Personalized brain network models for assessing structure-function relationships

Differences in fMRI-based connectivity during abstinence or interventions between heroin-dependent individuals and healthy controls

The substantial personal, societal, and economic impacts of opioid addiction drive research investigating how opioid addiction affects the brain, and whether therapies attenuate addiction-related metrics of brain function. Evaluating the connectivity between brain regions is a useful approach to characterise the effects of opioid addiction on the brain. This work is a systematic narrative review of studies investigating the effect of abstinence or interventions on connectivity in people who are dependent on heroin (HD) and healthy controls (HC). We found that HD typically showed weaker connectivity than HC between three functional networks: the Executive Control Network, Default Mode Network, and the Salience Network. Abstinence and Transcranial Magnetic Stimulation (TMS) both attenuated differences in connectivity between HD and HC, often by strengthening connectivity in HD. We observed that increased connectivity due to abstinence or TMS consistently related to decreased craving/risk of relapse. Using these findings, we present an "urge and action framework" relating therapeutic factors contributing to craving/relapse, connectivity results, and neurobiological models of HD. To inform future research, we critically assessed the impact of study design and analysis methods on study results. We conclude that the weaker between-network connectivity in HD and HC and its relationship to craving/relapse merits further exploration as a biomarker and target for therapeutic interventions.

Beyond the usual suspects: multi-factorial computational models in the search for neurodegenerative disease mechanisms

From Alzheimer's disease to amyotrophic lateral sclerosis, the molecular cascades underlying neurodegenerative disorders remain poorly understood. The clinical view of neurodegeneration is confounded by symptomatic heterogeneity and mixed pathology in almost every patient. While the underlying physiological alterations originate, proliferate, and propagate potentially decades before symptomatic onset, the complexity and inaccessibility of the living brain limit direct observation over a patient's lifespan. Consequently, there is a critical need for robust computational methods to support the search for causal mechanisms of neurodegeneration by distinguishing pathogenic processes from consequential alterations, and inter-individual variability from intra-individual progression. Recently, promising advances have been made by data-driven spatiotemporal modeling of the brain, based on in vivo neuroimaging and biospecimen markers. These methods include disease progression models comparing the temporal evolution of various biomarkers, causal models linking interacting biological processes, network propagation models reproducing the spatial spreading of pathology, and biophysical models spanning cellular- to network-scale phenomena. In this review, we discuss various computational approaches for integrating cross-sectional, longitudinal, and multi-modal data, primarily from large observational neuroimaging studies, to understand (i) the temporal ordering of physiological alterations, i(i) their spatial relationships to the brain's molecular and cellular architecture, (iii) mechanistic interactions between biological processes, and (iv) the macroscopic effects of microscopic factors. We consider the extents to which computational models can evaluate mechanistic hypotheses, explore applications such as improving treatment selection, and discuss how model-informed insights can lay the groundwork for a pathobiological redefinition of neurodegenerative disorders.

Adolescent maturation of cortical excitation-inhibition balance based on individualized biophysical network modeling

The balance of excitation and inhibition is a key functional property of cortical microcircuits which changes through the lifespan. Adolescence is considered a crucial period for the maturation of excitation-inhibition balance. This has been primarily observed in animal studies, yet human in vivo evidence on adolescent maturation of the excitation-inhibition balance at the individual level is limited. Here, we developed an individualized in vivo marker of regional excitation-inhibition balance in human adolescents, estimated using large-scale simulations of biophysical network models fitted to resting-state functional magnetic resonance imaging data from two independent cross-sectional (N = 752) and longitudinal (N = 149) cohorts. We found a widespread relative increase of inhibition in association cortices paralleled by a relative age-related increase of excitation, or lack of change, in sensorimotor areas across both datasets. This developmental pattern co-aligned with multiscale markers of sensorimotor-association differentiation. The spatial pattern of excitation-inhibition development in adolescence was robust to inter-individual variability of structural connectomes and modeling configurations. Notably, we found that alternative simulation-based markers of excitation-inhibition balance show a variable sensitivity to maturational change. Taken together, our study highlights an increase of inhibition during adolescence in association areas using cross sectional and longitudinal data, and provides a robust computational framework to estimate microcircuit maturation in vivo at the individual level.

