Computational Neuroscience Research Articles

Exploring an EM-algorithm for banded regression in computational neuroscience

Abstract Regression is a principal tool for relating brain responses to stimuli or tasks in computational neuroscience. This often involves fitting linear models with predictors that can be divided into groups, such as distinct stimulus feature subsets in encoding models or features of different neural response channels in decoding models. When fitting such models, it can be relevant to allow differential shrinkage of the different groups of regression weights. Here, we explore a framework that allow for straightforward definition and estimation of such models. We present an expectation-maximization algorithm for tuning hyperparameters that control shrinkage of groups of weights. We highlight properties, limitations, and potential use-cases of the model using simulated data. Next, we explore the model in the context of a BOLD fMRI encoding analysis and an EEG decoding analysis. Finally, we discuss cases where the model can be useful and scenarios where regularization procedures complicate model interpretation.

ExaFlexHH: an exascale-ready, flexible multi-FPGA library for biologically plausible brain simulations

IntroductionIn-silico simulations are a powerful tool in modern neuroscience for enhancing our understanding of complex brain systems at various physiological levels. To model biologically realistic and detailed systems, an ideal simulation platform must possess: (1) high performance and performance scalability, (2) flexibility, and (3) ease of use for non-technical users. However, most existing platforms and libraries do not meet all three criteria, particularly for complex models such as the Hodgkin-Huxley (HH) model or for complex neuron-connectivity modeling such as gap junctions.MethodsThis work introduces ExaFlexHH, an exascale-ready, flexible library for simulating HH models on multi-FPGA platforms. Utilizing FPGA-based Data-Flow Engines (DFEs) and the dataflow programming paradigm, ExaFlexHH addresses all three requirements. The library is also parameterizable and compliant with NeuroML, a prominent brain-description language in computational neuroscience. We demonstrate the performance scalability of the platform by implementing a highly demanding extended-Hodgkin-Huxley (eHH) model of the Inferior Olive using ExaFlexHH.ResultsModel simulation results show linear scalability for unconnected networks and near-linear scalability for networks with complex synaptic plasticity, with a 1.99 × performance increase using two FPGAs compared to a single FPGA simulation, and 7.96 × when using eight FPGAs in a scalable ring topology. Notably, our results also reveal consistent performance efficiency in GFLOPS per watt, further facilitating exascale-ready computing speeds and pushing the boundaries of future brain-simulation platforms.DiscussionThe ExaFlexHH library shows superior resource efficiency, quantified in FLOPS per hardware resources, benchmarked against other competitive FPGA-based brain simulation implementations.

Computational Modeling of Extrasynaptic NMDA Receptors: Insights into Dendritic Signal Amplification Mechanisms

Dendritic structures play a pivotal role in the computational processes occurring within neurons. Signal propagation along dendrites relies on both passive conduction and active processes related to voltage-dependent ion channels. Among these channels, extrasynaptic N-methyl-D-aspartate channels (exNMDA) emerge as a significant contributor. Prior studies have mainly concentrated on interactions between synapses and nearby exNMDA (100 nm–10 µm from synapse), activated by presynaptic membrane glutamate. This study concentrates on the correlation between synaptic inputs and distal exNMDA (>100 µm), organized in clusters that function as signal amplifiers. Employing a computational model of a dendrite, we elucidate the mechanism underlying signal amplification in exNMDA clusters. Our findings underscore the pivotal role of the optimal spatial positioning of the NMDA cluster in determining signal amplification efficiency. Additionally, we demonstrate that exNMDA subunits characterized by a large conduction decay constant. Specifically, NR2B subunits exhibit enhanced effectiveness in signal amplification compared to subunits with steeper conduction decay. This investigation extends our understanding of dendritic computational processes by emphasizing the significance of distant exNMDA clusters as potent signal amplifiers. The implications of our computational model shed light on the spatial considerations and subunit characteristics that govern the efficiency of signal amplification in dendritic structures, offering valuable insights for future studies in neurobiology and computational neuroscience.

