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Neural decoding is a tool for understanding how activities from a population of neurons inside the brain relate to the outside world and for engineering applications such as brain-machine interfaces. However, neural decoding studies mainly focused on different decoding algorithms rather than different neuron types which could use different coding strategies. In this study, we used two-photon calcium imaging to assess three auditory spatial decoders (space map, opponent channel, and population pattern) in excitatory and inhibitory neurons in the dorsal inferior colliculus of male and female mice. Our findings revealed a clustering of excitatory neurons that prefer similar interaural level difference (ILD), the primary spatial cues in mice, while inhibitory neurons showed random local ILD organization. We found that inhibitory neurons displayed lower decoding variability under the opponent channel decoder, while excitatory neurons achieved higher decoding accuracy under the space map and population pattern decoders. Further analysis revealed that the inhibitory neurons' preference for ILD off the midline and the excitatory neurons' heterogeneous ILD tuning account for their decoding differences. Additionally, we discovered a sharper ILD tuning in the inhibitory neurons. Our computational model, linking this to increased presynaptic inhibitory inputs, was corroborated using monaural and binaural stimuli. Overall, this study provides experimental and computational insight into how excitatory and inhibitory neurons uniquely contribute to the coding of sound locations. [ABSTRACT FROM AUTHOR]

Background/Objectives: Neural decoding methods are often limited by the performance of brain encoders, which map complex brain signals into a latent representation space of perception information. These brain encoders are constrained by the limited amount of paired brain and stimuli data available for training, making it challenging to learn rich neural representations. Methods: To address this limitation, we present a novel multimodal training approach using paired image and functional magnetic resonance imaging (fMRI) data to establish a brain masked autoencoder that learns the interactions between images and brain activities. Subsequently, we employ a diffusion model conditioned on brain data to decode realistic images. Results: Our method achieves high-quality decoding results in semantic contents and low-level visual attributes, outperforming previous methods both qualitatively and quantitatively, while maintaining computational efficiency. Additionally, our method is applied to decode artificial patterns across region of interests (ROIs) to explore their functional properties. We not only validate existing knowledge concerning ROIs but also unveil new insights, such as the synergy between early visual cortex and higher-level scene ROIs, as well as the competition within the higher-level scene ROIs. Conclusions: These findings provide valuable insights for future directions in the field of neural decoding. [ABSTRACT FROM AUTHOR]

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 spectrospatial 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 nonadditive 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. [ABSTRACT FROM AUTHOR]

Decoding the activity of individual neural cells during natural behaviours allows neuroscientists to study how the nervous system generates and controls movements. Contrary to other neural cells, the activity of spinal motor neurons can be determined non-invasively (or minimally invasively) from the decomposition of electromyographic (EMG) signals into motor unit firing activities. For some interfacing and neuro-feedback investigations, EMG decomposition needs to be performed in real time. Here, we introduce an open-source software that performs real-time decoding of motor neurons using a blind-source separation approach for multichannel EMG signal processing. Separation vectors (motor unit filters) are optimised for each motor unit from baseline contractions and then re-applied in real time during test contractions. In this way, the firing activity of multiple motor neurons can be provided through different forms of visual feedback. We provide a complete framework with guidelines and examples of recordings to guide researchers who aim to study movement control at the motor neuron level. We first validated the software with synthetic EMG signals generated during a range of isometric contraction patterns. We then tested the software on data collected using either surface or intramuscular electrode arrays from five lower limb muscles (gastrocnemius lateralis and medialis, vastus lateralis and medialis, and tibialis anterior). We assessed how the muscle or variation of contraction intensity between the baseline contraction and the test contraction impacted the accuracy of the real-time decomposition. This open-source software provides a set of tools for neuroscientists to design experimental paradigms where participants can receive real-time feedback on the output of the spinal cord circuits.

Epifluorescence miniature microscopes ('miniscopes') are widely used for in vivo calcium imaging of neural population activity. Imaging data are typically collected during a behavioral task and stored for later offline analysis, but emerging techniques for online imaging can support novel closed-loop experiments in which neural population activity is decoded in real time to trigger neurostimulation or sensory feedback. To achieve short feedback latencies, online imaging systems must be optimally designed to maximize computational speed and efficiency while minimizing errors in population decoding. Here we introduce DeCalciOn, an open-source device for real-time imaging and population decoding of in vivo calcium signals that is hardware compatible with all miniscopes that use the UCLA Data Acquisition (DAQ) interface. DeCalciOn performs online motion stabilization, neural enhancement, calcium trace extraction, and decoding of up to 1024 traces per frame at latencies of

