Neuroscience is undergoing faster changes than ever before. Over 100 years our field qualitatively described and invasively manipulated single or few organisms to gain anatomical, physiological, and pharmacological insights. In the last 10 years neuroscience spawned quantitative big-sample datasets on microanatomy, synaptic connections, optogenetic brain-behavior assays, and high-level cognition. While growing data availability and information granularity have been amply discussed, we direct attention to a routinely neglected question: How will the unprecedented data richness shape data analysis practices? Statistical reasoning is becoming more central to distill neurobiological knowledge from healthy and pathological brain recordings. We believe that large-scale data analysis will use more models that are non-parametric, generative, mixing frequentist and Bayesian aspects, and grounded in different statistical inferences.
Neuroimaging research has predominantly drawn conclusions based on classical statistics, including null-hypothesis testing, t-tests, and ANOVA. Throughout recent years, statistical learning methods enjoy increasing popularity, including cross-validation, pattern classification, and sparsity-inducing regression. These two methodological families used for neuroimaging data analysis can be viewed as two extremes of a continuum. Yet, they originated from different historical contexts, build on different theories, rest on different assumptions, evaluate different outcome metrics, and permit differe…
Many studies in biomedical and health sciences involve small sample sizes due to logistic or financial constraints. Often, identifying weak (but scientifically interesting) associations between a set of predictors and a response necessitates pooling datasets from multiple diverse labs or groups. While there is a rich literature in statistical machine learning to address distributional shifts and inference in multi-site datasets, it is less clear ${\it when}$ such pooling is guaranteed to help (and when it does not) -- independent of the inference algorithms we use. In this paper, we present a …
We organized a workshop on the "Present and Future Frameworks of Theoretical Neuroscience", with the support of the National Science Foundation. The objective was to identify the challenges and strategies that this field will need to tackle in order to incorporate vast and multi-scale streams of experimental data from the technologies developed by the BRAIN initiative. The participants, divided in workgroups, identified five key areas that, while not exhaustive, cover multiple aspects of current challenges needed to be developed: Dynamics-statistics; multi-scale integration; coding; brain-body…
Many experimental paradigms in neuroscience involve driving the nervous system with periodic sensory stimuli. Neural signals recorded using a variety of techniques will then include phase-locked oscillations at the stimulation frequency. The analysis of such data often involves standard univariate statistics such as T-tests, conducted on the Fourier amplitude components (ignoring phase), either to test for the presence of a signal, or to compare signals across different conditions. However, the assumptions of these tests will sometimes be violated because amplitudes are not normally distribute…
Mammalian brain is one of the most complex objects in the known universe, as it governs every aspect of animal's and human behavior. It is fair to say that we have a very limited knowledge of how the brain operates and functions. Computational Neuroscience is a scientific discipline that attempts to understand and describe the brain in terms of mathematical modeling. This user-friendly review tries to introduce this relatively new field to mathematicians and physicists by showing examples of recent trends. It also discusses briefly future prospects for constructing an integrated theory of brai…
This essay is presented with two principal objectives in mind: first, to document the prevalence of fractals at all levels of the nervous system, giving credence to the notion of their functional relevance; and second, to draw attention to the as yet still unresolved issues of the detailed relationships among power law scaling, self-similarity, and self-organized criticality. As regards criticality, I will document that it has become a pivotal reference point in Neurodynamics. Furthermore, I will emphasize the not yet fully appreciated significance of allometric control processes. For dynamic …
Neuroscience is undergoing dramatic progress because of the vast data streams derived from the new technologies product of the BRAIN initiative and other enterprises. As any other scientific field, neuroscience benefits from having clear definitions of its theoretical components and their interactions. This allows generating theories that integrate knowledge, provide mechanistic insights, and predict results under new experimental conditions. However, theoretical neuroscience is a heterogeneous field that has not yet agreed on how to build theories or whether it is desirable to have an overarc…
The last decades saw dramatic progress in brain research. These advances were often buttressed by probing single variables to make circumscribed discoveries, typically through null hypothesis significance testing. New ways for generating massive data fueled tension between the traditional methodology, used to infer statistically relevant effects in carefully-chosen variables, and pattern-learning algorithms, used to identify predictive signatures by searching through abundant information. In this article, we detail the antagonistic philosophies behind two quantitative approaches: certifying ro…
Functional optical imaging in neuroscience is rapidly growing with the development of new optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. In this review, we cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.
