related central processing changes affect hearing in noisy environments, we used a mouse model (Thy1-GCaMP6s X CBA) that has excellent peripheral hearing in old age. We used in vivo two-photon Ca2+ imaging to measure the responses of neuronal populations in auditory cortex (ACtx) of adult (2-6 months, nine male, six female, 4180 neurons) and aging mice (15-17 months, six male, three female, 1055 neurons) while listening to tones in noisy backgrounds. We found that ACtx neurons in aging mice showed larger responses to tones and have less suppressed responses consistent with reduced inhibition. Aging neurons also showed less sensitivity to temporal changes. Population analysis showed that neurons in aging mice showed higher pairwise activity correlations and showed a reduced diversity in responses to sound stimuli. Using neural decoding techniques, we show a loss of information in neuronal populations in the aging brain. Thus, aging not only affects the responses of single neurons but also affects how these neurons jointly represent stimuli.SIGNIFICANCE STATEMENT Aging results in hearing deficits particularly under challenging listening conditions. We show that auditory cortex contains distinct subpopulations of excitatory neurons that preferentially encode different stimulus features and that aging selectively reduces certain subpopulations. We also show that aging increases correlated activity between neurons and thereby reduces the response diversity in auditory cortex. The loss of population response diversity leads to a decrease of stimulus information and deficits in sound encoding, especially in noisy backgrounds. Future work determining the identities of circuits affected by aging could provide new targets for therapeutic strategies.

Representational drift in the mouse visual cortex

Recent studies have shown that neuronal representations gradually change over time despite no changes in the stimulus, environment, or behavior. However, such representational drift has been assumed to be a property of high-level brain structures, whereas earlier circuits, such as sensory cortices, have been assumed to stably encode information over time. Here, we analyzed large-scale optical and electrophysiological recordings from six visual cortical areas in behaving mice that were repeatedly presented with the same natural movies. Contrary to the prevailing notion, we found representational drift over timescales spanning minutes to days across multiple visual areas, cortical layers, and cell types. Notably, neural-code stability did not reflect the hierarchy of information flow across areas. Although individual neurons showed time-dependent changes in their coding properties, the structure of the relationships between population activity patterns remained stable and stereotypic. Such population-level organization may underlie stable visual perception despite continuous changes in neuronal responses.

The population doctrine in cognitive neuroscience

A major shift is happening within neurophysiology: a population doctrine is drawing level with the single-neuron doctrine that has long dominated the field. Population-level ideas have so far had their greatest impact in motor neuroscience, but they hold great promise for resolving open questions in cognition as well. Here, we codify the population doctrine and survey recent work that leverages this view to specifically probe cognition. Our discussion is organized around five core concepts that provide a foundation for population-level thinking: (1) state spaces, (2) manifolds, (3) coding dimensions, (4) subspaces, and (5) dynamics. The work we review illustrates the progress and promise that population-level thinking holds for cognitive neuroscience-for delivering new insight into attention, working memory, decision-making, executive function, learning, and reward processing.

A direct neural measure of variable precision representations in visual working memory

Visual working memory (VWM) is an active representation enabling the manipulation of item information even in the absence of visual input. A common way to investigate VWM is to analyze the performance at later recall. This approach, however, leaves uncertainties about whether the variation of recall performance is attributable to item encoding and maintenance or to the testing of memorized information. Here, we record the contralateral delay activity (CDA), an established electrophysiological measure of item storage and maintenance, in human subjects performing a delayed orientation precision estimation task. This allows us to link the fluctuation of recall precision directly to the process of item encoding and maintenance. We show that for two sequentially encoded orientation items, the CDA amplitude reflects the precision of orientation recall of both items, with higher precision being associated with a larger amplitude. Furthermore, we show that the CDA amplitudes for the items vary independently from each other, suggesting that the precision of memory representations fluctuates independently.NEW & NOTEWORTHY The present work demonstrates for the first time that the contralateral delay activity (CDA), an online electrophysiological measure of the number of representations maintained in memory, is also a reliable measure of the precision of memory representations. Furthermore, we show that the CDA fluctuates independently for individual items held in memory, thereby providing unambiguous direct neurophysiological support for independently fluctuating memory representations.

Uncovering structured responses of neural populations recorded from macaque monkeys with linear support vector machines

When a mammal, such as a macaque monkey, sees a complex natural image, many neurons in its visual cortex respond simultaneously. Here, we provide a protocol for studying the structure of population responses in laminar recordings with a machine learning model, the linear support vector machine. To unravel the role of single neurons in population responses and the structure of noise correlations, we use a multivariate decoding technique on time-averaged responses.

For complete details on the use and execution of this protocol, please refer to Koren et al. (2020a).