Neural decoding is a powerful method to analyze neural activity. However, the code needed to run a decoding analysis can be complex, which can present a barrier to using the method. In this paper we introduce a package that makes it easy to perform decoding analyses in the R programing language. We describe how the package is designed in a modular fashion which allows researchers to easily implement a range of different analyses. We also discuss how to format data to be able to use the package, and we give two examples of how to use the package to analyze real data. We believe that this package, combined with the rich data analysis ecosystem in R, will make it significantly easier for researchers to create reproducible decoding analyses, which should help increase the pace of neuroscience discoveries. [ABSTRACT FROM AUTHOR]

Decoding visual information, such as visual imagery and perception, from EEG data can be used to improve understanding of the neural representation of visual information and to provide commands for BCI systems. The appeal of EEG as a neuroimaging tool lies in its high temporal resolution, cost-effectiveness, and portability. Nevertheless, the feasibility of using EEG for visual information decoding remains a subject of ongoing inquiry. In this review, we explore the neural correlates of this visual information, specifically focusing on visual features such as colour, shapes, texture, and also naturalistic whole objects. We begin to examine which visual features can be effectively measured using EEG, taking into account its inherent characteristics, such as its measurement depth, limited spatial resolution, and high temporal resolution. Using a systematic approach, the review provides an in-depth analysis of the current state-of-the-art in EEG-based decoding of visual features for BCI purposes. Finally, we address some potential methodological improvements that can be made to the experimental design in EEG visual information decoding studies, such as palette cleansing, augmentation to bolster dataset size, and fusion of neuroimaging techniques. [ABSTRACT FROM AUTHOR]

In motor cortex, behaviorally relevant neural responses are entangled with irrelevant signals, which complicates the study of encoding and decoding mechanisms. It remains unclear whether behaviorally irrelevant signals could conceal some critical truth. One solution is to accurately separate behaviorally relevant and irrelevant signals at both single-neuron and single-trial levels, but this approach remains elusive due to the unknown ground truth of behaviorally relevant signals. Therefore, we propose a framework to define, extract, and validate behaviorally relevant signals. Analyzing separated signals in three monkeys performing different reaching tasks, we found neural responses previously considered to contain little information actually encode rich behavioral information in complex nonlinear ways. These responses are critical for neuronal redundancy and reveal movement behaviors occupy a higher-dimensional neural space than previously expected. Surprisingly, when incorporating often-ignored neural dimensions, behaviorally relevant signals can be decoded linearly with comparable performance to nonlinear decoding, suggesting linear readout may be performed in motor cortex. Our findings prompt that separating behaviorally relevant signals may help uncover more hidden cortical mechanisms.

Objective: Speech brain-computer interfaces (speech BCIs), which convert brain signals into spoken words or sentences, have demonstrated great potential for high-performance BCI communication. Phonemes are the basic pronunciation units. For monosyllabic languages such as Chinese Mandarin, where a word usually contains less than three phonemes, accurate decoding of phonemes plays a vital role. We found that in the neural representation space, phonemes with similar pronunciations are often inseparable, leading to confusion in phoneme classification. Methods: We mapped the neural signals of phoneme pronunciation into a hyperbolic space for a more distinct phoneme representation. Critically, we proposed a hyperbolic hierarchical clustering approach to specifically learn a phoneme-level structure to guide the representation. Results: We found such representation facilitated greater distance between similar phonemes, effectively reducing confusion. In the phoneme decoding task, our approach demonstrated an average accuracy of 75.21% for 21 phonemes and outperformed existing methods across different experimental days. Conclusion: Our approach showed high accuracy in phoneme classification. By learning the phoneme-level neural structure, the representations of neural signals were more discriminative and interpretable. Significance: Our approach can potentially facilitate high-performance speech BCIs for Chinese and other monosyllabic languages.

Neural decoding is still a challenging and a hot topic in neurocomputing science. Recently, many studies have shown that brain network patterns containing rich spatiotemporal structural information represent the brain’s activation information under external stimuli. In the traditional method, brain network features are directly obtained using the standard machine learning method and provide to a classifier, subsequently decoding external stimuli. However, this method cannot effectively extract the multidimensional structural information hidden in the brain network. Furthermore, studies on tensors have show that the tensor decomposition model can fully mine unique spatiotemporal structural characteristics of a spatiotemporal structure in data with a multidimensional structure. This research proposed a stimulus-constrained Tensor Brain Network (s-TBN) model that involves the tensor decomposition and stimulus category-constraint information. The model was verified on real neuroimaging data obtained via magnetoencephalograph and functional mangetic resonance imaging). Experimental results show that the s-TBN model achieve accuracy matrices of greater than 11.06% and 18.46% on the accuracy matrix compared with other methods on two modal datasets. These results prove the superiority of extracting discriminative characteristics using the STN model, especially for decoding object stimuli with semantic information.

