Biology subjects

Kopec, C. D.

Publications and source records attributed to Kopec, C. D..

12 recordsLinked to original sources

bioRxiv2025

FixGrower: An efficient and robust curriculum for shaping fixation behavior in rodents

Center-port fixation is a common prerequisite for many freely-moving rodent tasks in neuroscience and psychology. However, typical protocols for shaping this behavior are non-standardized and inefficient. Moreover, motor errors in fixation termed violations often account for a significant fraction of experimental trials, leading to notable data loss during experiments. In light of this, we developed FixGrower, a standardized protocol for center-port fixation training. FixGrower (1) requires a longer initial fixation requirement, (2) increases the required fixation duration at session boundaries customized to each animals performance, and (3) delays the introduction of violation penalties until the end of training. We demonstrate FixGrower decreases training time by 61%, yields low violation rates, and generalizes across rodent species and task difficulty. Moreover, the success of this curriculum is well supported by theories of operant conditioning and reinforcement learning. Our findings establish FixGrower as an efficient and broadly applicable curriculum for training fixation behavior in rodents, thereby accelerating training of many tasks in the field.

animal behavior and cognition↗

bioRxiv2024

Coordinated cross-brain activity during accumulation of sensory evidence and decision commitment

Decision-making is thought to involve two phases: first, evidence accumulation, then, decision commitment. Accumulation is represented broadly in the brain, but whether this best matches single versus multiple accumulator models is unknown. Here, analysis of simultaneous, bilateral recordings across sensory, association, and motor regions, in both cortex and subcortical structures, strongly supports a single accumulator, and suggests that accumulated noise (diffusion) originates frontally. Decision commitment can occur internally, without an overt report. Long-standing competing models of covert commitment disagree as to whether it is abrupt or continuous. Temporally aligning data on a single-trial estimator of internal, covert commitment ("nTc") revealed a rapid ([≤]50 ms) drop in the accumulators sensitivity to incoming sensory evidence, favoring abrupt transition models, and indicating a discrete cross-brain state change at nTc that was first detectable in motor regions. These data discriminate between decades-old models of accumulation, and between decades-old models of the transition to commitment.

neuroscience↗

bioRxiv2024

To integrate or not to integrate: Testing degenerate strategies for solving an accumulation of perceptual evidence decision-making task

A common approach in the study of cognition is to train subjects to perform a task that requires a particular cognitive process to solve. Analysis of the subjects response behavior while they perform these tasks can offer valuable insight into the underlying mechanisms that give rise to cognition. However, if subjects are able to accurately perform such a task by using a strategy that doesnt involve the targeted cognitive process, data from those experiments becomes more difficult to interpret. A number of perceptual decision-making tasks have been designed to study the accumulation of evidence, i.e. how noisy information presented over time is used to form a decision. Recent work, however, has highlighted how a variety of non-integration strategies can by some measures yield strikingly near-optimal performance on such tasks, raising the possibility that past conclusions from these experiments may be incorrect. Here we assemble the largest data set of animals performing one such task - the "Poisson Clicks" task - which is optimally solved by the gradual integration of pulsatile auditory noise. To investigate whether rats are in fact using this strategy, we compiled data from 515 rats performing over 35 million trials. We compare performance of 3 degenerate strategies (that circumvent the need to integrate evidence) to the optimal (integration) strategy. We demonstrate that the pulsatile nature of the stimuli used in the Poisson Clicks Task makes it possible to distinguish which strategy subjects use. Overwhelmingly, we find the rats are using an integration strategy when performing the Poisson Clicks Task.

animal behavior and cognition↗

bioRxiv2024

A multi-region recurrent circuit for evidence accumulation in rats

Decision-making based on noisy evidence requires accumulating evidence and categorizing it to form a choice. Here we evaluate a proposed feedforward and modular mapping of this process in rats: evidence accumulated in anterodorsal striatum (ADS) is categorized in prefrontal cortex (frontal orienting fields, FOF). Contrary to this, we show that both regions appear to be indistinguishable in their encoding/decoding of accumulator value and communicate this information bidirectionally. Consistent with a role for FOF in accumulation, silencing FOF to ADS projections impacted behavior throughout the accumulation period, even while nonselective FOF silencing did not. We synthesize these findings into a multi-region recurrent neural network trained with a novel approach. In-silico experiments reveal that multiple scales of recurrence in the cortico-striatal circuit rescue computation upon nonselective FOF perturbations. These results suggest that ADS and FOF accumulate evidence in a recurrent and distributed manner, yielding redundant representations and robustness to certain perturbations.

neuroscience↗

bioRxiv2024

A cognitive process model captures near-optimal confidence-guided waiting in rats