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Linear support vector machine (SVM) is an efficient model for decoding from neural data

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Permutation test is a rigorous method for testing the significance of results

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Neural responses along the cortical depth are heterogeneous

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Decoding weights and noise correlations share a similar structure

Bridging neuronal correlations and dimensionality reduction

Two commonly used approaches to study interactions among neurons are spike count correlation, which describes pairs of neurons, and dimensionality reduction, applied to a population of neurons. Although both approaches have been used to study trial-to-trial neuronal variability correlated among neurons, they are often used in isolation and have not been directly related. We first established concrete mathematical and empirical relationships between pairwise correlation and metrics of population-wide covariability based on dimensionality reduction. Applying these insights to macaque V4 population recordings, we found that the previously reported decrease in mean pairwise correlation associated with attention stemmed from three distinct changes in population-wide covariability. Overall, our work builds the intuition and formalism to bridge between pairwise correlation and population-wide covariability and presents a cautionary tale about the inferences one can make about population activity by using a single statistic, whether it be mean pairwise correlation or dimensionality.

Decoding of Attentional State Using High-Frequency Local Field Potential Is As Accurate As Using Spikes

Local field potentials (LFPs) in visual cortex are reliably modulated when the subject's focus of attention is cued into versus out of the receptive field of the recorded sites, similar to modulation of spikes. However, human psychophysics studies have used an additional attention condition, neutral cueing, for decades. The effect of neutral cueing on spikes was examined recently and found to be intermediate between cued and uncued conditions. However, whether LFPs are also precise enough to represent graded states of attention is unknown. We found in rhesus monkeys that LFPs during neutral cueing were also intermediate between cued and uncued conditions. For a single electrode, attention was more discriminable using high frequency (>30 Hz) LFP power than spikes, which is expected because LFP represents a population signal and therefore is expected to be less noisy than spikes. However, previous studies have shown that when multiple electrodes are used, spikes can outperform LFPs. Surprisingly, in our study, spikes did not outperform LFPs when discriminability was computed using multiple electrodes, even though the LFP activity was highly correlated across electrodes compared with spikes. These results constrain the spatial scale over which attention operates and highlight the usefulness of LFPs in studying attention.

Optimal policy for attention-modulated decisions explains human fixation behavior

Traditional accumulation-to-bound decision-making models assume that all choice options are processed with equal attention. In real life decisions, however, humans alternate their visual fixation between individual items to efficiently gather relevant information (Yang et al., 2016). These fixations also causally affect one's choices, biasing them toward the longer-fixated item (Krajbich et al., 2010). We derive a normative decision-making model in which attention enhances the reliability of information, consistent with neurophysiological findings (Cohen and Maunsell, 2009). Furthermore, our model actively controls fixation changes to optimize information gathering. We show that the optimal model reproduces fixation-related choice biases seen in humans and provides a Bayesian computational rationale for this phenomenon. This insight led to additional predictions that we could confirm in human data. Finally, by varying the relative cognitive advantage conferred by attention, we show that decision performance is benefited by a balanced spread of resources between the attended and unattended items.

Behavior needs neural variability

Human and non-human animal behavior is highly malleable and adapts successfully to internal and external demands. Such behavioral success stands in striking contrast to the apparent instability in neural activity (i.e., variability) from which it arises. Here, we summon the considerable evidence across scales, species, and imaging modalities that neural variability represents a key, undervalued dimension for understanding brain-behavior relationships at inter- and intra-individual levels. We believe that only by incorporating a specific focus on variability will the neural foundation of behavior be comprehensively understood.

Rules warp feature encoding in decision-making circuits

We have the capacity to follow arbitrary stimulus-response rules, meaning simple policies that guide our behavior. Rule identity is broadly encoded across decision-making circuits, but there are less data on how rules shape the computations that lead to choices. One idea is that rules could simplify these computations. When we follow a rule, there is no need to encode or compute information that is irrelevant to the current rule, which could reduce the metabolic or energetic demands of decision-making. However, it is not clear if the brain can actually take advantage of this computational simplicity. To test this idea, we recorded from neurons in 3 regions linked to decision-making, the orbitofrontal cortex (OFC), ventral striatum (VS), and dorsal striatum (DS), while macaques performed a rule-based decision-making task. Rule-based decisions were identified via modeling rules as the latent causes of decisions. This left us with a set of physically identical choices that maximized reward and information, but could not be explained by simple stimulus-response rules. Contrasting rule-based choices with these residual choices revealed that following rules (1) decreased the energetic cost of decision-making; and (2) expanded rule-relevant coding dimensions and compressed rule-irrelevant ones. Together, these results suggest that we use rules, in part, because they reduce the costs of decision-making through a distributed representational warping in decision-making circuits.