Background/Objectives: Neural decoding methods are often limited by the performance of brain encoders, which map complex brain signals into a latent representation space of perception information. These brain encoders are constrained by the limited amount of paired brain and stimuli data available for training, making it challenging to learn rich neural representations. Methods: To address this limitation, we present a novel multimodal training approach using paired image and functional magnetic resonance imaging (fMRI) data to establish a brain masked autoencoder that learns the interactions between images and brain activities. Subsequently, we employ a diffusion model conditioned on brain data to decode realistic images. Results: Our method achieves high-quality decoding results in semantic contents and low-level visual attributes, outperforming previous methods both qualitatively and quantitatively, while maintaining computational efficiency. Additionally, our method is applied to decode artificial patterns across region of interests (ROIs) to explore their functional properties. We not only validate existing knowledge concerning ROIs but also unveil new insights, such as the synergy between early visual cortex and higher-level scene ROIs, as well as the competition within the higher-level scene ROIs. Conclusions: These findings provide valuable insights for future directions in the field of neural decoding.

Brain signal patterns generated in the central nervous system of brain-computer interface (BCI) users are closely related to BCI paradigms and neural coding. In BCI systems, BCI paradigms and neural coding are critical elements for BCI research. However, so far there have been few references that clearly and systematically elaborated on the definition and design principles of the BCI paradigm as well as the definition and modeling principles of BCI neural coding. Therefore, these contents are expounded and the existing main BCI paradigms and neural coding are introduced in the review. Finally, the challenges and future research directions of BCI paradigm and neural coding were discussed, including user-centered design and evaluation for BCI paradigms and neural coding, revolutionizing the traditional BCI paradigms, breaking through the existing techniques for collecting brain signals and combining BCI technology with advanced AI technology to improve brain signal decoding performance. It is expected that the review will inspire innovative research and development of the BCI paradigm and neural coding. [ABSTRACT FROM AUTHOR]

Brain‐computer interfaces (BCIs) can be used to control assistive devices by patients with neurological disorders like amyotrophic lateral sclerosis (ALS) that limit speech and movement. For assistive control, it is desirable for BCI systems to be accurate and reliable, preferably with minimal setup time. In this study, a participant with severe dysarthria due to ALS operates computer applications with six intuitive speech commands via a chronic electrocorticographic (ECoG) implant over the ventral sensorimotor cortex. Speech commands are accurately detected and decoded (median accuracy: 90.59%) throughout a 3‐month study period without model retraining or recalibration. Use of the BCI does not require exogenous timing cues, enabling the participant to issue self‐paced commands at will. These results demonstrate that a chronically implanted ECoG‐based speech BCI can reliably control assistive devices over long time periods with only initial model training and calibration, supporting the feasibility of unassisted home use. [ABSTRACT FROM AUTHOR]

ObjectiveUnderstanding 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.ApproachWe 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 resultsSpectro-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.SignificanceTo 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.

Abstract Objective Noninvasive neural decoding enables predicting motor output from neural activities without physically damaging the human body. A recent study demonstrated the applicability of functional near-infrared spectroscopy (fNIRS) to decode muscle force production from hemodynamic signals measured in the male brain. However, given the sex differences in cerebral blood flow and muscle physiology, whether the fNIRS approach can also be applied to the female brain remains elusive. Therefore, this study aimed to evaluate whether fNIRS can be used to identify the optimal cortical region and hemodynamic predictor to decode muscle force output in females. Results Statistical group analysis for eight healthy female adults showed that the cortical region for wrist control was topologically dorsal to that for finger control over the primary sensorimotor cortex. This cortical area was maximally activated while the wrist flexor muscles were contracted to hold a load on the subject’s palm, as was the case for males. However, the dynamics of oxyhemoglobin concentration measured from the most activated cortical area differed between females and males. The signal intensity during 100% maximal voluntary contraction and the signal increase rate at 50% maximal voluntary contraction was lower and faster in females. Eight predictors were used to characterize hemodynamic signals’ amplitude and temporal variation in the female cortex. Unlike the case for males, only the trajectory predictors for the amplitude of oxyhemoglobin concentration change were strongly correlated with the strengths of force produced by the wrist flexor muscles, showing a linear relationship. These results suggest gender-specific hemodynamics must be considered for decoding low-level motor control with fNIRS in females.

