A cryptography-based approach for movement decoding

Dimensionality reduction beyond neural subspaces with slice tensor component analysis

Recent work has argued that large-scale neural recordings are often well described by patterns of coactivation across neurons. Yet the view that neural variability is constrained to a fixed, low-dimensional subspace may overlook higher-dimensional structure, including stereotyped neural sequences or slowly evolving latent spaces. Here we argue that task-relevant variability in neural data can also cofluctuate over trials or time, defining distinct 'covariability classes' that may co-occur within the same dataset. To demix these covariability classes, we develop sliceTCA (slice tensor component analysis), a new unsupervised dimensionality reduction method for neural data tensors. In three example datasets, including motor cortical activity during a classic reaching task in primates and recent multiregion recordings in mice, we show that sliceTCA can capture more task-relevant structure in neural data using fewer components than traditional methods. Overall, our theoretical framework extends the classic view of low-dimensional population activity by incorporating additional classes of latent variables capturing higher-dimensional structure.

Unsupervised Neural Manifold Alignment for Stable Decoding of Movement from Cortical Signals

The stable decoding of movement parameters using neural activity is crucial for the success of brain-machine interfaces (BMIs). However, neural activity can be unstable over time, leading to changes in the parameters used for decoding movement, which can hinder accurate movement decoding. To tackle this issue, one approach is to transfer neural activity to a stable, low-dimensional manifold using dimensionality reduction techniques and align manifolds across sessions by maximizing correlations of the manifolds. However, the practical use of manifold stabilization techniques requires knowledge of the true subject intentions such as target direction or behavioral state. To overcome this limitation, an automatic unsupervised algorithm is proposed that determines movement target intention before manifold alignment in the presence of manifold rotation and scaling across sessions. This unsupervised algorithm is combined with a dimensionality reduction and alignment method to overcome decoder instabilities. The effectiveness of the BMI stabilizer method is represented by decoding the two-dimensional (2D) hand velocity of two rhesus macaque monkeys during a center-out-reaching movement task. The performance of the proposed method is evaluated using correlation coefficient and R-squared measures, demonstrating higher decoding performance compared to a state-of-the-art unsupervised BMI stabilizer. The results offer benefits for the automatic determination of movement intents in long-term BMI decoding. Overall, the proposed method offers a promising automatic solution for achieving stable and accurate movement decoding in BMI applications.

Preserved neural dynamics across animals performing similar behaviour

Animals of the same species exhibit similar behaviours that are advantageously adapted to their body and environment. These behaviours are shaped at the species level by selection pressures over evolutionary timescales. Yet, it remains unclear how these common behavioural adaptations emerge from the idiosyncratic neural circuitry of each individual. The overall organization of neural circuits is preserved across individuals1 because of their common evolutionarily specified developmental programme2-4. Such organization at the circuit level may constrain neural activity5-8, leading to low-dimensional latent dynamics across the neural population9-11. Accordingly, here we suggested that the shared circuit-level constraints within a species would lead to suitably preserved latent dynamics across individuals. We analysed recordings of neural populations from monkey and mouse motor cortex to demonstrate that neural dynamics in individuals from the same species are surprisingly preserved when they perform similar behaviour. Neural population dynamics were also preserved when animals consciously planned future movements without overt behaviour12 and enabled the decoding of planned and ongoing movement across different individuals. Furthermore, we found that preserved neural dynamics extend beyond cortical regions to the dorsal striatum, an evolutionarily older structure13,14. Finally, we used neural network models to demonstrate that behavioural similarity is necessary but not sufficient for this preservation. We posit that these emergent dynamics result from evolutionary constraints on brain development and thus reflect fundamental properties of the neural basis of behaviour.