Low rank mechanisms underlying flexible visual representations

Neuronal population responses to sensory stimuli are remarkably flexible. The responses of neurons in visual cortex have heterogeneous dependence on stimulus properties (e.g., contrast), processes that affect all stages of visual processing (e.g., adaptation), and cognitive processes (e.g., attention or task switching). Understanding whether these processes affect similar neuronal populations and whether they have similar effects on entire populations can provide insight into whether they utilize analogous mechanisms. In particular, it has recently been demonstrated that attention has low rank effects on the covariability of populations of visual neurons, which impacts perception and strongly constrains mechanistic models. We hypothesized that measuring changes in population covariability associated with other sensory and cognitive processes could clarify whether they utilize similar mechanisms or computations. Our experimental design included measurements in multiple visual areas using four distinct sensory and cognitive processes. We found that contrast, adaptation, attention, and task switching affect the variability of responses of populations of neurons in primate visual cortex in a similarly low rank way. These results suggest that a given circuit may use similar mechanisms to perform many forms of modulation and likely reflects a general principle that applies to a wide range of brain areas and sensory, cognitive, and motor processes.

Slow Drift of Neural Activity as a Signature of Impulsivity in Macaque Visual and Prefrontal Cortex

An animal's decision depends not only on incoming sensory evidence but also on its fluctuating internal state. This state embodies multiple cognitive factors, such as arousal and fatigue, but it is unclear how these factors influence the neural processes that encode sensory stimuli and form a decision. We discovered that, unprompted by task conditions, animals slowly shifted their likelihood of detecting stimulus changes over the timescale of tens of minutes. Neural population activity from visual area V4, as well as from prefrontal cortex, slowly drifted together with these behavioral fluctuations. We found that this slow drift, rather than altering the encoding of the sensory stimulus, acted as an impulsivity signal, overriding sensory evidence to dictate the final decision. Overall, this work uncovers an internal state embedded in population activity across multiple brain areas and sheds further light on how internal states contribute to the decision-making process.

Spike Timing in the Attention Network Predicts Behavioral Outcome Prior to Target Selection

There has been little evidence linking changes in spiking activity that occur prior to a spatially predictable target (i.e., prior to target selection) to behavioral outcomes, despite such preparatory changes being widely assumed to enhance the sensitivity of sensory processing. We simultaneously recorded from frontal and parietal nodes of the attention network while macaques performed a spatial cueing task. When anticipating a spatially predictable target, different patterns of coupling between spike timing and the oscillatory phase in local field potentials-but not changes in spike rate-were predictive of different behavioral outcomes. These behaviorally relevant differences in local and between-region synchronization occurred among specific cell types that were defined based on their sensory and motor properties, providing insight into the mechanisms underlying enhanced sensory processing prior to target selection. We propose that these changes in neural synchronization reflect differential anticipatory engagement of the network nodes and functional units that shape attention-related sampling.

Learning to control the brain through adaptive closed-loop patterned stimulation

OBJECTIVE

Stimulation of neural activity is an important scientific and clinical tool, causally testing hypotheses and treating neurodegenerative and neuropsychiatric diseases. However, current stimulation approaches cannot flexibly control the pattern of activity in populations of neurons. To address this, we developed a model-free, adaptive, closed-loop stimulation (ACLS) system that learns to use multi-site electrical stimulation to control the pattern of activity of a population of neurons.

APPROACH

The ACLS system combined multi-electrode electrophysiological recordings with multi-site electrical stimulation to simultaneously record the activity of a population of 5-15 multiunit neurons and deliver spatially-patterned electrical stimulation across 4-16 sites. Using a closed-loop learning system, ACLS iteratively updated the pattern of stimulation to reduce the difference between the observed neural response and a specific target pattern of firing rates in the recorded multiunits.

MAIN RESULTS

In silico and in vivo experiments showed ACLS learns to produce specific patterns of neural activity (in ∼15 min) and was robust to noise and drift in neural responses. In visual cortex of awake mice, ACLS learned electrical stimulation patterns that produced responses similar to the natural response evoked by visual stimuli. Similar to how repetition of a visual stimulus causes an adaptation in the neural response, the response to electrical stimulation was adapted when it was preceded by the associated visual stimulus.

SIGNIFICANCE

Our results show an ACLS system that can learn, in real-time, to generate specific patterns of neural activity. This work provides a framework for using model-free closed-loop learning to control neural activity.

A modular high-density μECoG system on macaque vlPFC for auditory cognitive decoding

OBJECTIVE

A fundamental goal of the auditory system is to parse the auditory environment into distinct perceptual representations. Auditory perception is mediated by the ventral auditory pathway, which includes the ventrolateral prefrontal cortex (vlPFC). Because large-scale recordings of auditory signals are quite rare, the spatiotemporal resolution of the neuronal code that underlies vlPFC's contribution to auditory perception has not been fully elucidated. Therefore, we developed a modular, chronic, high-resolution, multi-electrode array system with long-term viability in order to identify the information that could be decoded from μECoG vlPFC signals.

APPROACH

We molded three separate μECoG arrays into one and implanted this system in a non-human primate. A custom 3D-printed titanium chamber was mounted on the left hemisphere. The molded 294-contact μECoG array was implanted subdurally over the vlPFC. μECoG activity was recorded while the monkey participated in a 'hearing-in-noise' task in which they reported hearing a 'target' vocalization from a background 'chorus' of vocalizations. We titrated task difficulty by varying the sound level of the target vocalization, relative to the chorus (target-to-chorus ratio, TCr).