Objective. Electrical recordings of neural activity from brain surface have been widely employed in basic neuroscience research and clinical practice for investigations of neural circuit functions, brain-computer interfaces, and treatments for neurological disorders. Traditionally, these surface potentials have been believed to mainly reflect local neural activity. It is not known how informative the locally recorded surface potentials are for the neural activities across multiple cortical regions.Approach. To investigate that, we perform simultaneous local electrical recording and wide-field calcium imaging in awake head-fixed mice. Using a recurrent neural network model, we try to decode the calcium fluorescence activity of multiple cortical regions from local electrical recordings.Main results. The mean activity of different cortical regions could be decoded from locally recorded surface potentials. Also, each frequency band of surface potentials differentially encodes activities from multiple cortical regions so that including all the frequency bands in the decoding model gives the highest decoding performance. Despite the close spacing between recording channels, surface potentials from different channels provide complementary information about the large-scale cortical activity and the decoding performance continues to improve as more channels are included. Finally, we demonstrate the successful decoding of whole dorsal cortex activity at pixel-level using locally recorded surface potentials.Significance. These results show that the locally recorded surface potentials indeed contain rich information of the large-scale neural activities, which could be further demixed to recover the neural activity across individual cortical regions. In the future, our cross-modality inference approach could be adapted to virtually reconstruct cortex-wide brain activity, greatly expanding the spatial reach of surface electrical recordings without increasing invasiveness. Furthermore, it could be used to facilitate imaging neural activity across the whole cortex in freely moving animals, without requirement of head-fixed microscopy configurations.

Recent developments in the biology of malignant gliomas have demonstrated that glioma cells interact with neurons through both paracrine signaling and electrochemical synapses. Glioma-neuron interactions consequently modulate the excitability of local neuronal circuits, and it is unclear the extent to which glioma-infiltrated cortex can meaningfully participate in neural computations. For example, gliomas may result in a local disorganization of activity that impedes the transient synchronization of neural oscillations. Alternatively, glioma-infiltrated cortex may retain the ability to engage in synchronized activity in a manner similar to normal-appearing cortex but exhibit other altered spatiotemporal patterns of activity with subsequent impact on cognitive processing. Here, we use subdural electrocorticography to sample both normal-appearing and glioma-infiltrated cortex during speech. We find that glioma-infiltrated cortex engages in synchronous activity during task performance in a manner similar to normal-appearing cortex but recruits a diffuse spatial network. On a temporal scale, we show that signals from glioma-infiltrated cortex have decreased entropy, which may affect its ability to encode information during nuanced tasks such as production of monosyllabic versus polysyllabic words. Furthermore, we show that temporal decoding strategies for distinguishing monosyllabic from polysyllabic words were feasible for signals arising from normal-appearing cortex but not from glioma-infiltrated cortex. These findings inform our understanding of cognitive processing in chronic disease states and have implications for neuromodulation and prosthetics in patients with malignant gliomas.

Neural decoding is a powerful method to analyze neural activity. However, the code needed to run a decoding analysis can be complex, which can present a barrier to using the method. In this paper we introduce a package that makes it easy to perform decoding analyses in the R programing language. We describe how the package is designed in a modular fashion which allows researchers to easily implement a range of different analyses. We also discuss how to format data to be able to use the package, and we give two examples of how to use the package to analyze real data. We believe that this package, combined with the rich data analysis ecosystem in R, will make it significantly easier for researchers to create reproducible decoding analyses, which should help increase the pace of neuroscience discoveries.

Abstract Brain‐computer interfaces (BCIs) can be used to control assistive devices by patients with neurological disorders like amyotrophic lateral sclerosis (ALS) that limit speech and movement. For assistive control, it is desirable for BCI systems to be accurate and reliable, preferably with minimal setup time. In this study, a participant with severe dysarthria due to ALS operates computer applications with six intuitive speech commands via a chronic electrocorticographic (ECoG) implant over the ventral sensorimotor cortex. Speech commands are accurately detected and decoded (median accuracy: 90.59%) throughout a 3‐month study period without model retraining or recalibration. Use of the BCI does not require exogenous timing cues, enabling the participant to issue self‐paced commands at will. These results demonstrate that a chronically implanted ECoG‐based speech BCI can reliably control assistive devices over long time periods with only initial model training and calibration, supporting the feasibility of unassisted home use.