Technological advances have dramatically expanded our ability to probe multi-neuronal dynamics and connectivity in the brain. However, our ability to extract a simple conceptual understanding from complex data is increasingly hampered by the lack of theoretically principled data analytic procedures, as well as theoretical frameworks for how circuit connectivity and dynamics can conspire to generate emergent behavioral and cognitive functions. We review and outline potential avenues for progress, including new theories of high dimensional data analysis, the need to analyze complex artificial ne…
Connectomics and network neuroscience offer quantitative scientific frameworks for modeling and analyzing networks of structurally and functionally interacting neurons, neuronal populations, and macroscopic brain areas. This shift in perspective and emphasis on distributed brain function has provided fundamental insight into the role played by the brain's network architecture in cognition, disease, development, and aging. In this chapter, we review the core concepts of human connectomics at the macroscale. From the construction of networks using functional and diffusion MRI data, to their subs…
A common feature in many neuroscience datasets is the presence of hierarchical data structures, most commonly recording the activity of multiple neurons in multiple animals across multiple trials. Accordingly, the measurements constituting the dataset are not independent, even though the traditional statistical analyses often applied in such cases (e.g., Students t-test) treat them as such. The hierarchical bootstrap has been shown to be an effective tool to accurately analyze such data and while it has been used extensively in the statistical literature, its use is not widespread in neuroscie…
This paper presents the first comprehensive tutorial on a promising research field located at the frontier of two well-established domains: Neurosciences and wireless communications, motivated by the ongoing efforts to define how the sixth generation of mobile networks (6G) will be. In particular, this tutorial first provides a novel integrative approach that bridges the gap between these two, seemingly disparate fields. Then, we present the state-of-the-art and key challenges of these two topics. In particular, we propose a novel systematization that divides the contributions into two groups,…
The field of neuroscience is facing an unprecedented expanse in the volume and diversity of available data. Traditionally, network models have provided key insights into the structure and function of the brain. With the advent of big data in neuroscience, both more sophisticated models capable of characterizing the increasing complexity of the data and novel methods of quantitative analysis are needed. Recently multilayer networks, a mathematical extension of traditional networks, have gained increasing popularity in neuroscience due to their ability to capture the full information of multi-mo…
Data-driven techniques for translational neuroscience and personalized neuro-health
University of Maryland Baltimore County（马里兰大学巴尔的摩郡分校）；Texas Tech University（得克萨斯理工大学）；University of Minnesota（明尼苏达大学）；University of Nebraska Lincoln（内布拉斯加大学林肯分校）
We extracted and processed abstract data from the SFN annual meeting abstracts during the period 2001-2006, using techniques and software from natural language processing, database management, and data visualization and analysis. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. The resulting co-author graph in 2006, for example, had 39,645 nodes (with an estimated 6% error rate in our disambiguation of similar author nam…
To learn how cognition is implemented in the brain, we must build computational models that can perform cognitive tasks, and test such models with brain and behavioral experiments. Cognitive science has developed computational models of human cognition, decomposing task performance into computational components. However, its algorithms still fall short of human intelligence and are not grounded in neurobiology. Computational neuroscience has investigated how interacting neurons can implement component functions of brain computation. However, it has yet to explain how those components interact …
Istanbul Technical University（伊斯坦布尔理工大学）；University of Dundee（邓迪大学）；University of Sousse（苏塞大学）
Noninvasive medical neuroimaging has yielded many discoveries about the brain connectivity. Several substantial techniques mapping morphological, structural and functional brain connectivities were developed to create a comprehensive road map of neuronal activities in the human brain -namely brain graph. Relying on its non-Euclidean data type, graph neural network (GNN) provides a clever way of learning the deep graph structure and it is rapidly becoming the state-of-the-art leading to enhanced performance in various network neuroscience tasks. Here we review current GNN-based methods, highlig…
Linguistics and Human Brain: A Perspective of Computational Neuroscience
