Flow-field inference from neural data using deep recurrent networks.

Computations involved in processes such as decision-making, working memory, and motor control are thought to emerge from the dynamics governing the collective activity of neurons in large populations. But the estimation of these dynamics remains a significant challenge. Here we introduce Flow-field Inference from Neural Data using deep Recurrent networks (FINDR), an unsupervised deep learning method that can infer low-dimensional nonlinear stochastic dynamics underlying neural population activity. Using population spike train data from frontal brain regions of rats performing an auditory decision-making task, we demonstrate that FINDR outperforms existing methods in capturing the heterogeneous responses of individual neurons. We further show that FINDR can discover interpretable low-dimensional dynamics when it is trained to disentangle task-relevant and irrelevant components of the neural population activity. Importantly, the low-dimensional nature of the learned dynamics allows for explicit visualization of flow fields and attractor structures. We suggest FINDR as a powerful method for revealing the low-dimensional task-relevant dynamics of neural populations and their associated computations.

Transitions in dynamical regime and neural mode 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 networks 1,2 . However, whether attractor dynamics underlie decision behavior and the complex neuronal responses remains unclear. Here we use an unsupervised, deep learning-based method to discover decision-related dynamics from the simultaneous activity of neurons in frontal cortex and striatum of rats while they accumulate pulsatile auditory evidence. We show that contrary to prevailing hypotheses, attractors play a role only after a transition from a regime in the dynamics that is strongly driven by inputs to one dominated by the intrinsic dynamics. The initial regime mediates evidence accumulation, and the subsequent intrinsic-dominant regime subserves decision commitment. This regime transition is coupled to a rapid reorganization in the representation of the decision process in the neural population (a change in the "neural mode" along which the process develops). A simplified model approximating the coupled transition in the dynamics and neural mode allows inferring, from each trial's neural activity, the internal decision commitment time in that trial, and captures diverse and complex single-neuron temporal profiles, such as ramping and stepping 3-5 . It also captures trial-averaged curved trajectories 6-8 , and reveals distinctions between brain regions. 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, and suggest pairing deep learning and parsimonious models as a promising approach for understanding complex data.

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.

Attention can be subdivided into neurobiological components corresponding to distinct behavioral effects.

Attention is a common but highly complex term associated with a large number of distinct behavioral and perceptual phenomena. In the brain, attention-related changes in neuronal activity are observed in widespread structures. The many distinct behavioral and neuronal phenomena related to attention suggest that it might be subdivided into components corresponding to distinct biological mechanisms. Recent neurophysiological studies in monkeys have isolated behavioral changes related to attention along the 2 indices of signal detection theory and found that these 2 behavioral changes are associated with distinct neuronal changes in different brain areas. These results support the view that attention is made up of distinct neurobiological mechanisms.

Attentional Changes in Either Criterion or Sensitivity Are Associated with Robust Modulations in Lateral Prefrontal Cortex.

Visual attention is associated with neuronal changes across the brain, and these widespread signals are generally assumed to underlie a unitary mechanism of attention. However, using signal detection theory, attention-related effects on performance can be partitioned into changes in either the subject's criterion or sensitivity. Neuronal modulations associated with only sensitivity changes were previously observed in visual cortex, raising questions about which structures mediate attention-related changes in criterion and whether individual neurons are involved in multiple components of attention. Here, we recorded from monkey lateral prefrontal cortex (LPFC) and found that, in contrast to visual cortex, neurons in LPFC changed their firing rates, pairwise correlation, and Fano factor when subjects changed either their criterion or their sensitivity. These results indicate that attention-related neuronal modulations in separate brain regions are not a monolithic signal and instead can be linked to distinct behavioral changes.

Neuronal Modulations in Visual Cortex Are Associated with Only One of Multiple Components of Attention.

Neuronal signals related to visual attention are found in widespread brain regions, and these signals are generally assumed to participate in a common mechanism of attention. However, the behavioral effects of attention in detection can be separated into two distinct components: spatially selective shifts in either the criterion or sensitivity of the subject. Here we show that a paradigm used by many single-neuron studies of attention conflates behavioral changes in the subject's criterion and sensitivity. Then, using a task designed to dissociate these two components, we found that multiple aspects of attention-related neuronal modulations in area V4 of monkey visual cortex corresponded to behavioral shifts in sensitivity, but not criterion. This result suggests that separate components of attention are associated with signals in different brain regions and that attention is not a unitary process in the brain, but instead consists of distinct neurobiological mechanisms.