Rational decision-makers invest more time pursuing rewards they are more confident they will eventually receive. A series of studies have therefore used willingness to wait for delayed rewards as a proxy for decision confidence. However, interpretation of waiting behavior is limited because it is unclear how environmental statistics influence optimal waiting, and how sources of internal variability influence subjects behavior. We trained rats to perform a confidence-guided waiting task, and derived expressions for optimal waiting that make relevant environmental statistics explicit, including travel time incurred traveling from one reward opportunity to another. We found that rats waited longer than fully optimal agents, but that their behavior was closely matched by optimal agents with travel times constrained to match their own. We developed a process model describing the decision to stop waiting as an accumulation to bound process, which allowed us to compare the effects of multiple sources of internal variability on waiting. Surprisingly, although mean wait times grew with confidence, variability did not, inconsistent with scalar invariant timing, and best explained by variability in the stopping bound. Our results describe a tractable process model that can capture the influence of environmental statistics and internal sources of variability on subjects decision process during confidence-guided waiting.

animal behavior and cognition↗

bioRxiv2023

Non-canonical attractor dynamics underlie perceptual decision-making

Perceptual decision-making is the process by which an animal uses sensory stimuli to choose an action or mental proposition. This process is thought to be mediated by neurons organized as attractor networks1,2. However, whether attractor dynamics underlie decision behavior and the complex neuronal responses remains unclear. Here we use simultaneous recordings from hundreds of neurons, together with an unsupervised, deep learning-based method, to discover decision-related neural dynamics in frontal cortex and striatum of rats while the subjects accumulate pulsatile auditory evidence. We found that trajectories evolved along two sequential regimes, the first dominated by sensory inputs, and the second dominated by the autonomous dynamics, with flow in a direction (i.e., "neural mode") largely orthogonal to that in the first regime. We propose that the transition to the second regime corresponds to the moment of decision commitment. We developed a simplified model that approximates the coupled transition in dynamics and neural mode and allows precise inference, from each trials large-scale neural population activity, of a putative neurally-inferred time of commitment ("nTc") on that trial. The simplified model captures diverse and complex single-neuron temporal profiles, such as ramping and stepping3-5, as well as trial-averaged curved trajectories6-8, and reveals distinctions between brain regions. The estimated nTc times were not time-locked to stimulus onset or offset, or to response onset, but were instead broadly distributed across trials. If nTc marks the moment of decision commitment, sensory evidence before nTc should affect the decision, while evidence afterward should not. Behavioral analysis of trials aligned to their estimated nTc times confirmed this prediction. Our results show that the formation of a perceptual choice involves a rapid, coordinated transition in both the dynamical regime and the neural mode of the decision process that corresponds to commitment to a decision, and suggest this moment as a useful entry point for dissecting mechanisms underlying rapid changes in internal state.

neuroscience↗

bioRxiv2023

Trial-history biases in evidence accumulation can give rise to apparent lapses

Trial history biases and lapses are two of the most common suboptimalities observed during perceptual decision-making. These suboptimalities are routinely assumed to arise from distinct processes. However, several hints in the literature suggest that they covary in their prevalence and that their proposed neural substrates overlap - what could underlie these links? Here we demonstrate that history biases and apparent lapses can both arise from a common cognitive process that is normative under misbeliefs about non-stationarity in the world. This corresponds to an accumulation- to-bound model with history-dependent updates to the initial state of the accumulator. We test our models predictions about the relative prevalence of history biases and lapses, and show that they are robustly borne out in two distinct rat decision-making datasets, including data from a novel reaction time task. Our model improves the ability to precisely predict decision-making dynamics within and across trials, by positing a process through which agents can generate quasi-stochastic choices.

animal behavior and cognition↗

bioRxiv2020

An approach for long-term, multi-probe Neuropixels recordings in unrestrained rats

The use of Neuropixels probes for chronic neural recordings is in its infancy and initial studies leave questions about long-term stability and probe reusability unaddressed. Here we demonstrate a new approach for chronic Neuropixels recordings over a period of months in freely moving rats. Our approach allows multiple probes per rat and multiple cycles of probe reuse. We found that hundreds of units could be recorded for multiple months, but that yields depended systematically on anatomical position. Explanted probes displayed a small increase in noise compared to unimplanted probes, but this was insufficient to impair future single-unit recordings. We conclude that cost-effective, multi-region, and multi-probe Neuropixels recordings can be carried out with high yields over multiple months in rats or other similarly sized animals. Our methods and observations may facilitate the standardization of chronic recording from Neuropixels probes in freely moving animals.

neuroscience↗

bioRxiv2019

Orbitofrontal cortex promotes trial-by-trial learning of risky, but not spatial, biases