A high-performance speech neuroprosthesis

Speech brain-computer interfaces (BCIs) have the potential to restore rapid communication to people with paralysis by decoding neural activity evoked by attempted speech into text1,2 or sound3,4. Early demonstrations, although promising, have not yet achieved accuracies sufficiently high for communication of unconstrained sentences from a large vocabulary1-7. Here we demonstrate a speech-to-text BCI that records spiking activity from intracortical microelectrode arrays. Enabled by these high-resolution recordings, our study participant-who can no longer speak intelligibly owing to amyotrophic lateral sclerosis-achieved a 9.1% word error rate on a 50-word vocabulary (2.7 times fewer errors than the previous state-of-the-art speech BCI2) and a 23.8% word error rate on a 125,000-word vocabulary (the first successful demonstration, to our knowledge, of large-vocabulary decoding). Our participant's attempted speech was decoded  at 62 words per minute, which is 3.4 times as fast as the previous record8 and begins to approach the speed of natural conversation (160 words per minute9). Finally, we highlight two aspects of the neural code for speech that are encouraging for speech BCIs: spatially intermixed tuning to speech articulators that makes accurate decoding possible from only a small region of cortex, and a detailed articulatory representation of phonemes that persists years after paralysis. These results show a feasible path forward for restoring rapid communication to people with paralysis who can no longer speak.

A high-performance speech neuroprosthesis

Speech brain-computer interfaces (BCIs) have the potential to restore rapid communication to people with paralysis by decoding neural activity evoked by attempted speaking movements into text or sound. Early demonstrations, while promising, have not yet achieved accuracies high enough for communication of unconstrainted sentences from a large vocabulary. Here, we demonstrate the first speech-to-text BCI that records spiking activity from intracortical microelectrode arrays. Enabled by these high-resolution recordings, our study participant, who can no longer speak intelligibly due amyotrophic lateral sclerosis (ALS), achieved a 9.1% word error rate on a 50 word vocabulary (2.7 times fewer errors than the prior state of the art speech BCI2) and a 23.8% word error rate on a 125,000 word vocabulary (the first successful demonstration of large-vocabulary decoding). Our BCI decoded speech at 62 words per minute, which is 3.4 times faster than the prior record for any kind of BCI and begins to approach the speed of natural conversation (160 words per minute). Finally, we highlight two aspects of the neural code for speech that are encouraging for speech BCIs: spatially intermixed tuning to speech articulators that makes accurate decoding possible from only a small region of cortex, and a detailed articulatory representation of phonemes that persists years after paralysis. These results show a feasible path forward for using intracortical speech BCIs to restore rapid communication to people with paralysis who can no longer speak.

Rapid adaptation of brain-computer interfaces to new neuronal ensembles or participants via generative modelling

For brain-computer interfaces (BCIs), obtaining sufficient training data for algorithms that map neural signals onto actions can be difficult, expensive or even impossible. Here we report the development and use of a generative model-a model that synthesizes a virtually unlimited number of new data distributions from a learned data distribution-that learns mappings between hand kinematics and the associated neural spike trains. The generative spike-train synthesizer is trained on data from one recording session with a monkey performing a reaching task and can be rapidly adapted to new sessions or monkeys by using limited additional neural data. We show that the model can be adapted to synthesize new spike trains, accelerating the training and improving the generalization of BCI decoders. The approach is fully data-driven, and hence, applicable to applications of BCIs beyond motor control.

How our understanding of memory replay evolves

Memory reactivations and replay, widely reported in the hippocampus and cortex across species, have been implicated in memory consolidation, planning, and spatial and skill learning. Technological advances in electrophysiology, calcium imaging, and human neuroimaging techniques have enabled neuroscientists to measure large-scale neural activity with increasing spatiotemporal resolution and have provided opportunities for developing robust analytic methods to identify memory replay. In this article, we first review a large body of historically important and representative memory replay studies from the animal and human literature. We then discuss our current understanding of memory replay functions in learning, planning, and memory consolidation and further discuss the progress in computational modeling that has contributed to these improvements. Next, we review past and present analytic methods for replay analyses and discuss their limitations and challenges. Finally, looking ahead, we discuss some promising analytic methods for detecting nonstereotypical, behaviorally nondecodable structures from large-scale neural recordings. We argue that seamless integration of multisite recordings, real-time replay decoding, and closed-loop manipulation experiments will be essential for delineating the role of memory replay in a wide range of cognitive and motor functions.