Coarse graining and criticality in the human connectome

In the face of the stupefying complexity of the human brain, network analysis is a most useful tool that allows one to greatly simplify the problem, typically by approximating the billions of neurons making up the brain by means of a coarse-grained picture with a practicable number of nodes. But even such relatively small and coarse networks, such as the human connectome with its 100-1000 nodes, may present challenges for some computationally demanding analyses that are incapable of handling networks with more than a handful of nodes. With such applications in mind, we set out to study the extent to which dynamical behavior and critical phenomena in the brain may be preserved following a severe coarse-graining procedure. Thus we proceeded to further coarse grain the human connectome by taking a modularity-based approach, the goal being to produce a network of a relatively small number of modules. After finding that the qualitative dynamical behavior of the coarse-grained networks reflected that of the original networks, albeit to a less pronounced extent, we then formulated a hypothesis based on the coarse-grained networks in the context of criticality in the Wilson-Cowan and Ising models, and we verified the hypothesis, which connected a transition value of the former with the critical temperature of the latter, using the original networks. This preservation of dynamical and critical behavior following a severe coarse-graining procedure, in principle, allows for the drawing of similar qualitative conclusions by analyzing much smaller networks, which opens the door for studying the human connectome in contexts typically regarded as computationally intractable, such as Integrated Information Theory and quantum models of the human brain.

Open datasets and code for multi-scale relations on structure, function and neuro-genetics in the human brain

The human brain is an extremely complex network of structural and functional connections that operate at multiple spatial and temporal scales. Investigating the relationship between these multi-scale connections is critical to advancing our comprehension of brain function and disorders. However, accurately predicting structural connectivity from its functional counterpart remains a challenging pursuit. One of the major impediments is the lack of public repositories that integrate structural and functional networks at diverse resolutions, in conjunction with modular transcriptomic profiles, which are essential for comprehensive biological interpretation. To mitigate this limitation, our contribution encompasses the provision of an open-access dataset consisting of derivative matrices of functional and structural connectivity across multiple scales, accompanied by code that facilitates the investigation of their interrelations. We also provide additional resources focused on neuro-genetic associations of module-level network metrics, which present promising opportunities to further advance research in the field of network neuroscience, particularly concerning brain disorders.

Macroscopic resting-state brain dynamics are best described by linear models

It is typically assumed that large networks of neurons exhibit a large repertoire of nonlinear behaviours. Here we challenge this assumption by leveraging mathematical models derived from measurements of local field potentials via intracranial electroencephalography and of whole-brain blood-oxygen-level-dependent brain activity via functional magnetic resonance imaging. We used state-of-the-art linear and nonlinear families of models to describe spontaneous resting-state activity of 700 participants in the Human Connectome Project and 122 participants in the Restoring Active Memory project. We found that linear autoregressive models provide the best fit across both data types and three performance metrics: predictive power, computational complexity and the extent of the residual dynamics unexplained by the model. To explain this observation, we show that microscopic nonlinear dynamics can be counteracted or masked by four factors associated with macroscopic dynamics: averaging over space and over time, which are inherent to aggregated macroscopic brain activity, and observation noise and limited data samples, which stem from technological limitations. We therefore argue that easier-to-interpret linear models can faithfully describe macroscopic brain dynamics during resting-state conditions.

Personalized dynamic network models of the human brain as a future tool for planning and optimizing epilepsy therapy

Epilepsy is a common neurological disorder, with one third of patients not responding to currently available antiepileptic drugs. The proportion of pharmacoresistant epilepsies has remained unchanged for many decades. To cure epilepsy and control seizures requires a paradigm shift in the development of new approaches to epilepsy diagnosis and treatment. Contemporary medicine has benefited from the exponential growth of computational modeling, and the application of network dynamics theory to understanding and treating human brain disorders. In epilepsy, the introduction of these approaches has led to personalized epileptic network modeling that can explore the patient's seizure genesis and predict the functional impact of resection on its individual network's propensity to seize. The application of the dynamic systems approach to neurostimulation therapy of epilepsy allows designing stimulation strategies that consider the patient's seizure dynamics and long-term fluctuations in the stability of their epileptic networks. In this article, we review, in a nontechnical fashion suitable for a broad neuroscientific audience, recent progress in personalized dynamic brain network modeling that is shaping the future approach to the diagnosis and treatment of epilepsy.

PPA: Principal parcellation analysis for brain connectomes and multiple traits

Our understanding of the structure of the brain and its relationships with human traits is largely determined by how we represent the structural connectome. Standard practice divides the brain into regions of interest (ROIs) and represents the connectome as an adjacency matrix having cells measuring connectivity between pairs of ROIs. Statistical analyses are then heavily driven by the (largely arbitrary) choice of ROIs. In this article, we propose a human trait prediction framework utilizing a tractography-based representation of the brain connectome, which clusters fiber endpoints to define a data-driven white matter parcellation targeted to explain variation among individuals and predict human traits. This leads to Principal Parcellation Analysis (PPA), representing individual brain connectomes by compositional vectors building on a basis system of fiber bundles that captures the connectivity at the population level. PPA eliminates the need to choose atlases and ROIs a priori, and provides a simpler, vector-valued representation that facilitates easier statistical analysis compared to the complex graph structures encountered in classical connectome analyses. We illustrate the proposed approach through applications to data from the Human Connectome Project (HCP) and show that PPA connectomes improve power in predicting human traits over state-of-the-art methods based on classical connectomes, while dramatically improving parsimony and maintaining interpretability. Our PPA package is publicly available on GitHub, and can be implemented routinely for diffusion image data.