MAIN RESULTS

We decoded the TCr and the monkey's behavioral choices from the μECoG signal. We analyzed decoding accuracy as a function of number of electrodes, spatial resolution, and time from implantation. Over a one-year period, we found significant decoding with individual electrodes that increased significantly as we decoded simultaneously more electrodes. Further, we found that the decoding for behavioral choice was better than the decoding of TCr. Finally, because the decoding accuracy of individual electrodes varied on a day-by-day basis, electrode arrays with high channel counts ensure robust decoding in the long term.

SIGNIFICANCE

Our results demonstrate the utility of high-resolution and high-channel-count, chronic µECoG recording. We developed a surface electrode array that can be scaled to cover larger cortical areas without increasing the chamber footprint.

Prefrontal attentional saccades explore space rhythmically

Recent studies suggest that attention samples space rhythmically through oscillatory interactions in the frontoparietal network. How these attentional fluctuations coincide with spatial exploration/displacement and exploitation/selection by a dynamic attentional spotlight under top-down control is unclear. Here, we show a direct contribution of prefrontal attention selection mechanisms to a continuous space exploration. Specifically, we provide a direct high spatio-temporal resolution prefrontal population decoding of the covert attentional spotlight. We show that it continuously explores space at a 7-12 Hz rhythm. Sensory encoding and behavioral reports are increased at a specific optimal phase w/ to this rhythm. We propose that this prefrontal neuronal rhythm reflects an alpha-clocked sampling of the visual environment in the absence of eye movements. These attentional explorations are highly flexible, how they spatially unfold depending both on within-trial and across-task contingencies. These results are discussed in the context of exploration-exploitation strategies and prefrontal top-down attentional control.

Activity in LIP, But not V4, Matches Performance When Attention is Spread

The enhancement of neuronal responses in many visual areas while animals perform spatial attention tasks has widely been thought to be the neural correlate of visual attention, but it is unclear whether the presence or absence of this modulation contributes to our striking inability to notice changes in change blindness examples. We asked whether neuronal responses in visual area V4 and the lateral intraparietal area (LIP) in posterior parietal cortex could explain the limited ability of subjects to attend multiple items in a display. We trained animals to perform a change detection task in which they had to compare 2 arrays of stimuli separated briefly in time and found that each animal's performance decreased as function of set-size. Neuronal discriminability in V4 was consistent across set-sizes, but decreased for higher set-sizes in LIP. The introduction of a reward bias produced attentional enhancement in V4, but this could not explain the vast improvement in performance, whereas the enhancement in LIP responses could. We suggest that behavioral set-size effects and the marked improvement in performance with focused attention may not be related to response enhancement in V4 but, instead, may occur in or on the way to LIP.

Selective Changes in Noise Correlations Contribute to an Enhanced Representation of Saccadic Targets in Prefrontal Neuronal Ensembles

An ensemble of neurons can provide a dynamic representation of external stimuli, ongoing processes, or upcoming actions. This dynamic representation could be achieved by changes in the activity of individual neurons and/or their interactions. To investigate these possibilities, we simultaneously recorded from ensembles of prefrontal neurons in non-human primates during a memory-guided saccade task. Using both decoding and encoding methods, we examined changes in the information content of individual neurons and that of ensembles between visual encoding and saccadic target selection. We found that individual neurons maintained their limited spatial sensitivity between these cognitive states, whereas the ensemble selectively improved its encoding of spatial locations far from the neurons’ preferred locations. This population-level “encoding expansion” was not due to the ceiling effect at the preferred locations and was accompanied by selective changes in noise correlations for non-preferred locations. Moreover, the encoding expansion was observed for ensembles of different types of neurons and could not be explained by shifts in the preferred location of individual neurons. Our results demonstrate that the representation of space by neuronal ensembles is dynamically enhanced prior to saccades, and this enhancement occurs alongside changes in noise correlations more than changes in the activity of individual neurons.

Interneuronal correlations at longer time scales predict decision signals for bistable structure-from-motion perception

Perceptual decisions are thought to depend on the activation of task-relevant neurons, whose activity is often correlated in time. Here, we examined how the temporal structure of shared variability in neuronal firing relates to perceptual choices. We recorded stimulus-selective neurons from visual area V5/MT while two monkeys (Macaca mulatta) made perceptual decisions about the rotation direction of structure-from-motion cylinders. Interneuronal correlations for a perceptually ambiguous cylinder stimulus were significantly higher than those for unambiguous cylinders or for random 2D motion during passive viewing. Much of the difference arose from correlations at relatively long timescales (hundreds of milliseconds). Choice-related neural activity (quantified as choice probability; CP) for ambiguous cylinders was positively correlated with interneuronal correlations and was specifically associated with their long timescale component. Furthermore, the slope of the long timescale - but not the instantaneous - component of the correlation predicted higher CPs towards the end of the trial i.e. close to the decision. Our results suggest that the perceptual stability of structure-from-motion cylinders may be controlled by enhanced interneuronal correlations on longer timescales. We propose this as a potential signature of top-down influences onto V5/MT processing that shape and stabilize the appearance of 3D-motion percepts.