Long-term unsupervised recalibration of cursor BCIs

Intracortical brain-computer interfaces (iBCIs) require frequent recalibration to maintain robust performance due to changes in neural activity that accumulate over time. Compensating for this nonstationarity would enable consistently high performance without the need for supervised recalibration periods, where users cannot engage in free use of their device. Here we introduce a hidden Markov model (HMM) to infer what targets users are moving toward during iBCI use. We then retrain the system using these inferred targets, enabling unsupervised adaptation to changing neural activity. Our approach outperforms the state of the art in large-scale, closed-loop simulations over two months and in closed-loop with a human iBCI user over one month. Leveraging an offline dataset spanning five years of iBCI recordings, we further show how recently proposed data distribution-matching approaches to recalibration fail over long time scales; only target-inference methods appear capable of enabling long-term unsupervised recalibration. Our results demonstrate how task structure can be used to bootstrap a noisy decoder into a highly-performant one, thereby overcoming one of the major barriers to clinically translating BCIs.

The science and engineering behind sensitized brain-controlled bionic hands

Advances in our understanding of brain function, along with the development of neural interfaces that allow for the monitoring and activation of neurons, have paved the way for brain-machine interfaces (BMIs), which harness neural signals to reanimate the limbs via electrical activation of the muscles or to control extracorporeal devices, thereby bypassing the muscles and senses altogether. BMIs consist of reading out motor intent from the neuronal responses monitored in motor regions of the brain and executing intended movements with bionic limbs, reanimated limbs, or exoskeletons. BMIs also allow for the restoration of the sense of touch by electrically activating neurons in somatosensory regions of the brain, thereby evoking vivid tactile sensations and conveying feedback about object interactions. In this review, we discuss the neural mechanisms of motor control and somatosensation in able-bodied individuals and describe approaches to use neuronal responses as control signals for movement restoration and to activate residual sensory pathways to restore touch. Although the focus of the review is on intracortical approaches, we also describe alternative signal sources for control and noninvasive strategies for sensory restoration.

Feel Your Reach: An EEG-Based Framework to Continuously Detect Goal-Directed Movements and Error Processing to Gate Kinesthetic Feedback Informed Artificial Arm Control

Establishing the basic knowledge, methodology, and technology for a framework for the continuous decoding of hand/arm movement intention was the aim of the ERC-funded project “Feel Your Reach”. In this work, we review the studies and methods we performed and implemented in the last 6 years, which build the basis for enabling severely paralyzed people to non-invasively control a robotic arm in real-time from electroencephalogram (EEG). In detail, we investigated goal-directed movement detection, decoding of executed and attempted movement trajectories, grasping correlates, error processing, and kinesthetic feedback. Although we have tested some of our approaches already with the target populations, we still need to transfer the “Feel Your Reach” framework to people with cervical spinal cord injury and evaluate the decoders’ performance while participants attempt to perform upper-limb movements. While on the one hand, we made major progress towards this ambitious goal, we also critically discuss current limitations.

Drop, Swap, and Generate: A Self-Supervised Approach for Generating Neural Activity

Meaningful and simplified representations of neural activity can yield insights into how and what information is being processed within a neural circuit. However, without labels, finding representations that reveal the link between the brain and behavior can be challenging. Here, we introduce a novel unsupervised approach for learning disentangled representations of neural activity called Swap-VAE. Our approach combines a generative modeling framework with an instance-specific alignment loss that tries to maximize the representational similarity between transformed views of the input (brain state). These transformed (or augmented) views are created by dropping out neurons and jittering samples in time, which intuitively should lead the network to a representation that maintains both temporal consistency and invariance to the specific neurons used to represent the neural state. Through evaluations on both synthetic data and neural recordings from hundreds of neurons in different primate brains, we show that it is possible to build representations that disentangle neural datasets along relevant latent dimensions linked to behavior.