Institute of AI and Robotics, College of Intelligent Robotics and Advanced Manufacturing, Fudan University（人工智能与机器人研究院，智能机器人与先进制造学院，复旦大学）；Department of Language Science and Technology, The Hong Kong Polytechnic University（语言科学与技术系，香港理工大学）；Department of Computing, The Hong Kong Polytechnic University（计算系，香港理工大学）
Neuroscience is undergoing a period of rapid experimental progress and expansion. New mathematical tools, previously unknown in the neuroscience community, are now being used to tackle fundamental questions and analyze emerging data sets. Consistent with this trend, the last decade has seen an uptick in the use of topological ideas and methods in neuroscience. In this talk I will survey recent applications of topology in neuroscience, and explain why topology is an especially natural tool for understanding neural codes. Note: This is a write-up of my talk for the Current Events Bulletin, held …
When designing experimental studies with human participants, experimenters must decide how many trials each participant will complete, as well as how many participants to test. Most discussion of statistical power (the ability of a study design to detect an effect) has focussed on sample size, and assumed sufficient trials. Here we explore the influence of both factors on statistical power, represented as a two-dimensional plot on which iso-power contours can be visualised. We demonstrate the conditions under which the number of trials is particularly important, i.e. when the within-participan…
Neuroscientists frequently use a certain statistical reasoning to establish the existence of distinct neuronal processes in the brain. We show that this reasoning is flawed and that the large corresponding literature needs reconsideration. We illustrate the fallacy with a recent study that received an enormous press coverage because it concluded that humans detect deceit better if they use unconscious processes instead of conscious deliberations. The study was published under a new open-data policy that enabled us to reanalyze the data with more appropriate methods. We found that unconscious p…
Neuroscience has focused on the detailed implementation of computation, studying neural codes, dynamics and circuits. In machine learning, however, artificial neural networks tend to eschew precisely designed codes, dynamics or circuits in favor of brute force optimization of a cost function, often using simple and relatively uniform initial architectures. Two recent developments have emerged within machine learning that create an opportunity to connect these seemingly divergent perspectives. First, structured architectures are used, including dedicated systems for attention, recursion and var…
While probabilistic models describe the dependence structure between observed variables, causal models go one step further: they predict, for example, how cognitive functions are affected by external interventions that perturb neuronal activity. In this review and perspective article, we introduce the concept of causality in the context of cognitive neuroscience and review existing methods for inferring causal relationships from data. Causal inference is an ambitious task that is particularly challenging in cognitive neuroscience. We discuss two difficulties in more detail: the scarcity of int…
Given the constant rise in quantity and quality of data obtained from neural systems on many scales ranging from molecular to systems', information-theoretic analyses became increasingly necessary during the past few decades in the neurosciences. Such analyses can provide deep insights into the functionality of such systems, as well as a rigid mathematical theory and quantitative measures of information processing in both healthy and diseased states of neural systems. This chapter will present a short introduction to the fundamentals of information theory, especially suited for people having a…
"Task-relevant autoencoding" enhances machine learning for human neuroscience
University of California, Irvine（加州大学欧文分校）；Université de Montréal（蒙特利尔大学）；Centre de recherche de l’institut universitaire en santé mentale de Montréal（蒙特利尔大学精神健康研究所研究中心）；ATR Computational Neuroscience Laboratories（ATR计算神经科学实验室）；University of Florida（佛罗里达大学）；University of California Los Angeles（加州大学洛杉矶分校）；RIKEN Center for Brain Science（理化学研究所脑科学中心）
In order to gain a mechanistic understanding of how tinnitus emerges in the brain, we must build biologically plausible computational models that mimic both tinnitus development and perception, and test the tentative models with brain and behavioral experiments. With a special focus on tinnitus research, we review recent work at the intersection of artificial intelligence, psychology and neuroscience, indicating a new research agenda that follows the idea that experiments will yield theoretical insight only when employed to test brain-computational models. This view challenges the popular beli…