Neural interfaces for stable access to the spinal cord (SC) electrical activity can benefit patients with motor dysfunctions. Invasive high‐density electrodes can directly extract signals from SC neuronal populations that can be used for the facilitation, adjustment, and reconstruction of motor actions. However, developing neural interfaces that can achieve high channel counts and long‐term intraspinal recording remains technically challenging. Here, a biocompatible SC hyperflexible electrode array (SHEA) with an ultrathin structure that minimizes mechanical mismatch between the interface and SC tissue and enables stable single‐unit recording for more than 2 months in mice is demonstrated. These results show that SHEA maintains stable impedance, signal‐to‐noise ratio, single‐unit yield, and spike amplitude after implantation into mouse SC. Gait analysis and histology show that SHEA implantation induces negligible behavioral effects and Inflammation. Additionally, multi‐unit signals recorded from the SC ventral horn can predict the mouse's movement trajectory with a high decoding coefficient of up to 0.95. Moreover, during step cycles, it is found that the neural trajectory of spikes and low‐frequency local field potential (LFP) signal exhibits periodic geometry patterns. Thus, SHEA can offer an efficient and reliable SC neural interface for monitoring and potentially modulating SC neuronal activity associated with motor dysfunctions. [ABSTRACT FROM AUTHOR]

Objective: Noninvasive neural decoding enables predicting motor output from neural activities without physically damaging the human body. A recent study demonstrated the applicability of functional near-infrared spectroscopy (fNIRS) to decode muscle force production from hemodynamic signals measured in the male brain. However, given the sex differences in cerebral blood flow and muscle physiology, whether the fNIRS approach can also be applied to the female brain remains elusive. Therefore, this study aimed to evaluate whether fNIRS can be used to identify the optimal cortical region and hemodynamic predictor to decode muscle force output in females. Results: Statistical group analysis for eight healthy female adults showed that the cortical region for wrist control was topologically dorsal to that for finger control over the primary sensorimotor cortex. This cortical area was maximally activated while the wrist flexor muscles were contracted to hold a load on the subject's palm, as was the case for males. However, the dynamics of oxyhemoglobin concentration measured from the most activated cortical area differed between females and males. The signal intensity during 100% maximal voluntary contraction and the signal increase rate at 50% maximal voluntary contraction was lower and faster in females. Eight predictors were used to characterize hemodynamic signals' amplitude and temporal variation in the female cortex. Unlike the case for males, only the trajectory predictors for the amplitude of oxyhemoglobin concentration change were strongly correlated with the strengths of force produced by the wrist flexor muscles, showing a linear relationship. These results suggest gender-specific hemodynamics must be considered for decoding low-level motor control with fNIRS in females. [ABSTRACT FROM AUTHOR]

Everyday speech communication often occurs in environments with background noise, and the impact of noise on speech recognition can vary depending on factors such as noise type, noise intensity, and the listener's hearing ability. However, the extent to which neural mechanisms in speech understanding are influenced by different types and levels of noise remains unknown. This study aims to investigate whether individuals exhibit distinct neural responses and attention strategies depending on noise conditions. We recorded electroencephalography (EEG) data from 20 participants with normal hearing (13 males) and evaluated both neural tracking of speech envelopes and behavioral performance in speech understanding in the presence of varying types of background noise. Participants engaged in an EEG experiment consisting of two separate sessions. The first session involved listening to a 12-min story presented binaurally without any background noise. In the second session, speech understanding scores were measured using matrix sentences presented under speech-shaped noise (SSN) and Story noise background noise conditions at noise levels corresponding to sentence recognitions score (SRS). We observed differences in neural envelope correlation depending on noise type but not on its level. Interestingly, the impact of noise type on the variation in envelope tracking was more significant among participants with higher speech perception scores, while those with lower scores exhibited similarities in envelope correlation regardless of the noise condition. The findings suggest that even individuals with normal hearing could adopt different strategies to understand speech in challenging listening environments, depending on the type of noise. [ABSTRACT FROM AUTHOR]

The complexity and high dimensionality of neuroimaging data pose problems for decoding information with machine learning (ML) models because the number of features is often much larger than the number of observations. Feature selection is one of the crucial steps for determining meaningful target features in decoding; however, optimizing the feature selection from such high-dimensional neuroimaging data has been challenging using conventional ML models. Here, we introduce an efficient and high-performance decoding package incorporating a forward variable selection (FVS) algorithm and hyper-parameter optimization that automatically identifies the best feature pairs for both classification and regression models, where a total of 18 ML models are implemented by default. First, the FVS algorithm evaluates the goodness-of-fit across different models using the k-fold cross-validation step that identifies the best subset of features based on a predefined criterion for each model. Next, the hyperparameters of each ML model are optimized at each forward iteration. Final outputs highlight an optimized number of selected features (brain regions of interest) for each model with its accuracy. Furthermore, the toolbox can be executed in a parallel environment for efficient computation on a typical personal computer. With the optimized forward variable selection decoder (oFVSD) pipeline, we verified the effectiveness of decoding sex classification and age range regression on 1,113 structural magnetic resonance imaging (MRI) datasets. Compared to ML models without the FVS algorithm and with the Boruta algorithm as a variable selection counterpart, we demonstrate that the oFVSD significantly outperformed across all of the ML models over the counterpart models without FVS (approximately 0.20 increase in correlation coefficient, r, with regression models and 8% increase in classification models on average) and with Boruta variable selection algorithm (approximately 0.07 improvement in regression and 4% in classification models). Furthermore, we confirmed the use of parallel computation considerably reduced the computational burden for the high-dimensional MRI data. Altogether, the oFVSD toolbox efficiently and effectively improves the performance of both classification and regression ML models, providing a use case example on MRI datasets. With its flexibility, oFVSD has the potential for many other modalities in neuroimaging. This open-source and freely available Python package makes it a valuable toolbox for research communities seeking improved decoding accuracy. [ABSTRACT FROM AUTHOR]

