AJILE12: Long-term naturalistic human intracranial neural recordings and pose

A Generalist Intracortical Motor Decoder

Mapping the relationship between neural activity and motor behavior is a central aim of sensorimotor neuroscience and neurotechnology. While most progress to this end has relied on restricting complexity, the advent of foundation models instead proposes integrating a breadth of data as an alternate avenue for broadly advancing downstream modeling. We quantify this premise for motor decoding from intracortical microelectrode data, pretraining an autoregressive Transformer on 2000 hours of neural population spiking activity paired with diverse motor covariates from over 30 monkeys and humans. The resulting model is broadly useful, benefiting decoding on 8 downstream decoding tasks and generalizing to a variety of neural distribution shifts. However, we also highlight that scaling autoregressive Transformers seems unlikely to resolve limitations stemming from sensor variability and output stereotypy in neural datasets. Code: https://github.com/joel99/ndt3.

Generating realistic neurophysiological time series with denoising diffusion probabilistic models

Denoising diffusion probabilistic models (DDPMs) have recently been shown to accurately generate complicated data such as images, audio, or time series. Experimental and clinical neuroscience also stand to benefit from this progress, as the accurate generation of neurophysiological time series can enable or improve many neuroscientific applications. Here, we present a flexible DDPM-based method for modeling multichannel, densely sampled neurophysiological recordings. DDPMs can generate realistic synthetic data for a variety of datasets from different species and recording techniques. The generated data capture important statistics, such as frequency spectra and phase-amplitude coupling, as well as fine-grained features such as sharp wave ripples. Furthermore, data can be generated based on additional information such as experimental conditions. We demonstrate the flexibility of DDPMs in several applications, including brain-state classification and missing-data imputation. In summary, DDPMs can serve as accurate generative models of neurophysiological recordings and have broad utility in the probabilistic generation of synthetic recordings for neuroscientific applications.

Open Data In Neurophysiology: Advancements, Solutions & Challenges

Across the life sciences, an ongoing effort over the last 50 years has made data and methods more reproducible and transparent. This openness has led to transformative insights and vastly accelerated scientific progress1,2. For example, structural biology3 and genomics4,5 have undertaken systematic collection and publication of protein sequences and structures over the past half-century, and these data have led to scientific breakthroughs that were unthinkable when data collection first began (e.g.6). We believe that neuroscience is poised to follow the same path, and that principles of open data and open science will transform our understanding of the nervous system in ways that are impossible to predict at the moment. To this end, new social structures along with active and open scientific communities are essential7 to facilitate and expand the still limited adoption of open science practices in our field8. Unified by shared values of openness, we set out to organize a symposium for Open Data in Neuroscience (ODIN) to strengthen our community and facilitate transformative neuroscience research at large. In this report, we share what we learned during this first ODIN event. We also lay out plans for how to grow this movement, document emerging conversations, and propose a path toward a better and more transparent science of tomorrow.

Consistent spectro-spatial features of human ECoG successfully decode naturalistic behavioral states

Objective

Understanding the neural correlates of naturalistic behavior is critical for extending and confirming the results obtained from trial-based experiments and designing generalizable brain-computer interfaces that can operate outside laboratory environments. In this study, we aimed to pinpoint consistent spectro-spatial features of neural activity in humans that can discriminate between naturalistic behavioral states.

Approach

We analyzed data from five participants using electrocorticography (ECoG) with broad spatial coverage. Spontaneous and naturalistic behaviors such as "Talking" and "Watching TV" were labeled from manually annotated videos. Linear discriminant analysis (LDA) was used to classify the two behavioral states. The parameters learned from the LDA were then used to determine whether the neural signatures driving classification performance are consistent across the participants.

Main results

Spectro-spatial feature values were consistently discriminative between the two labeled behavioral states across participants. Mainly, θ, α, and low and high γ in the postcentral gyrus, precentral gyrus, and temporal lobe showed significant classification performance and feature consistency across participants. Subject-specific performance exceeded 70%. Combining neural activity from multiple cortical regions generally does not improve decoding performance, suggesting that information regarding the behavioral state is non-additive as a function of the cortical region.