A flexible readout mechanism of human sensory representations

Attention can both enhance and suppress cortical sensory representations. However, changing sensory representations can also be detrimental to behavior. Behavioral consequences can be avoided by flexibly changing sensory readout, while leaving the representations unchanged. Here, we asked human observers to attend to and report about either one of two features which control the visibility of motion while making concurrent measurements of cortical activity with BOLD imaging (fMRI). We extend a well-established linking model to account for the relationship between these measurements and find that changes in sensory representation during directed attention are insufficient to explain perceptual reports. Adding a flexible downstream readout is necessary to best explain our data. Such a model implies that observers should be able to recover information about ignored features, a prediction which we confirm behaviorally. Thus, flexible readout is a critical component of the cortical implementation of human adaptive behavior.

Lasting connectivity increase and anxiety reduction via transcranial alternating current stimulation

Growing evidence of transcranial alternating current stimulation (tACS) modulating intrinsic neural oscillations has spawned interest in applying tACS to treat psychiatric disorders associated with aberrant neural oscillations. The alpha rhythmic activity is known to dominate neural oscillations at the awake, restful state, while attenuated resting-state alpha activity has been implicated in anxious mood. Administering repeated alpha-frequency tACS (α-tACS; at individual peak alpha frequency; 8–12 Hz) over four consecutive days (in the experiment group, sham stimulation in the control group), we demonstrated immediate and lasting (>24 h) increases in resting-state posterior ➔frontal connectivity in the alpha frequency, quantified by Granger causality. Critically, this connectivity enhancement was accompanied by sustained reductions in both anxious arousal and negative perception of sensory stimuli. Resting-state alpha power also increased, albeit only transiently, reversing to the baseline level within 24 h after tACS. Therefore, the lasting enhancement of long-range alpha connectivity due to α-tACS differs from local alpha activity that is nonetheless conserved, highlighting the adaptability of alpha oscillatory networks. In light of increasing recognition of large-scale network dysfunctions as a transdiagnostic pathophysiology of psychiatric disorders, this enduring connectivity plasticity, along with the behavioral improvements, paves the way for tACS applications in clinical interventions of psychiatric ‘oscillopathies’.

Routing information flow by separate neural synchrony frequencies allows for "functionally labeled lines" in higher primate cortex

Dynamical coordination of the neural activity between individual neurons is known to have a key role in the efficient transfer of sensory information to associative areas. Here, we report a role of interneuronal synchrony within the high-gamma (180 to 220 Hz) frequency range of activity in macaque area MT (a visual area in the dorsal visual pathway) in determining behavioral performance. This is, however, in contrast to previous reports for the ventral visual pathway (such as area V4), where only gamma range (40 to 70 Hz) was observed to play a role. We propose that such a difference between the functional coordination in different visual pathways might be used to unambiguously identify the source of input to the higher areas.

Efficient transfer of sensory information to higher (motor or associative) areas in primate visual cortical areas is crucial for transforming sensory input into behavioral actions. Dynamically increasing the level of coordination between single neurons has been suggested as an important contributor to this efficiency. We propose that differences between the functional coordination in different visual pathways might be used to unambiguously identify the source of input to the higher areas, ensuring a proper routing of the information flow. Here we determined the level of coordination between neurons in area MT in macaque visual cortex in a visual attention task via the strength of synchronization between the neurons’ spike timing relative to the phase of oscillatory activities in local field potentials. In contrast to reports on the ventral visual pathway, we observed the synchrony of spikes only in the range of high gamma (180 to 220 Hz), rather than gamma (40 to 70 Hz) (as reported previously) to predict the animal’s reaction speed. This supports a mechanistic role of the phase of high-gamma oscillatory activity in dynamically modulating the efficiency of neuronal information transfer. In addition, for inputs to higher cortical areas converging from the dorsal and ventral pathway, the distinct frequency bands of these inputs can be leveraged to preserve the identity of the input source. In this way source-specific oscillatory activity in primate cortex can serve to establish and maintain “functionally labeled lines” for dynamically adjusting cortical information transfer and multiplexing converging sensory signals.

Optogenetically induced low-frequency correlations impair perception

Deployment of covert attention to a spatial location can cause large decreases in low-frequency correlated variability among neurons in macaque area V4 whose receptive-fields lie at the attended location. It has been estimated that this reduction accounts for a substantial fraction of the attention-mediated improvement in sensory processing. These estimates depend on assumptions about how population signals are decoded and the conclusion that correlated variability impairs perception, is purely hypothetical. Here we test this proposal directly by optogenetically inducing low-frequency fluctuations, to see if this interferes with performance in an attention-demanding task. We find that low-frequency optical stimulation of neurons in V4 elevates correlations among pairs of neurons and impairs the animal’s ability to make fine sensory discriminations. Stimulation at higher frequencies does not impair performance, despite comparable modulation of neuronal responses. These results support the hypothesis that attention-dependent reductions in correlated variability contribute to improved perception of attended stimuli.