Complete reaching movements involve target sensing, motor planning, and arm movement execution, and this process requires the integration and communication of various brain regions. Previously, reaching movements have been decoded successfully from the motor cortex (M1) and applied to prosthetic control. However, most studies attempted to decode neural activities from a single brain region, resulting in reduced decoding accuracy during visually guided reaching motions. To enhance the decoding accuracy of visually guided forelimb reaching movements, we propose a parallel computing neural network using both M1 and medial agranular cortex (AGm) neural activities of rats to predict forelimb-reaching movements. The proposed network decodes M1 neural activities into the primary components of the forelimb movement and decodes AGm neural activities into internal feedforward information to calibrate the forelimb movement in a goal-reaching movement. We demonstrate that using AGm neural activity to calibrate M1 predicted forelimb movement can improve decoding performance significantly compared to neural decoders without calibration. We also show that the M1 and AGm neural activities contribute to controlling forelimb movement during goal-reaching movements, and we report an increase in the power of the local field potential (LFP) in beta and gamma bands over AGm in response to a change in the target distance, which may involve sensorimotor transformation and communication between the visual cortex and AGm when preparing for an upcoming reaching movement. The proposed parallel computing neural network with the internal feedback model improves prediction accuracy for goal-reaching movements. [ABSTRACT FROM AUTHOR]

Reconstructing visual experience from brain responses measured by functional magnetic resonance imaging (fMRI) is a challenging yet important research topic in brain decoding, especially it has proved more difficult to decode visually similar stimuli, such as faces. Although face attributes are known as the key to face recognition, most existing methods generally ignore how to decode facial attributes more precisely in perceived face reconstruction, which often leads to indistinguishable reconstructed faces. To solve this problem, we propose a novel neural decoding framework called VSPnet (voxel2style2pixel) by establishing hierarchical encoding and decoding networks with disentangled latent representations as media, so that to recover visual stimuli more elaborately. And we design a hierarchical visual encoder (named HVE) to pre-extract features containing both high-level semantic knowledge and low-level visual details from stimuli. The proposed VSPnet consists of two networks: Multi-branch cognitive encoder and style-based image generator. The encoder network is constructed by multiple linear regression branches to map brain signals to the latent space provided by the pre-extracted visual features and obtain representations containing hierarchical information consistent to the corresponding stimuli. We make the generator network inspired by StyleGAN to untangle the complexity of fMRI representations and generate images. And the HVE network is composed of a standard feature pyramid over a ResNet backbone. Extensive experimental results on the latest public datasets have demonstrated the reconstruction accuracy of our proposed method outperforms the state-of-the-art approaches and the identifiability of different reconstructed faces has been greatly improved. In particular, we achieve feature editing for several facial attributes in fMRI domain based on the multiview (i.e. , visual stimuli and evoked fMRI) latent representations. • A style-oriented decoding framework is proposed to reconstruct perceived faces from brain activity. • Facial information captured through a multi-regression model can be disentangled by feature hierarchy. • Reconstructions of different faces can be distinguished more accurately than the state-of-the-art. • Feature editing can be performed in fMRI domain for the first time to control human face attributes. [ABSTRACT FROM AUTHOR]

Persistent cohomology is a powerful technique for discovering topological structure in data. Strategies for its use in neuroscience are still undergoing development. We comprehensively and rigorously assess its performance in simulated neural recordings of the brain's spatial representation system. Grid, head direction, and conjunctive cell populations each span low-dimensional topological structures embedded in high-dimensional neural activity space. We evaluate the ability for persistent cohomology to discover these structures for different dataset dimensions, variations in spatial tuning, and forms of noise. We quantify its ability to decode simulated animal trajectories contained within these topological structures. We also identify regimes under which mixtures of populations form product topologies that can be detected. Our results reveal how dataset parameters affect the success of topological discovery and suggest principles for applying persistent cohomology, as well as persistent homology, to experimental neural recordings.