Significance

To the best of our knowledge, this is the first attempt to identify specific spectro-spatial neural correlates that consistently decode naturalistic and active behavioral states. The aim of this work is to serve as an initial starting point for developing brain-computer interfaces that can be generalized in a realistic setting and to further our understanding of the neural correlates of naturalistic behavior in humans.

A comparison of neuroelectrophysiology databases

As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics.

Neural Data Transformer 2: Multi-context Pretraining for Neural Spiking Activity

The neural population spiking activity recorded by intracortical brain-computer interfaces (iBCIs) contain rich structure. Current models of such spiking activity are largely prepared for individual experimental contexts, restricting data volume to that collectable within a single session and limiting the effectiveness of deep neural networks (DNNs). The purported challenge in aggregating neural spiking data is the pervasiveness of context-dependent shifts in the neural data distributions. However, large scale unsupervised pretraining by nature spans heterogeneous data, and has proven to be a fundamental recipe for successful representation learning across deep learning. We thus develop Neural Data Transformer 2 (NDT2), a spatiotemporal Transformer for neural spiking activity, and demonstrate that pretraining can leverage motor BCI datasets that span sessions, subjects, and experimental tasks. NDT2 enables rapid adaptation to novel contexts in downstream decoding tasks and opens the path to deployment of pretrained DNNs for iBCI control. Code: https://github.com/joel99/context_general_bci.

A Comparison of Neuroelectrophysiology Databases

As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics.

The Neurodata Without Borders ecosystem for neurophysiological data science

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB's impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states

In analyzing the neural correlates of naturalistic and unstructured behaviors, features of neural activity that are ignored in a trial-based experimental paradigm can be more fully studied and investigated. Here, we analyze neural activity from two patients using electrocorticography (ECoG) and stereo-electroencephalography (sEEG) recordings, and reveal that multiple neural signal characteristics exist that discriminate between unstructured and naturalistic behavioral states such as “engaging in dialogue” and “using electronics”. Using the high gamma amplitude as an estimate of neuronal firing rate, we demonstrate that behavioral states in a naturalistic setting are discriminable based on long-term mean shifts, variance shifts, and differences in the specific neural activity’s covariance structure. Both the rapid and slow changes in high gamma band activity separate unstructured behavioral states. We also use Gaussian process factor analysis (GPFA) to show the existence of salient spatiotemporal features with variable smoothness in time. Further, we demonstrate that both temporally smooth and stochastic spatiotemporal activity can be used to differentiate unstructured behavioral states. This is the first attempt to elucidate how different neural signal features contain information about behavioral states collected outside the conventional experimental paradigm.

Learning neural decoders without labels using multiple data streams

OBJECTIVE

Recent advances in neural decoding have accelerated the development of brain-computer interfaces aimed at assisting users with everyday tasks such as speaking, walking, and manipulating objects. However, current approaches for training neural decoders commonly require large quantities of labeled data, which can be laborious or infeasible to obtain in real-world settings. Alternatively, self-supervised models that share self-generated pseudo-labels between two data streams have shown exceptional performance on unlabeled audio and video data, but it remains unclear how well they extend to neural decoding.

APPROACH

We learn neural decoders without labels by leveraging multiple simultaneously recorded data streams, including neural, kinematic, and physiological signals. Specifically, we apply cross-modal, self-supervised deep clustering to train decoders that can classify movements from brain recordings. After training, we then isolate the decoders for each input data stream and compare the accuracy of decoders trained using cross-modal deep clustering against supervised and unimodal, self-supervised models.

MAIN RESULTS

We find that sharing pseudo-labels between two data streams during training substantially increases decoding performance compared to unimodal, self-supervised models, with accuracies approaching those of supervised decoders trained on labeled data. Next, we extend cross-modal decoder training to three or more modalities, achieving state-of-the-art neural decoding accuracy that matches or slightly exceeds the performance of supervised models. Significance: We demonstrate that cross-modal, self-supervised decoding can be applied to train neural decoders when few or no labels are available and extend the cross-modal framework to share information among three or more data streams, further improving self-supervised training.