Neural Variability Limits Adolescent Skill Learning

Skill learning is fundamental to the acquisition of many complex behaviors that emerge during development. For example, years of practice give rise to perceptual improvements that contribute to mature speech and language skills. While fully honed learning skills might be thought to offer an advantage during the juvenile period, the ability to learn actually continues to develop through childhood and adolescence, suggesting that the neural mechanisms that support skill learning are slow to mature. To address this issue, we asked whether the rate and magnitude of perceptual learning varies as a function of age as male and female gerbils trained on an auditory task. Adolescents displayed a slower rate of perceptual learning compared with their young and mature counterparts. We recorded auditory cortical neuron activity from a subset of adolescent and adult gerbils as they underwent perceptual training. While training enhanced the sensitivity of most adult units, the sensitivity of many adolescent units remained unchanged, or even declined across training days. Therefore, the average rate of cortical improvement was significantly slower in adolescents compared with adults. Both smaller differences between sound-evoked response magnitudes and greater trial-to-trial response fluctuations contributed to the poorer sensitivity of individual adolescent neurons. Together, these findings suggest that elevated sensory neural variability limits adolescent skill learning.SIGNIFICANCE STATEMENT The ability to learn new skills emerges gradually as children age. This prolonged development, often lasting well into adolescence, suggests that children, teens, and adults may rely on distinct neural strategies to improve their sensory and motor capabilities. Here, we found that practice-based improvement on a sound detection task is slower in adolescent gerbils than in younger or older animals. Neural recordings made during training revealed that practice enhanced the sound sensitivity of adult cortical neurons, but had a weaker effect in adolescents. This latter finding was partially explained by the fact that adolescent neural responses were more variable than in adults. Our results suggest that one mechanistic basis of adult-like skill learning is a reduction in neural response variability.

Bridging large-scale neuronal recordings and large-scale network models using dimensionality reduction

A long-standing goal in neuroscience has been to bring together neuronal recordings and neural network modeling to understand brain function. Neuronal recordings can inform the development of network models, and network models can in turn provide predictions for subsequent experiments. Traditionally, neuronal recordings and network models have been related using single-neuron and pairwise spike train statistics. We review here recent studies that have begun to relate neuronal recordings and network models based on the multi-dimensional structure of neuronal population activity, as identified using dimensionality reduction. This approach has been used to study working memory, decision making, motor control, and more. Dimensionality reduction has provided common ground for incisive comparisons and tight interplay between neuronal recordings and network models.

An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability

Animals are not simple input-output machines. Their responses to even very similar stimuli are variable. A key, long-standing question in neuroscience is to understand the neural correlates of such behavioral variability. To reveal these correlates, behavior and neural population activity must be related to one another on single trials. Such analysis is challenging due to the dynamical nature of brain function (e.g., in decision making), heterogeneity across neurons and limited sampling of the relevant neural population. By analyzing population recordings from mouse frontal cortex in perceptual decision-making tasks, we show that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal previously unrecognized structure in the organization of population activity. This structure is similar on error and correct trials, suggesting dynamics that may be constrained by the underlying circuitry, is able to predict multiple aspects of behavioral variability and reveals long time-scale modulation of population activity.

Distinct population codes for attention in the absence and presence of visual stimulation

Visual neurons respond more vigorously to an attended stimulus than an unattended one. How the brain prepares for response gain in anticipation of that stimulus is not well understood. One prominent proposal is that anticipation is characterized by gain-like modulations of spontaneous activity similar to gains in stimulus responses. Here we test an alternative idea: anticipation is characterized by a mixture of both increases and decreases of spontaneous firing rates. Such a strategy would be adaptive as it supports a simple linear scheme for disentangling internal, modulatory signals from external, sensory inputs. We recorded populations of V4 neurons in monkeys performing an attention task, and found that attention states are signaled by different mixtures of neurons across the population in the presence or absence of a stimulus. Our findings support a move from a stimulation-invariant account of anticipation towards a richer view of attentional modulation in a diverse neuronal population.

Attention affects stimulus response gain, but its impact without sensory drive is less known. Here, the authors show that attention is coded diversely in a population and is distinct between unstimulated and stimulated contexts, providing a contrast to normalized gain models of attention.

Neural Activity Predicts Reaction in Primates Long Before a Behavioral Response

How neural activity is linked to behavior is a critical question in neural engineering and cognitive neurosciences. It is crucial to predict behavior as early as possible, to plan a machine response in real-time brain computer interactions. However, previous studies have studied the neural readout of behavior only within a short time before the action is performed. This leaves unclear, if the neural activity long before a decision could predict the upcoming behavior. By recording extracellular neural activities from the visual cortex of behaving rhesus monkeys, we show that: (1) both, local field potentials (LFPs) and the rate of neural spikes long before (>2 s) a monkey responds to a change, foretell its behavioral performance in a spatially selective manner; (2) LFPs, the more accessible component of extracellular activity, are a stronger predictor of behavior; and (3) LFP amplitude is positively correlated while spiking activity is negatively correlated with behavioral reaction time (RT). These results suggest that field potentials could be used to predict behavior way before it is performed, an observation that could potentially be useful for brain computer interface applications, and that they contribute to the sensory neural circuit’s speed in information processing.