Neural decoding is useful to explore the timing and source location in which the brain encodes information. Higher classification accuracy means that an analysis is more likely to succeed in extracting useful information from noises. In this paper, we present the application of a nonlinear, nonstationary signal decomposition technique-the empirical mode decomposition (EMD), on MEG data. We discuss the fundamental concepts and importance of nonlinear methods when it comes to analyzing brainwave signals and demonstrate the procedure on a set of open-source MEG facial recognition task dataset. The improved clarity of data allowed further decoding analysis to capture distinguishing features between conditions that were formerly over-looked in the existing literature, while raising interesting questions concerning hemispheric dominance to the encoding process of facial and identity information.

Abstract Neural interfaces for stable access to the spinal cord (SC) electrical activity can benefit patients with motor dysfunctions. Invasive high‐density electrodes can directly extract signals from SC neuronal populations that can be used for the facilitation, adjustment, and reconstruction of motor actions. However, developing neural interfaces that can achieve high channel counts and long‐term intraspinal recording remains technically challenging. Here, a biocompatible SC hyperflexible electrode array (SHEA) with an ultrathin structure that minimizes mechanical mismatch between the interface and SC tissue and enables stable single‐unit recording for more than 2 months in mice is demonstrated. These results show that SHEA maintains stable impedance, signal‐to‐noise ratio, single‐unit yield, and spike amplitude after implantation into mouse SC. Gait analysis and histology show that SHEA implantation induces negligible behavioral effects and Inflammation. Additionally, multi‐unit signals recorded from the SC ventral horn can predict the mouse's movement trajectory with a high decoding coefficient of up to 0.95. Moreover, during step cycles, it is found that the neural trajectory of spikes and low‐frequency local field potential (LFP) signal exhibits periodic geometry patterns. Thus, SHEA can offer an efficient and reliable SC neural interface for monitoring and potentially modulating SC neuronal activity associated with motor dysfunctions.

Zero-shot neural decoding aims to decode image categories, which were not previously trained, from functional magnetic resonance imaging (fMRI) activity evoked when a person views images. However, having insufficient training data due to the difficulty in collecting fMRI data causes poor generalization capability. Thus, models suffer from the projection domain shift problem when novel target categories are decoded. In this paper, we propose a zero-shot neural decoding approach with semi-supervised multi-view embedding. We introduce the semi-supervised approach that utilizes additional images related to the target categories without fMRI activity patterns. Furthermore, we project fMRI activity patterns into a multi-view embedding space, i.e., visual and semantic feature spaces of viewed images to effectively exploit the complementary information. We define several source and target groups whose image categories are very different and verify the zero-shot neural decoding performance. The experimental results demonstrate that the proposed approach rectifies the projection domain shift problem and outperforms existing methods. [ABSTRACT FROM AUTHOR]

Generativity, the ability to create and evaluate novel constructions, is a fundamental property of human language and cognition. The productivity of generative processes is determined by the scope of the representations they engage. Here we examine the neural representation of reduplication, a productive phonological process that can create novel forms through patterned syllable copying (e.g. ba-mih → ba-ba-mih, ba-mih-mih, or ba-mih-ba). Using MRI-constrained source estimates of combined MEG/EEG data collected during an auditory artificial grammar task, we identified localised cortical activity associated with syllable reduplication pattern contrasts in novel trisyllabic nonwords. Neural decoding analyses identified a set of predominantly right hemisphere temporal lobe regions whose activity reliably discriminated reduplication patterns evoked by untrained, novel stimuli. Effective connectivity analyses suggested that sensitivity to abstracted reduplication patterns was propagated between these temporal regions. These results suggest that localised temporal lobe activity patterns function as abstract representations that support linguistic generativity. [ABSTRACT FROM AUTHOR]