Go with the FLOW: visualizing spatiotemporal dynamics in optical widefield calcium imaging

Widefield calcium imaging has recently emerged as a powerful experimental technique to record coordinated large-scale brain activity. These measurements present a unique opportunity to characterize spatiotemporally coherent structures that underlie neural activity across many regions of the brain. In this work, we leverage analytic techniques from fluid dynamics to develop a visualization framework that highlights features of flow across the cortex, mapping wavefronts that may be correlated with behavioural events. First, we transform the time series of widefield calcium images into time-varying vector fields using optic flow. Next, we extract concise diagrams summarizing the dynamics, which we refer to as FLOW (flow lines in optical widefield imaging) portraits. These FLOW portraits provide an intuitive map of dynamic calcium activity, including regions of initiation and termination, as well as the direction and extent of activity spread. To extract these structures, we use the finite-time Lyapunov exponent technique developed to analyse time-varying manifolds in unsteady fluids. Importantly, our approach captures coherent structures that are poorly represented by traditional modal decomposition techniques. We demonstrate the application of FLOW portraits on three simple synthetic datasets and two widefield calcium imaging datasets, including cortical waves in the developing mouse and spontaneous cortical activity in an adult mouse.

High-performance brain-to-text communication via handwriting

Brain-computer interfaces (BCIs) can restore communication to people who have lost the ability to move or speak. So far, a major focus of BCI research has been on restoring gross motor skills, such as reaching and grasping^1-5 or point-and-click typing with a computer cursor^6,7. However, rapid sequences of highly dexterous behaviours, such as handwriting or touch typing, might enable faster rates of communication. Here we developed an intracortical BCI that decodes attempted handwriting movements from neural activity in the motor cortex and translates it to text in real time, using a recurrent neural network decoding approach. With this BCI, our study participant, whose hand was paralysed from spinal cord injury, achieved typing speeds of 90 characters per minute with 94.1% raw accuracy online, and greater than 99% accuracy offline with a general-purpose autocorrect. To our knowledge, these typing speeds exceed those reported for any other BCI, and are comparable to typical smartphone typing speeds of individuals in the age group of our participant (115 characters per minute)⁸. Finally, theoretical considerations explain why temporally complex movements, such as handwriting, may be fundamentally easier to decode than point-to-point movements. Our results open a new approach for BCIs and demonstrate the feasibility of accurately decoding rapid, dexterous movements years after paralysis.

Brain microvasculature has a common topology with local differences in geometry that match metabolic load

The microvasculature underlies the supply networks that support neuronal activity within heterogeneous brain regions. What are common versus heterogeneous aspects of the connectivity, density, and orientation of capillary networks? To address this, we imaged, reconstructed, and analyzed the microvasculature connectome in whole adult mice brains with sub-micrometer resolution. Graph analysis revealed common network topology across the brain that leads to a shared structural robustness against the rarefaction of vessels. Geometrical analysis, based on anatomically accurate reconstructions, uncovered a scaling law that links length density, i.e., the length of vessel per volume, with tissue-to-vessel distances. We then derive a formula that connects regional differences in metabolism to differences in length density and, further, predicts a common value of maximum tissue oxygen tension across the brain. Last, the orientation of capillaries is weakly anisotropic with the exception of a few strongly anisotropic regions; this variation can impact the interpretation of fMRI data.

Multi-source domain adaptation for decoder calibration of intracortical brain-machine interface

OBJECTIVE

For nonstationarity of neural recordings, daily retraining is required in the decoder calibration of intracortical brain-machine interfaces (iBMIs). Domain adaptation has started to be applied in iBMIs to solve the problem of daily retraining by taking advantage of historical data. However, previous domain adaptation studies used only a single source domain, which might lead to performance instability. In this study, we proposed a multi-source domain adaptation algorithm, by fully utilizing the historical data, to achieve a better and more robust decoding performance while reducing the decoder calibration time.

APPROACH

The neural signals were recorded from two rhesus macaques using intracortical electrodes to decode the reaching and grasping movements. A principal component analysis-based multi-source domain adaptation algorithm was proposed to apply the feature transfer to diminish the disparities between the target domain and each source domain. Moreover, the multiple weighted sub-classifiers based on multi-source domain data and small current sample set were constructed to accomplish the decoding.