Attentional fluctuations induce shared variability in macaque primary visual cortex

Variability in neuronal responses to identical stimuli is frequently correlated across a population. Attention is thought to reduce these correlations by suppressing noisy inputs shared by the population. However, even with precise control of the visual stimulus, the subject’s attentional state varies across trials. While these state fluctuations are bound to induce some degree of correlated variability, it is currently unknown how strong their effect is, as previous studies generally do not dissociate changes in attentional strength from changes in attentional state variability. We designed a novel paradigm that does so and find both a pronounced effect of attentional fluctuations on correlated variability at long timescales and attention-dependent reductions in correlations at short timescales. These effects predominate in layers 2/3, as expected from a feedback signal such as attention. Thus, significant portions of correlated variability can be attributed to fluctuations in internally generated signals, like attention, rather than noise.

Attention reduces correlated variability in population activity, however the effect of fluctuations in attentional state has not been studied. Here, the authors report in a novel visual task that fluctuations in attentional allocation have a pronounced effect on correlated variability at longer timescales.

Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis

Perceptions, thoughts, and actions unfold over millisecond timescales, while learned behaviors can require many days to mature. While recent experimental advances enable large-scale and long-term neural recordings with high temporal fidelity, it remains a formidable challenge to extract unbiased and interpretable descriptions of how rapid single-trial circuit dynamics change slowly over many trials to mediate learning. We demonstrate a simple tensor component analysis (TCA) can meet this challenge by extracting three interconnected, low-dimensional descriptions of neural data: neuron factors, reflecting cell assemblies; temporal factors, reflecting rapid circuit dynamics mediating perceptions, thoughts, and actions within each trial; and trial factors, describing both long-term learning and trial-to-trial changes in cognitive state. We demonstrate the broad applicability of TCA by revealing insights into diverse datasets derived from artificial neural networks, large-scale calcium imaging of rodent prefrontal cortex during maze navigation, and multielectrode recordings of macaque motor cortex during brain machine interface learning.

The Magnitude, But Not the Sign, of MT Single-Trial Spike-Time Correlations Predicts Motion Detection Performance

Spike-time correlations capture the short timescale covariance between the activity of neurons on a single trial. These correlations can significantly vary in magnitude and sign from trial to trial, and have been proposed to contribute to information encoding in visual cortex. While monkeys performed a motion-pulse detection task, we examined the behavioral impact of both the magnitude and sign of single-trial spike-time correlations between two nonoverlapping pools of middle temporal (MT) neurons. We applied three single-trial measures of spike-time correlation between our multiunit MT spike trains (Pearson's, absolute value of Pearson's, and mutual information), and examined the degree to which they predicted a subject's performance on a trial-by-trial basis. We found that on each trial, positive and negative spike-time correlations were almost equally likely, and, once the correlational sign was accounted for, all three measures were similarly predictive of behavior. Importantly, just before the behaviorally relevant motion pulse occurred, single-trial spike-time correlations were as predictive of the performance of the animal as single-trial firing rates. While firing rates were positively associated with behavioral outcomes, the presence of either strong positive or negative correlations had a detrimental effect on behavior. These correlations occurred on short timescales, and the strongest positive and negative correlations modulated behavioral performance by ∼9%, compared with trials with no correlations. We suggest a model where spike-time correlations are associated with a common noise source for the two MT pools, which in turn decreases the signal-to-noise ratio of the integrated signals that drive motion detection.SIGNIFICANCE STATEMENT Previous work has shown that spike-time correlations occurring on short timescales can affect the encoding of visual inputs. Although spike-time correlations significantly vary in both magnitude and sign across trials, their impact on trial-by-trial behavior is not fully understood. Using neural recordings from area MT (middle temporal) in monkeys performing a motion-detection task using a brief stimulus, we found that both positive and negative spike-time correlations predicted behavioral responses as well as firing rate on a trial-by-trial basis. We propose that strong positive and negative spike-time correlations decreased behavioral performance by reducing the signal-to-noise ratio of integrated MT neural signals.

Normalization and the Cholinergic Microcircuit: A Unified Basis for Attention

Attention alters three key properties of population neural activity - firing rate, rate variability, and shared variability between neurons. All three properties are well explained by a single canonical computation - normalization - that acts across hierarchically integrated brain systems. Combining data from rodents and nonhuman primates, we argue that cortical cholinergic modulation originating from the basal forebrain closely mimics the effects of directed attention on these three properties of population neural activity. Cholinergic modulation of the cortical microcircuit underlying normalization may represent a key biological basis for the rapid and flexible changes in population neuronal coding that are required by directed attention.