Neuromorphic Perception and Navigation for Mobile Robots: A Review

With the fast and unstoppable evolution of robotics and artificial intelligence, effective autonomous navigation in real-world scenarios has become one of the most pressing challenges in the literature. However, demanding requirements, such as real-time operation, energy and computational efficiency, robustness, and reliability, make most current solutions unsuitable for real-world challenges. Thus, researchers are fostered to seek innovative approaches, such as bio-inspired solutions. Indeed, animals have the intrinsic ability to efficiently perceive, understand, and navigate their unstructured surroundings. To do so, they exploit self-motion cues, proprioception, and visual flow in a cognitive process to map their environment and locate themselves within it. Computational neuroscientists aim to answer “how” and “why” such cognitive processes occur in the brain, to design novel neuromorphic sensors and methods that imitate biological processing. This survey aims to comprehensively review the application of brain-inspired strategies to autonomous navigation. Considering neuromorphic perception and asynchronous event processing, energy-efficient and adaptive learning, or the imitation of the working principles of brain areas that play a crucial role in navigation such as the hippocampus or the entorhinal cortex.

Exploring contactless techniques in multimodal emotion recognition: insights into diverse applications, challenges, solutions, and prospects

In recent years, emotion recognition has received significant attention, presenting a plethora of opportunities for application in diverse fields such as human–computer interaction, psychology, and neuroscience, to name a few. Although unimodal emotion recognition methods offer certain benefits, they have limited ability to encompass the full spectrum of human emotional expression. In contrast, Multimodal Emotion Recognition (MER) delivers a more holistic and detailed insight into an individual's emotional state. However, existing multimodal data collection approaches utilizing contact-based devices hinder the effective deployment of this technology. We address this issue by examining the potential of contactless data collection techniques for MER. In our tertiary review study, we highlight the unaddressed gaps in the existing body of literature on MER. Through our rigorous analysis of MER studies, we identify the modalities, specific cues, open datasets with contactless cues, and unique modality combinations. This further leads us to the formulation of a comparative schema for mapping the MER requirements of a given scenario to a specific modality combination. Subsequently, we discuss the implementation of Contactless Multimodal Emotion Recognition (CMER) systems in diverse use cases with the help of the comparative schema which serves as an evaluation blueprint. Furthermore, this paper also explores ethical and privacy considerations concerning the employment of contactless MER and proposes the key principles for addressing ethical and privacy concerns. The paper further investigates the current challenges and future prospects in the field, offering recommendations for future research and development in CMER. Our study serves as a resource for researchers and practitioners in the field of emotion recognition, as well as those intrigued by the broader outcomes of this rapidly progressing technology.

Bridging the Gap Between Biological Plausibility and Practicality in Neuron Modeling: Challenges and Perspectives

Neuron modeling has been a fundamental approach in computational neuroscience for understanding the dynamics and function of the central nervous system (CNS). Over the past decades, a plethora of mathematical models, ranging from the seminal Hodgkin-Huxley model to more complex multicompartmental and stochastic models, have been developed to capture the intricate behavior of neurons and their interactions. However, despite the significant advances in modeling, there remains a substantial disconnect between the complexity of the models and their practical applicability in day-to-day medical and laboratory settings. This article explores the challenges and limitations of current neuron modeling approaches, particularly focusing on the trade-off between biological realism and computational tractability. I discuss the variability of neuronal properties within and across different regions of the brain, which poses a significant challenge for developing models that can accurately represent the full complexity of the CNS. I also highlight the computational bottlenecks associated with simulating highly detailed, which often require extensive computational resources and specialized software. Considering these challenges, we emphasize the need for a balance between biological plausibility and practicality in neuron modeling. We discuss the role of simplified models, such as the leaky integrate-and-fire (LIF) and Izhikevich models, which sacrifice some biological detail in favor of computational efficiency and ease of use. These models have proven valuable for large-scale simulations of neural networks and have provided important insights into the collective behavior of neuronal populations. Furthermore, I explore the potential of data-driven approaches, such as machine learning and artificial neural networks, in bridging the gap between biological realism and practical applicability. These approaches can learn the dynamics of neuronal systems directly from experimental data, bypassing the need for explicit mathematical models. I present a simple example using linear regression to predict neuronal firing rates based on input features, showcasing the potential of machine learning techniques in capturing the complex relationships between neuronal variables. I also highlight the need for more extensive validation of models against experimental data and the development of standardized benchmarks for assessing model performance. In conclusion, while the quest for biologically plausible neuron models has driven significant advances in our understanding of the CNS, the disconnect between model complexity and practical applicability remains a major challenge. By embracing simplified models, data-driven approaches, and interdisciplinary collaborations, we can work towards the development of more efficient and practical neuron models that can bridge the gap between biological realism and computational feasibility, ultimately facilitating the translation of theoretical insights into clinical and experimental applications.

Linking fast and slow: The case for generative models.