Sparse coding networks, which utilize unsupervised learning to maximize coding efficiency, have successfully reproduced response properties found in primary visual cortex \cite{AN:OlshausenField96}. However, conventional sparse coding models require that the coding circuit can fully sample the sensory data in a one-to-one fashion, a requirement not supported by experimental data from the thalamo-cortical projection. To relieve these strict wiring requirements, we propose a sparse coding network constructed by introducing synaptic learning in the framework of compressed sensing. We demonstrate …
Researchers within the Human Brain Project and related projects have in the last couple of years expanded their needs for high-performance computing infrastructures. The needs arise from a diverse set of science challenges that range from large-scale simulations of brain models to processing of extreme-scale experimental data sets. The ICEI project, which is in the process of creating a distributed infrastructure optimised for brain research, started to build-up a set of benchmarks that reflect the diversity of applications in this field. In this paper we analyse the performance of some select…
University of Padova（帕多瓦大学）；Jahangirnagar University（贾汉吉尔纳加尔大学）；American International University - Bangladesh（孟加拉美国国际大学）；University of Sheffield（谢菲尔德大学）；Anglia Ruskin University（安格利亚鲁斯金大学）；Saitama University（埼玉大学）；University of Stirling（斯特灵大学）
Rapid popularity of Internet of Things (IoT) and cloud computing permits neuroscientists to collect multilevel and multichannel brain data to better understand brain functions, diagnose diseases, and devise treatments. To ensure secure and reliable data communication between end-to-end (E2E) devices supported by current IoT and cloud infrastructure, trust management is needed at the IoT and user ends. This paper introduces a Neuro-Fuzzy based Brain-inspired trust management model (TMM) to secure IoT devices and relay nodes, and to ensure data reliability. The proposed TMM utilizes node behavio…
We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes---neural connectivity maps of the brain---using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at http://openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive com…
The human brain is a complex network that supports mental function. The nascent field of network neuroscience applies tools from mathematics to neuroimaging data in the hopes of shedding light on cognitive function. A critical question arising from these empirical studies is how to modulate a human brain network to treat cognitive deficits or enhance mental abilities. While historically a number of tools have been employed to modulate mental states (such as cognitive behavioral therapy and brain stimulation), theoretical frameworks to guide these interventions - and to optimize them for clinic…
If modern computers are sometimes superior to humans in some specialized tasks such as playing chess or browsing a large database, they can't beat the efficiency of biological vision for such simple tasks as recognizing and following an object in a complex cluttered background. We present in this paper our attempt at outlining the dynamical, parallel and event-based representation for vision in the architecture of the central nervous system. We will illustrate this on static natural images by showing that in a signal matching framework, a L/LN (linear/non-linear) cascade may efficiently transf…
Integrative neurocybernetic modeling in the era of large-scale neuroscience
Champalimaud Centre for the Unknown（Champalimaud 未知中心）；Janelia Research Campus（Janelia 研究campus）；Harvard University（哈佛大学）；Yale University（哥伦比亚大学）；École Polytechnique Fédérale de Lausanne (EPFL)（瑞士联邦理工学院）；RyvivyR Inc（RyvivyR 公司）
TRACE: Contrastive learning for multi-trial time-series data in neuroscience
Hertie Institute for AI in Brain Health, University of Tübingen（蒂耶脑健康人工智能研究所，蒂宾根大学）；Institute for Ophthalmic Research, University of Tübingen（眼科学研究 institute，蒂宾根大学）；Centre for Integrative Neuroscience, University of Tübingen（整合神经科学中心，蒂宾根大学）；Department of Neuroscience, Baylor College of Medicine（贝勒医学院神经科学系）；Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine（贝勒医学院神经科学与人工智能中心）；Institute for Computer Science and Campus Institute Data Science, University of Göttingen（哥廷根大学计算机科学研究所与校园数据科学研究所）；Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine（斯坦福大学医学院拜尔斯眼科研究所眼科系）；Stanford Bio-X, Stanford University（斯坦福大学生物-X项目，斯坦福大学）；Wu Tsai Neurosciences Institute, Stanford University（斯坦福大学吴氏神经科学研究所）；Department of Electrical Engineering, Stanford University（斯坦福大学电气工程系）
We are entering an age of `big' computational neuroscience, in which neural network models are increasing in size and in numbers of underlying data sets. Consolidating the zoo of models into large-scale models simultaneously consistent with a wide range of data is only possible through the effort of large teams, which can be spread across multiple research institutions. To ensure that computational neuroscientists can build on each other's work, it is important to make models publicly available as well-documented code. This chapter describes such an open-source model, which relates the connect…