MAIN RESULTS

Our algorithm was able to make use of the multi-source domain data and achieve better and more robust decoding performance compared with other methods. Only a small current sample set was needed by our algorithm in order for the decoder calibration time to be effectively reduced.

SIGNIFICANCE

(1) The idea of the multi-source domain adaptation was introduced into the iBMIs to solve the problem of time consumption in the daily decoder retraining. (2) Instead of using only single-source domain data in the previous study, our algorithm made use of multi-day historical data, resulting in better and more robust decoding performance. (3) Our algorithm could be accomplished with only a small current sample set, and it can effectively reduce the decoder calibration time, which is important for further clinical applications.

A comprehensive model-based framework for optimal design of biomimetic patterns of electrical stimulation for prosthetic sensation

OBJECTIVE

Touch and proprioception are essential to motor function as shown by the movement deficits that result from the loss of these senses, e.g. due to neuropathy of sensory nerves. To achieve a high-performance brain-controlled prosthetic arm/hand thus requires the restoration of somatosensation, perhaps through intracortical microstimulation (ICMS) of somatosensory cortex (S1). The challenge is to generate patterns of neuronal activation that evoke interpretable percepts. We present a framework to design optimal spatiotemporal patterns of ICMS (STIM) that evoke naturalistic patterns of neuronal activity and demonstrate performance superior to four previous approaches.

APPROACH

We recorded multiunit activity from S1 during a center-out reach task (from proprioceptive neurons in Brodmann's area 2) and during application of skin indentations (from cutaneous neurons in Brodmann's area 1). We implemented a computational model of a cortical hypercolumn and used a genetic algorithm to design STIM that evoked patterns of model neuron activity that mimicked their experimentally-measured counterparts. Finally, from the ICMS patterns, the evoked neuronal activity, and the stimulus parameters that gave rise to it, we trained a recurrent neural network (RNN) to learn the mapping function between the physical stimulus and the biomimetic stimulation pattern, i.e. the sensory encoder to be integrated into a neuroprosthetic device.

MAIN RESULTS

We identified ICMS patterns that evoked simulated responses that closely approximated the measured responses for neurons within 50 µm of the electrode tip. The RNN-based sensory encoder generalized well to untrained limb movements or skin indentations. STIM designed using the model-based optimization approach outperformed STIM designed using existing linear and nonlinear mappings.

SIGNIFICANCE

The proposed framework produces an encoder that converts limb state or patterns of pressure exerted onto the prosthetic hand into STIM that evoke naturalistic patterns of neuronal activation.

Decoding hand kinematics from population responses in sensorimotor cortex during grasping

OBJECTIVE

The hand-a complex effector comprising dozens of degrees of freedom of movement-endows us with the ability to flexibly, precisely, and effortlessly interact with objects. The neural signals associated with dexterous hand movements in primary motor cortex (M1) and somatosensory cortex (SC) have received comparatively less attention than have those associated with proximal upper limb control.

APPROACH

To fill this gap, we trained two monkeys to grasp objects varying in size and shape while tracking their hand postures and recording single-unit activity from M1 and SC. We then decoded their hand kinematics across tens of joints from population activity in these areas.

MAIN RESULTS

We found that we could accurately decode kinematics with a small number of neural signals and that different cortical fields carry different amounts of information about hand kinematics. In particular, neural signals in rostral M1 led to better performance than did signals in caudal M1, whereas Brodmann's area 3a outperformed areas 1 and 2 in SC. Moreover, decoding performance was higher for joint angles than joint angular velocities, in contrast to what has been found with proximal limb decoders.

SIGNIFICANCE

We conclude that cortical signals can be used for dexterous hand control in brain machine interface applications and that postural representations in SC may be exploited via intracortical stimulation to close the sensorimotor loop.