A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable longer, more naturalistic neuronal recordings. The implicit opportunity for understanding the self-organised brain calls for new analysis methods that link temporal scales: from the order of milliseconds over which neuronal dynamics evolve, to the order of minutes, days, or even years over which experimental observations unfold. This review article demonstrates how hierarchical generative models and Bayesian inference help to characterise neuronal activity across different time scales. Crucially, these methods go beyond describing statistical associations among observations and enable inference about underlying mechanisms. We offer an overview of fundamental concepts in state-space modeling and suggest a taxonomy for these methods. Additionally, we introduce key mathematical principles that underscore a separation of temporal scales, such as the slaving principle, and review Bayesian methods that are being used to test hypotheses about the brain with multiscale data. We hope that this review will serve as a useful primer for experimental and computational neuroscientists on the state of the art and current directions of travel in the complex systems modelling literature.

Computational Language Modeling and the Promise of In Silico Experimentation

Abstract Language neuroscience currently relies on two major experimental paradigms: controlled experiments using carefully hand-designed stimuli, and natural stimulus experiments. These approaches have complementary advantages which allow them to address distinct aspects of the neurobiology of language, but each approach also comes with drawbacks. Here we discuss a third paradigm—in silico experimentation using deep learning-based encoding models—that has been enabled by recent advances in cognitive computational neuroscience. This paradigm promises to combine the interpretability of controlled experiments with the generalizability and broad scope of natural stimulus experiments. We show four examples of simulating language neuroscience experiments in silico and then discuss both the advantages and caveats of this approach.

Exploring Flip Flop memories and beyond: training Recurrent Neural Networks with key insights.

Training neural networks to perform different tasks is relevant across various disciplines. In particular, Recurrent Neural Networks (RNNs) are of great interest in Computational Neuroscience. Open-source frameworks dedicated to Machine Learning, such as Tensorflow and Keras have produced significant changes in the development of technologies that we currently use. This work contributes by comprehensively investigating and describing the application of RNNs for temporal processing through a study of a 3-bit Flip Flop memory implementation. We delve into the entire modeling process, encompassing equations, task parametrization, and software development. The obtained networks are meticulously analyzed to elucidate dynamics, aided by an array of visualization and analysis tools. Moreover, the provided code is versatile enough to facilitate the modeling of diverse tasks and systems. Furthermore, we present how memory states can be efficiently stored in the vertices of a cube in the dimensionally reduced space, supplementing previous results with a distinct approach.

Closing the loop: High-speed robotics with accelerated neuromorphic hardware.

The BrainScaleS-2 system is an established analog neuromorphic platform with versatile applications in the diverse fields of computational neuroscience and spike-based machine learning. In this work, we extend the system with a configurable realtime event interface that enables a tight coupling of its distinct analog network core to external sensors and actuators. The 1,000-fold acceleration of the emulated nerve cells allows us to target high-speed robotic applications that require precise timing on a microsecond scale. As a showcase, we present a closed-loop setup for commuting brushless DC motors: we utilize PyTorch to train a spiking neural network emulated on the analog substrate to control an electric motor from a sensory event stream. The presented system enables research in the area of event-driven controllers for high-speed robotics, including self-supervised and biologically inspired online learning for such applications.

Resolving uncertainty on the fly: modeling adaptive driving behavior as active inference.

Understanding adaptive human driving behavior, in particular how drivers manage uncertainty, is of key importance for developing simulated human driver models that can be used in the evaluation and development of autonomous vehicles. However, existing traffic psychology models of adaptive driving behavior either lack computational rigor or only address specific scenarios and/or behavioral phenomena. While models developed in the fields of machine learning and robotics can effectively learn adaptive driving behavior from data, due to their black box nature, they offer little or no explanation of the mechanisms underlying the adaptive behavior. Thus, generalizable, interpretable, computational models of adaptive human driving behavior are still rare. This paper proposes such a model based on active inference, a behavioral modeling framework originating in computational neuroscience. The model offers a principled solution to how humans trade progress against caution through policy selection based on the single mandate to minimize expected free energy. This casts goal-seeking and information-seeking (uncertainty-resolving) behavior under a single objective function, allowing the model to seamlessly resolve uncertainty as a means to obtain its goals. We apply the model in two apparently disparate driving scenarios that require managing uncertainty, (1) driving past an occluding object and (2) visual time-sharing between driving and a secondary task, and show how human-like adaptive driving behavior emerges from the single principle of expected free energy minimization.