Data-Driven Network Neuroscience: On Data Collection and Benchmark
Nanyang Technological University（南洋理工大学）；The University of Auckland（奥克兰大学）；General Electric Healthcare Magnetic Resonance（通用电气医疗磁共振）；Mātai Medical Research Institute（Mātai医学研究所）
Justus-Liebig University Giessen（吉森尤斯利比希大学）；Columbia University（哥伦比亚大学）
Neural network models can now recognise images, understand text, translate languages, and play many human games at human or superhuman levels. These systems are highly abstracted, but are inspired by biological brains and use only biologically plausible computations. In the coming years, neural networks are likely to become less reliant on learning from massive labelled datasets, and more robust and generalisable in their task performance. From their successes and failures, we can learn about the computational requirements of the different tasks at which brains excel. Deep learning also provid…
The cognitive frame in which most neuropsychological research on the neural basis of behavior is conducted contains the assumption that brain mechanisms per se fully suffice to explain all psychologically described phenomena. This assumption stems from the idea that the brain is made up entirely of material particles and fields, and that all causal mechanisms must therefore be formulated solely in terms of properties of these elements. One consequence of this stance is that psychological terms having intrinsic mentalistic and/or experiential content (terms such as "feeling," "knowing," and "ef…
Individual neurons often produce highly variable responses over nominally identical trials, reflecting a mixture of intrinsic "noise" and systematic changes in the animal's cognitive and behavioral state. Disentangling these sources of variability is of great scientific interest in its own right, but it is also increasingly inescapable as neuroscientists aspire to study more complex and naturalistic animal behaviors. In these settings, behavioral actions never repeat themselves exactly and may rarely do so even approximately. Thus, new statistical methods that extract reliable features of neur…
Generative causal testing to bridge data-driven models and scientific theories in language neuroscience
Computer Science Department, University of Texas at Austin（德克萨斯大学计算机科学系）；Microsoft Research（微软研究院）；Neurosurgery Department, University of California（加州大学神经外科系）；EECS Department, University of California（加州大学电子工程与计算机科学系）；Statistics Department, University of California（加州大学统计学系）；Center for Computational Biology, University of California（加州大学计算生物学中心）；Neuroscience Department, University of California（加州大学神经科学系）
The fast-growing field of Computational Cognitive Neuroscience is on track to meet its first crisis. A large number of papers in this nascent field are developing and testing novel analysis methods using the same stimuli and neuroimaging datasets. Publication bias and confirmatory exploration will result in overfitting to the limited available data. The field urgently needs to collect more good quality open neuroimaging data using a variety of experimental stimuli, to test the generalisability of current published results, and allow for more robust results in future work.
Despite the recent success of neural network models in mimicking animal performance on visual perceptual tasks, critics worry that these models fail to illuminate brain function. We take it that a central approach to explanation in systems neuroscience is that of mechanistic modeling, where understanding the system is taken to require fleshing out the parts, organization, and activities of a system, and how those give rise to behaviors of interest. However, it remains somewhat controversial what it means for a model to describe a mechanism, and whether neural network models qualify as explanat…
Multivariate pattern analysis (MVPA) or brain decoding methods have become standard practice in analysing fMRI data. Although decoding methods have been extensively applied in Brain Computing Interfaces (BCI), these methods have only recently been applied to time-series neuroimaging data such as MEG and EEG to address experimental questions in Cognitive Neuroscience. In a tutorial-style review, we describe a broad set of options to inform future time-series decoding studies from a Cognitive Neuroscience perspective. Using example MEG data, we illustrate the effects that different options in th…
CNeuroMod-THINGS, a densely-sampled fMRI dataset for visual neuroscience
Max Planck Institute for Human Cognitive and Brain Sciences（马克斯·普朗克人类认知与脑科学研究所）；Centre de recherche de l’Institut universitaire de gériatrie de Montréal（蒙特利尔大学老年医学研究中心）；Université de Montréal（蒙特利尔大学）；Martin Luther University Halle-Wittenberg（马丁·路德大学哈勒-维滕贝格）；Université de Genève（日内瓦大学）；Justus Liebig University Giessen（吉森尤斯图斯·李比希大学）；Center for Mind, Brain and Behavior (CMBB), Universities of Marburg, Giessen, and Darmstadt（心智、大脑与行为中心（马尔堡大学、吉森大学和达姆施塔特工业大学））