Alzheimer's Disease: Insights from Large-Scale Brain Dynamics Models

Alzheimer's disease (AD) is a degenerative brain disease, and the condition is difficult to assess. In the past, numerous brain dynamics models have made remarkable contributions to neuroscience and the brain from the microcosmic to the macroscopic scale. Recently, large-scale brain dynamics models have been developed based on dual-driven multimodal neuroimaging data and neurodynamics theory. These models bridge the gap between anatomical structure and functional dynamics and have played an important role in assisting the understanding of the brain mechanism. Large-scale brain dynamics have been widely used to explain how macroscale neuroimaging biomarkers emerge from potential neuronal population level disturbances associated with AD. In this review, we describe this emerging approach to studying AD that utilizes a biophysically large-scale brain dynamics model. In particular, we focus on the application of the model to AD and discuss important directions for the future development and analysis of AD models. This will facilitate the development of virtual brain models in the field of AD diagnosis and treatment and add new opportunities for advancing clinical neuroscience.

Global excitability and network structure in the human brain

We utilize a model of Wilson-Cowan oscillators to investigate structure-function relationships in the human brain by means of simulations of the spontaneous dynamics of brain networks generated through human connectome data. This allows us to establish relationships between the global excitability of such networks and global structural network quantities for connectomes of two different sizes for a number of individual subjects. We compare the qualitative behavior of such correlations between biological networks and shuffled networks, the latter generated by shuffling the pairwise connectivities of the former while preserving their distribution. Our results point towards a remarkable propensity of the brain to achieve a trade-off between low network wiring cost and strong functionality, and highlight the unique capacity of brain network topologies to exhibit a strong transition from an inactive state to a globally excited one.

Within-subject reproducibility varies in multi-modal, longitudinal brain networks

Network neuroscience provides important insights into brain function by analyzing complex networks constructed from diffusion Magnetic Resonance Imaging (dMRI), functional MRI (fMRI) and Electro/Magnetoencephalography (E/MEG) data. However, in order to ensure that results are reproducible, we need a better understanding of within- and between-subject variability over long periods of time. Here, we analyze a longitudinal, 8 session, multi-modal (dMRI, and simultaneous EEG-fMRI), and multiple task imaging data set. We first confirm that across all modalities, within-subject reproducibility is higher than between-subject reproducibility. We see high variability in the reproducibility of individual connections, but observe that in EEG-derived networks, during both rest and task, alpha-band connectivity is consistently more reproducible than connectivity in other frequency bands. Structural networks show a higher reliability than functional networks across network statistics, but synchronizability and eigenvector centrality are consistently less reliable than other network measures across all modalities. Finally, we find that structural dMRI networks outperform functional networks in their ability to identify individuals using a fingerprinting analysis. Our results highlight that functional networks likely reflect state-dependent variability not present in structural networks, and that the type of analysis should depend on whether or not one wants to take into account state-dependent fluctuations in connectivity.

Moving from phenomenological to predictive modelling: Progress and pitfalls of modelling brain stimulation in-silico

Brain stimulation is an increasingly popular neuromodulatory tool used in both clinical and research settings; however, the effects of brain stimulation, particularly those of non-invasive stimulation, are variable. This variability can be partially explained by an incomplete mechanistic understanding, coupled with a combinatorial explosion of possible stimulation parameters. Computational models constitute a useful tool to explore the vast sea of stimulation parameters and characterise their effects on brain activity. Yet the utility of modelling stimulation in-silico relies on its biophysical relevance, which needs to account for the dynamics of large and diverse neural populations and how underlying networks shape those collective dynamics. The large number of parameters to consider when constructing a model is no less than those needed to consider when planning empirical studies. This piece is centred on the application of phenomenological and biophysical models in non-invasive brain stimulation. We first introduce common forms of brain stimulation and computational models, and provide typical construction choices made when building phenomenological and biophysical models. Through the lens of four case studies, we provide an account of the questions these models can address, commonalities, and limitations across studies. We conclude by proposing future directions to fully realise the potential of computational models of brain stimulation for the design of personalized, efficient, and effective stimulation strategies.