Viscous dynamics associated with hypoexcitation and structural disintegration in neurodegeneration via generative whole-brain modeling.

Alzheimer's disease (AD) and behavioral variant frontotemporal dementia (bvFTD) lack mechanistic biophysical modeling in diverse, underrepresented populations. Electroencephalography (EEG) is a high temporal resolution, cost-effective technique for studying dementia globally, but lacks mechanistic models and produces non-replicable results. We developed a generative whole-brain model that combines EEG source-level metaconnectivity, anatomical priors, and a perturbational approach. This model was applied to Global South participants (AD, bvFTD, and healthy controls). Metaconnectivity outperformed pairwise connectivity and revealed more viscous dynamics in patients, with altered metaconnectivity patterns associated with multimodal disease presentation. The biophysical model showed that connectome disintegration and hypoexcitability triggered altered metaconnectivity dynamics and identified critical regions for brain stimulation. We replicated the main results in a second subset of participants for validation with unharmonized, heterogeneous recording settings. The results provide a novel agenda for developing mechanistic model-inspired characterization and therapies in clinical, translational, and computational neuroscience settings.

Digital Being: social media and the predictive mind.

Social media is implicated today in an array of mental health concerns. While concerns around social media have become mainstream, little is known about the specific cognitive mechanisms underlying the correlations seen in these studies or why we find it so hard to stop engaging with these platforms when things obviously begin to deteriorate for us. New advances in computational neuroscience, however, are now poised to shed light on this matter. In this paper, we approach the phenomenon of social media addiction through the lens of the active inference framework. According to this framework, predictive agents like us use a 'generative model' of the world to predict our own incoming sense data and act to minimize any discrepancy between the prediction and incoming signal (prediction error). In order to live well and be able to act effectively to minimize prediction error, it is vital that agents like us have a generative model, which not only accurately reflects the regularities of our complex environment but is also flexible and dynamic and able to stay accurate in volatile and turbulent circumstances. In this paper, we propose that some social media platforms are a spectacularly effective way of warping an agent's generative model and of arresting the model's ability to flexibly track and adapt to changes in the environment. We go on to investigate cases of digital tech, which do not have these adverse effects and suggest-based on the active inference framework-some ways to understand why some forms of digital technology pose these risks, while others do not.

Cognitive Computational Neuroscience of Language: Using Computational Models to Investigate Language Processing in the Brain

Cognitive Computational Neuroscience of Language: Using Computational Models to Investigate Language Processing in the Brain

Neural Field Dynamics: The Interplay of Local and Global Activity in Brain Function

Abstract: Recent advancements in neuroscience have spurred a paradigm shift away from strict localizationism towards an appreciation for the brain as a dynamic, interconnected network. This paper discusses the intricacies of neural field dynamics, emphasizing the role of local and global brain activities and their interplay in shaping cognitive processes and behaviors. We explore the concept of neural microfields and their collective influence at a distance, considering how even subthreshold electric currents generated by neural activity can modulate neuronal excitability and network states. The discussion extends to the brain's operation at the edge of criticality—a state theorized to optimize information processing and adaptability. We delve into how fluctuations in neural activity, potentially stemming from strong emotions or pathological states, can precipitate bifurcations in neuronal behavior, leading to various brain states or phase transitions. The implications of external electric fields, such as those used in neuromodulatory therapies, are also considered, highlighting their capacity to influence neuronal activity and alter systemic dynamics. This review integrates perspectives from computational neuroscience, dynamical systems theory, and electrophysiology to construct a holistic understanding of neural field dynamics and their significance in the functioning of the brain. The paper aims to theoretically contribute to the ongoing dialogue in neuroscience regarding the non-linear and emergent properties of neural networks, paving the way for future research and clinical innovations.

Deep latent variable joint cognitive modeling of neural signals and human behavior

As the field of computational cognitive neuroscience continues to expand and generate new theories, there is a growing need for more advanced methods to test the hypothesis of brain-behavior relationships. Recent progress in Bayesian cognitive modeling has enabled the combination of neural and behavioral models into a single unifying framework. However, these approaches require manual feature extraction, and lack the capability to discover previously unknown neural features in more complex data. Consequently, this would hinder the expressiveness of the models. To address these challenges, we propose a Neurocognitive Variational Autoencoder (NCVA) to conjoin high-dimensional EEG with a cognitive model in both generative and predictive modeling analyses. Importantly, our NCVA enables both the prediction of EEG signals given behavioral data and the estimation of cognitive model parameters from EEG signals. This novel approach can allow for a more comprehensive understanding of the triplet relationship between behavior, brain activity, and cognitive processes.