Individual choices are not made in isolation but are embedded in a series of past experiences, decisions, and outcomes. The effects of past experiences on choices, often called sequential biases, are ubiquitous in perceptual and value-based decision-making, but their neural substrates are unclear. We trained rats to choose between explicitly cued guaranteed and probabilistic rewards in a task in which outcomes on each trial were independent. Behavioral variability often reflected the effects of previous trials, including increased willingness to take risks following risky wins, and spatial \"win-stay/lose-shift\" biases. Electrophysiological recordings from lateral orbitofrontal cortex (lOFC) revealed strong encoding of reward history and receipt, and optogenetic inhibition of lOFC during choice reporting eliminated rats increased preference for risk on subsequent trials following risky wins, but spared other sequential effects. Our data show that different sequential biases are neurally dissociable, and that the lOFCs role in adaptive behavior promotes learning of more abstract, task-specific biases (here, biases for the risky option), but not spatial ones. These data are consistent with proposals that the OFC represents the animals location in an abstract representation of task states, and highlight the lOFCs role in learning.

neuroscience↗

bioRxiv2018

Collicular circuits for flexible sensorimotor routing

Historically, cognitive processing has been thought to rely on cortical areas such as prefrontal cortex (PFC), with the outputs of these areas modulating activity in lower, putatively simpler spatiomotor regions, such as the midbrain superior colliculus (SC). Using a rat task in which subjects switch rapidly between task contexts that demand changes in sensorimotor mappings, we report a surprising role for the SC in non-spatial cognitive processes. Before spatial response choices could be formed, neurons in SC encoded task context more strongly than neurons in PFC, and bilateral SC silencing impaired behavioral performance. Once spatial choices could begin to be formed, SC neurons encoded the choice faster than PFC, while bilateral SC silencing no longer impaired choices. A set of dynamical models of the SC replicates our findings. Our results challenge cortically-focused views of cognition, and suggest that ostensibly spatiomotor structures can play central roles in non-spatiomotor cognitive processes.

neuroscience↗

bioRxiv2018

Controlling for temporal discounting shifts rats from geometric to human-like arithmetic bisection

How our brains measure the passage of time is still largely open for debate. One behavioral task commonly used to study how durations are perceived is the Temporal Bisection Task, in which subjects categorize time durations as either \"short\" or \"long.\" The duration equally likely to be categorized as short or long is known as the bisection point. It has been consistently demonstrated that for humans, the bisection point is near the arithmetic mean of the longest and shortest durations the subject was trained on. In contrast, for non-human subjects it has been consistently found near the geometric mean. This difference implies that humans may process or represent temporal durations differently than other species. Here we present a behavioral model that reconciles the differences by demonstrating that rats performance on this task is driven not only by their noisy estimates of duration, but also by the temporally-discounted value of future rewards. The model correctly predicts shifts in the bisection point induced by unequal rewards and explains otherwise-paradoxical psychometric reversals documented three decades ago. Furthermore, as predicted by the model, we found that modifying the Temporal Bisection Task to eliminate the temporally-discounted reward component shifted the rats bisection point from the geometric mean to the arithmetic mean, thus bringing the rat results into line with the human results. We therefore propose that humans and rats (and perhaps other non-human subjects as well) process temporal information similarly, and that the difference between them in the Temporal Bisection Task may be simply due to rats weighing temporal discounting of future rewards more strongly than humans.

animal behavior and cognition↗

bioRxiv2017

Posterior parietal cortex represents sensory stimulus history and is necessary for its effects on behavior

Many models of cognition and of neural computations posit the use and estimation of prior stimulus statistics1-4: it has long been known that working memory and perception are strongly impacted by previous sensory experience, even when that sensory history is irrelevant for the current task at hand. Nevertheless, the neural mechanisms and brain regions necessary for computing and using such priors are unknown. Here we report that the posterior parietal cortex (PPC) is a critical locus for the representation and use of prior stimulus information. We trained rats in an auditory Parametric Working Memory (PWM) task, and found that rats displayed substantial and readily quantifiable behavioral effects of sensory stimulus history, similar to those observed in humans5,6 and monkeys7. Earlier proposals that PPC supports working memory8,9 predict that optogenetic silencing of this region would impair behavior in our working memory task. Contrary to this prediction, silencing PPC significantly improved performance. Quantitative analyses of behavior revealed that this improvement was due to the selective reduction of the effects of prior sensory stimuli. Electrophysiological recordings showed that PPC neurons carried far more information about sensory stimuli of previous trials than about stimuli of the current trial. Furthermore, the more information about previous trial sensory history in the neural firing rates of a given rats PPC, the greater the behavioral effect of sensory history in that rat, suggesting a tight link between behavior and PPC representations of stimulus history. Our results indicate that the PPC is a central component in the processing of sensory stimulus history, and open a window for neurobiological investigation of long-standing questions regarding how perception and working memory are affected by prior sensory information.

neuroscience↗