Processing incoming neural oscillatory signals in real-time and decoding from them relevant behavioral or pathological states is often required for adaptive Deep Brain Stimulation (aDBS) and other brain-computer interface (BCI) applications. Most current approaches rely on first extracting a set of predefined features, such as the power in canonical frequency bands or various time-domain features, and then training machine learning systems that use those predefined features as inputs and infer what the underlying brain state is at each given time point. However, whether this algorithmic approach is best suited to extract all available information contained within the neural waveforms remains an open question. Here, we aim to explore different algorithmic approaches in terms of their potential to yield improvements in decoding performance based on neural activity such as measured through local field potentials (LFPs) recordings or electroencephalography (EEG). In particular, we aim to explore the potential of end-to-end convolutional neural networks, and compare this approach with other machine learning methods that are based on extracting predefined feature sets. To this end, we implement and train a number of machine learning models, based either on manually constructed features or, in the case of deep learning-based models, on features directly learnt from the data. We benchmark these models on the task of identifying neural states using simulated data, which incorporates waveform features previously linked to physiological and pathological functions. We then assess the performance of these models in decoding movements based on local field potentials recorded from the motor thalamus of patients with essential tremor. Our findings, derived from both simulated and real patient data, suggest that end-to-end deep learning-based methods may surpass feature-based approaches, particularly when the relevant patterns within the waveform data are either unknown, difficult to quantify, or when there may be, from the point of view of the predefined feature extraction pipeline, unidentified features that could contribute to decoding performance. The methodologies proposed in this study might hold potential for application in adaptive deep brain stimulation (aDBS) and other brain-computer interface systems. [ABSTRACT FROM AUTHOR]

In the last decades, deep learning neural decoding algorithms have gained momentum in the field of neural interfaces and neural processing systems. However, to be deployed on low-budget portable devices while maintaining real-time operability, these models must withstand strict computational and power limitations. This work presents a spike decoding system implemented on a low-end Zynq-7010 FPGA, which includes a multiplier-less spike detection pipeline and a spiking-neural-network-based decoder mapped in the programmable logic. We tested the system on two publicly available datasets and achieved comparable results with state-of-the-art neural decoders that use more complex deep learning models. The system required 7.36 times fewer parameters than the smallest architecture tested on the same dataset. Moreover, by exploiting the spike sparsity property of the neural signal, the total amount of computations is reduced by about 90% during a test carried out on real recorded data. The low computational complexity of the chosen spike detection setup, combined with the power efficiency of spiking neural networks, makes this prototype a well-suited choice for low-power real-time neural decoding at the edge.

Brain-computer interfaces (BCI) can help people with motor disorders to regain their ability to communicate and interact with the surrounding environment. The majority of studies in this field pursue the development of BCI systems to enhance or restore the movement functionality of people with disability. Although the studies on the development of BCIs to restore hindlimb movements have shorter backgrounds compared to forelimb, several studies have investigated hindlimb BCIs and their results were promising. In the present study, we systematically reviewed the studies investigating the decoding of hindlimb movement parameters using intracortical signals. Three scientific databases (PubMed, Scopus, and Embase) were used to extract the articles and the experiment, recording, processing methods, and results of the included studies were discussed. Although several studies on upper-limb intracortical BCIs have been conducted on human subjects, almost all studies in hindlimb intracortical BCI field were performed on animal subjects. The most investigated task was walking on a treadmill, and the position of hindlimb joints and gait phase were the most studied continuous and discrete parameters, respectively. The included studies have mainly used spikes and linear decoders, which leaves the question of the effectiveness of using local field potentials and nonlinear decoders in this field unanswered. Although the results imply that hindlimb movement decoding using brain signals is feasible in laboratory conditions, further investigations are required to examine the hindlimb BCIs in real-life conditions.

Objective: This study proposes a new hybrid brain-computer interface (BCI) system to improve spelling accuracy and speed by stimulating P300 and steadystate visually evoked potential (SSVEP) in electroencephalography (EEG) signals. Methods: A frequency enhanced row and column (FERC) paradigm is proposed to incorporate the frequency coding into the row and column (RC) paradigm so that the P300 and SSVEP signals can be evoked simultaneously. A flicker (whiteblack) with a specific frequency from 6.0 to 11.5 Hz with an interval of 0.5 Hz is assigned to one row or column of a 6 x 6 layout, and the row/column flashes are carried out in a pseudorandom sequence. A wavelet and support vector machine (SVM) combination is adopted for P300 detection, an ensemble taskrelated component analysis (TRCA) method is used for SSVEP detection, and the two detection possibilities are fused using a weight control approach. Results: The implemented BCI speller achieved an accuracy of 94.29% and an information transfer rate (ITR) of 28.64 bit/min averaged across 10 subjects during the online tests. An accuracy of 96.86% is obtained during the offline calibration tests, higher than that of only using P300 (75.29%) or SSVEP (89.13%). The SVM in P300 outperformed the previous linear discrimination classifier and its variants (61.90-72.22%), and the ensemble TRCA in SSVEP outperformed the canonical correlation analysis method (73.33%). Conclusion: The proposed hybrid FERC stimulus paradigm can improve the performance of the speller compared with the classical single stimulus paradigm. The implemented speller can achieve comparable accuracy and ITR to its state-of-the-art counterparts with advanced detection algorithms. [ABSTRACT FROM AUTHOR]