Ten simple rules for pushing boundaries of inclusion at academic events.

Inclusion at academic events is facing increased scrutiny as the communities these events serve raise their expectations for who can practically attend. Active efforts in recent years to bring more diversity to academic events have brought progress and created momentum. However, we must reflect on these efforts and determine which underrepresented groups are being disadvantaged. Inclusion at academic events is important to ensure diversity of discourse and opinion, to help build networks, and to avoid academic siloing. All of these contribute to the development of a robust and resilient academic field. We have developed these Ten Simple Rules both to amplify the voices that have been speaking out and to celebrate the progress of many Equity, Diversity, and Inclusivity practices that continue to drive the organisation of academic events. The Rules aim to raise awareness as well as provide actionable suggestions and tools to support these initiatives further. This aims to support academic organisations such as the Deep Learning Indaba, Neuromatch Academy, the IBRO-Simons Computational Neuroscience Imbizo, Biodiversity Information Standards (TDWG), Arabs in Neuroscience, FAIRPoints, and OLS (formerly Open Life Science). This article is a call to action for organisers to reevaluate the impact and reach of their inclusive practices.

Probing the Structure and Functional Properties of the Dropout-Induced Correlated Variability in Convolutional Neural Networks.

Computational neuroscience studies have shown that the structure of neural variability to an unchanged stimulus affects the amount of information encoded. Some artificial deep neural networks, such as those with Monte Carlo dropout layers, also have variable responses when the input is fixed. However, the structure of the trial-by-trial neural covariance in neural networks with dropout has not been studied, and its role in decoding accuracy is unknown. We studied the above questions in a convolutional neural network model with dropout in both the training and testing phases. We found that trial-by-trial correlation between neurons (i.e., noise correlation) is positive and low dimensional. Neurons that are close in a feature map have larger noise correlation. These properties are surprisingly similar to the findings in the visual cortex. We further analyzed the alignment of the main axes of the covariance matrix. We found that different images share a common trial-by-trial noise covariance subspace, and they are aligned with the global signal covariance. This evidence that the noise covariance is aligned with signal covariance suggests that noise covariance in dropout neural networks reduces network accuracy, which we further verified directly with a trial-shuffling procedure commonly used in neuroscience. These findings highlight a previously overlooked aspect of dropout layers that can affect network performance. Such dropout networks could also potentially be a computational model of neural variability.

Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch.

Spiking neural network simulations are a central tool in Computational Neuroscience, Artificial Intelligence, and Neuromorphic Engineering research. A broad range of simulators and software frameworks for such simulations exist with different target application areas. Among these, PymoNNto is a recent Python-based toolbox for spiking neural network simulations that emphasizes the embedding of custom code in a modular and flexible way. While PymoNNto already supports GPU implementations, its backend relies on NumPy operations. Here we introduce PymoNNtorch, which is natively implemented with PyTorch while retaining PymoNNto's modular design. Furthermore, we demonstrate how changes to the implementations of common network operations in combination with PymoNNtorch's native GPU support can offer speed-up over conventional simulators like NEST, ANNarchy, and Brian 2 in certain situations. Overall, we show how PymoNNto's modular and flexible design in combination with PymoNNtorch's GPU acceleration and optimized indexing operations facilitate research and development of spiking neural networks in the Python programming language.

Mean-field method for generic conductance-based integrate-and-fire neurons with finite timescales.

The construction of transfer functions in theoretical neuroscience plays an important role in determining the spiking rate behavior of neurons in networks. These functions can be obtained through various fitting methods, but the biological relevance of the parameters is not always clear. However, for stationary inputs, such functions can be obtained without the adjustment of free parameters by using mean-field methods. In this work, we expand current Fokker-Planck approaches to account for the concurrent influence of colored and multiplicative noise terms on generic conductance-based integrate-and-fire neurons. We reduce the resulting stochastic system through the application of the diffusion approximation to a one-dimensional Langevin equation. An effective Fokker-Planck is then constructed using Fox Theory, which is solved numerically using a newly developed double integration procedure to obtain the transfer function and the membrane potential distribution. The solution is capable of reproducing the transfer function and the stationary voltage distribution of simulated neurons across a wide range of parameters. The method can also be easily extended to account for different sources of noise with various multiplicative terms, and it can be used in other types of problems in principle.