Stabilization of a brain-computer interface via the alignment of low-dimensional spaces of neural activity

The instability of neural recordings can render clinical brain-computer interfaces (BCIs) uncontrollable. Here, we show that the alignment of low-dimensional neural manifolds (low-dimensional spaces that describe specific correlation patterns between neurons) can be used to stabilize neural activity, thereby maintaining BCI performance in the presence of recording instabilities. We evaluated the stabilizer with non-human primates during online cursor control via intracortical BCIs in the presence of severe and abrupt recording instabilities. The stabilized BCIs recovered proficient control under different instability conditions and across multiple days. The stabilizer does not require knowledge of user intent and can outperform supervised recalibration. It stabilized BCIs even when neural activity contained little information about the direction of cursor movement. The stabilizer may be applicable to other neural interfaces and may improve the clinical viability of BCIs.

Cross-subject decoding of eye movement goals from local field potentials

OBJECTIVE

We consider the cross-subject decoding problem from local field potential (LFP) signals, where training data collected from the prefrontal cortex (PFC) of a source subject is used to decode intended motor actions in a destination subject.

APPROACH

We propose a novel supervised transfer learning technique, referred to as data centering, which is used to adapt the feature space of the source to the feature space of the destination. The key ingredients of data centering are the transfer functions used to model the deterministic component of the relationship between the source and destination feature spaces. We propose an efficient data-driven estimation approach for linear transfer functions that uses the first and second order moments of the class-conditional distributions.

MAIN RESULTS

We apply our data centering technique with linear transfer functions for cross-subject decoding of eye movement intentions in an experiment where two macaque monkeys perform memory-guided visual saccades to one of eight target locations. The results show peak cross-subject decoding performance of [Formula: see text], which marks a substantial improvement over random choice decoder. In addition to this, data centering also outperforms standard sampling-based methods in setups with imbalanced training data.

SIGNIFICANCE

The analyses presented herein demonstrate that the proposed data centering is a viable novel technique for reliable LFP-based cross-subject brain-computer interfacing and neural prostheses.

Long-term stability of cortical population dynamics underlying consistent behavior

Animals readily execute learned behaviors in a consistent manner over long periods of time, and yet no equally stable neural correlate has been demonstrated. How does the cortex achieve this stable control? Using the sensorimotor system as a model of cortical processing, we investigated the hypothesis that the dynamics of neural latent activity, which captures the dominant co-variation patterns within the neural population, must be preserved across time. We recorded from populations of neurons in premotor, primary motor and somatosensory cortices as monkeys performed a reaching task, for up to 2 years. Intriguingly, despite a steady turnover in the recorded neurons, the low-dimensional latent dynamics remained stable. The stability allowed reliable decoding of behavioral features for the entire timespan, while fixed decoders based directly on the recorded neural activity degraded substantially. We posit that stable latent cortical dynamics within the manifold are the fundamental building blocks underlying consistent behavioral execution.

Latent Factors and Dynamics in Motor Cortex and Their Application to Brain-Machine Interfaces

In the 1960s, Evarts first recorded the activity of single neurons in motor cortex of behaving monkeys (Evarts, 1968). In the 50 years since, great effort has been devoted to understanding how single neuron activity relates to movement. Yet these single neurons exist within a vast network, the nature of which has been largely inaccessible. With advances in recording technologies, algorithms, and computational power, the ability to study these networks is increasing exponentially. Recent experimental results suggest that the dynamical properties of these networks are critical to movement planning and execution. Here we discuss this dynamical systems perspective and how it is reshaping our understanding of the motor cortices. Following an overview of key studies in motor cortex, we discuss techniques to uncover the "latent factors" underlying observed neural population activity. Finally, we discuss efforts to use these factors to improve the performance of brain-machine interfaces, promising to make these findings broadly relevant to neuroengineering as well as systems neuroscience.

Generative models and abstractions for large-scale neuroanatomy datasets

Neural datasets are increasing rapidly in both resolution and volume. In neuroanatomy, this trend has been accelerated by innovations in imaging technology. As full datasets are impractical and unnecessary for many applications, it is important to identify abstractions that distill useful features of neural structure, organization, and anatomy. In this review article, we discuss several such abstractions and highlight recent algorithmic advances in working with these models. In particular, we discuss the use of generative models in neuroanatomy; such models may be considered 'meta-abstractions' that capture distributions over other abstractions.