Pupil Size Coupling to Cortical States Protects the Stability of Deep Sleep via Parasympathetic Modulation

During wakefulness, pupil diameter can reflect changes in attention, vigilance, and cortical states. How pupil size relates to cortical activity during sleep, however, remains unknown. Pupillometry during natural sleep is inherently challenging since the eyelids are usually closed. Here, we present a novel head-fixed sleep paradigm in combination with infrared back-illumination pupillometry (iBip) allowing robust tracking of pupil diameter in sleeping mice. We found that pupil size can be used as a reliable indicator of sleep states and that cortical activity becomes tightly coupled to pupil size fluctuations during non-rapid eye movement (NREM) sleep. Pharmacological blocking experiments indicate that the observed pupil size changes during sleep are mediated via the parasympathetic system. We furthermore found that constrictions of the pupil during NREM episodes might play a protective role for stability of sleep depth. These findings reveal a fundamental relationship between cortical activity and pupil size, which has so far been hidden behind closed eyelids.

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Infrared back-illumination allows accurate pupillometry in sleeping mice

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Brain activity and pupil diameter are tightly coupled during sleep

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The parasympathetic system is the main driver of pupillary changes during NREM sleep

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Pupillary constrictions might have a protective function to stabilize deep sleep

Exploration Disrupts Choice-Predictive Signals and Alters Dynamics in Prefrontal Cortex

In uncertain environments, decision-makers must balance two goals: they must "exploit" rewarding options but also "explore" in order to discover rewarding alternatives. Exploring and exploiting necessarily change how the brain responds to identical stimuli, but little is known about how these states, and transitions between them, change how the brain transforms sensory information into action. To address this question, we recorded neural activity in a prefrontal sensorimotor area while monkeys naturally switched between exploring and exploiting rewarding options. We found that exploration profoundly reduced spatially selective, choice-predictive activity in single neurons and delayed choice-predictive population dynamics. At the same time, reward learning was increased in brain and behavior. These results indicate that exploration is related to sudden disruptions in prefrontal sensorimotor control and rapid, reward-dependent reorganization of control dynamics. This may facilitate discovery through trial and error.

The effects of delay duration on visual working memory for orientation

We used a delayed-estimation paradigm to characterize the joint effects of set size (one, two, four, or six) and delay duration (1, 2, 3, or 6 s) on visual working memory for orientation. We conducted two experiments: one with delay durations blocked, another with delay durations interleaved. As dependent variables, we examined four model-free metrics of dispersion as well as precision estimates in four simple models. We tested for effects of delay time using analyses of variance, linear regressions, and nested model comparisons. We found significant effects of set size and delay duration on both model-free and model-based measures of dispersion. However, the effect of delay duration was much weaker than that of set size, dependent on the analysis method, and apparent in only a minority of subjects. The highest forgetting slope found in either experiment at any set size was a modest 1.14°/s. As secondary results, we found a low rate of nontarget reports, and significant estimation biases towards oblique orientations (but no dependence of their magnitude on either set size or delay duration). Relative stability of working memory even at higher set sizes is consistent with earlier results for motion direction and spatial frequency. We compare with a recent study that performed a very similar experiment.

Characterizing and interpreting the influence of internal variables on sensory activity

The concept of a tuning curve has been central for our understanding of how the responses of cortical neurons depend on external stimuli. Here, we describe how the influence of unobserved internal variables on sensory responses, in particular correlated neural variability, can be understood in a similar framework. We suggest that this will lead to deeper insights into the relationship between stimulus, sensory responses, and behavior. We review related recent work and discuss its implication for distinguishing feedforward from feedback influences on sensory responses, and for the information contained in those responses.

Decoupled choice-driven and stimulus-related activity in parietal neurons may be misrepresented by choice probabilities

Trial-by-trial correlations between neural responses and choices (choice probabilities) are often interpreted to reflect a causal contribution of neurons to task performance. However, choice probabilities may arise from top-down, rather than bottom-up, signals. We isolated distinct sensory and decision contributions to single-unit activity recorded from the dorsal medial superior temporal (MSTd) and ventral intraparietal (VIP) areas of monkeys during perception of self-motion. Superficially, neurons in both areas show similar tuning curves during task performance. However, tuning in MSTd neurons primarily reflects sensory inputs, whereas choice-related signals dominate tuning in VIP neurons. Importantly, the choice-related activity of VIP neurons is not predictable from their stimulus tuning, and these factors are often confounded in choice probability measurements. This finding was confirmed in a subset of neurons for which stimulus tuning was measured during passive fixation. Our findings reveal decoupled stimulus and choice signals in the VIP area, and challenge our understanding of choice signals in the brain.Choice-related signals in neuronal activity may reflect bottom-up sensory processes, top-down decision-related influences, or a combination of the two. Here the authors report that choice-related activity in VIP neurons is not predictable from their stimulus tuning, and that dominant choice signals can bias the standard metric of choice preference (choice probability).