Communication dynamics in the human connectome shape the cortex-wide propagation of direct electrical stimulation

Communication between gray matter regions underpins all facets of brain function. We study inter-areal communication in the human brain using intracranial EEG recordings, acquired following 29,055 single-pulse direct electrical stimulations in a total of 550 individuals across 20 medical centers (average of 87 ± 37 electrode contacts per subject). We found that network communication models-computed on structural connectivity inferred from diffusion MRI-can explain the causal propagation of focal stimuli, measured at millisecond timescales. Building on this finding, we show that a parsimonious statistical model comprising structural, functional, and spatial factors can accurately and robustly predict cortex-wide effects of brain stimulation (R²=46% in data from held-out medical centers). Our work contributes toward the biological validation of concepts in network neuroscience and provides insight into how connectome topology shapes polysynaptic inter-areal signaling. We anticipate that our findings will have implications for research on neural communication and the design of brain stimulation paradigms.

Multi-modal and multi-subject modular organization of human brain networks

The human brain is a complex network of anatomically interconnected brain areas. Spontaneous neural activity is constrained by this architecture, giving rise to patterns of statistical dependencies between the activity of remote neural elements. The non-trivial relationship between structural and functional connectivity poses many unsolved challenges about cognition, disease, development, learning and aging. While numerous studies have focused on statistical relationships between edge weights in anatomical and functional networks, less is known about dependencies between their modules and communities. In this work, we investigate and characterize the relationship between anatomical and functional modular organization of the human brain, developing a novel multi-layer framework that expands the classical concept of multi-layer modularity. By simultaneously mapping anatomical and functional networks estimated from different subjects into communities, this approach allows us to carry out a multi-subject and multi-modal analysis of the brain's modular organization. Here, we investigate the relationship between anatomical and functional modules during resting state, finding unique and shared structures. The proposed framework constitutes a methodological advance in the context of multi-layer network analysis and paves the way to further investigate the relationship between structural and functional network organization in clinical cohorts, during cognitively demanding tasks, and in developmental or lifespan studies.

Fully Bayesian estimation of virtual brain parameters with self-tuning Hamiltonian Monte Carlo

Virtual brain models are data-driven patient-specific brain models integrating individual brain imaging data with neural mass modeling in a single computational framework, capable of autonomously generating brain activity and its associated brain imaging signals. Along the example of epilepsy, we develop an efficient and accurate Bayesian methodology estimating the parameters linked to the extent of the epileptogenic zone. State-of-the-art advances in Bayesian inference using Hamiltonian Monte Carlo (HMC) algorithms have remained elusive for large-scale differential-equations based models due to their slow convergence. We propose appropriate priors and a novel reparameterization to facilitate efficient exploration of the posterior distribution in terms of computational time and convergence diagnostics. The methodology is illustrated for in-silico dataset and then, applied to infer the personalized model parameters based on the empirical stereotactic electroencephalography (SEEG) recordings of retrospective patients. This improved methodology may pave the way to render HMC methods sufficiently easy and efficient to use, thus applicable in personalized medicine.

Reliability and subject specificity of personalized whole-brain dynamical models

Dynamical whole-brain models were developed to link structural (SC) and functional connectivity (FC) together into one framework. Nowadays, they are used to investigate the dynamical regimes of the brain and how these relate to behavioral, clinical and demographic traits. However, there is no comprehensive investigation on how reliable and subject specific the modeling results are given the variability of the empirical FC. In this study, we show that the parameters of these models can be fitted with a "poor" to "good" reliability depending on the exact implementation of the modeling paradigm. We find, as a general rule of thumb, that enhanced model personalization leads to increasingly reliable model parameters. In addition, we observe no clear effect of the model complexity evaluated by separately sampling results for linear, phase oscillator and neural mass network models. In fact, the most complex neural mass model often yields modeling results with "poor" reliability comparable to the simple linear model, but demonstrates an enhanced subject specificity of the model similarity maps. Subsequently, we show that the FC simulated by these models can outperform the empirical FC in terms of both reliability and subject specificity. For the structure-function relationship, simulated FC of individual subjects may be identified from the correlations with the empirical SC with an accuracy up to 70%, but not vice versa for non-linear models. We sample all our findings for 8 distinct brain parcellations and 6 modeling conditions and show that the parcellation-induced effect is much more pronounced for the modeling results than for the empirical data. In sum, this study provides an exploratory account on the reliability and subject specificity of dynamical whole-brain models and may be relevant for their further development and application. In particular, our findings suggest that the application of the dynamical whole-brain modeling should be tightly connected with an estimate of the reliability of the results.

Exploring Parameter and Hyper-Parameter Spaces of Neuroscience Models on High Performance Computers With Learning to Learn

Neuroscience models commonly have a high number of degrees of freedom and only specific regions within the parameter space are able to produce dynamics of interest. This makes the development of tools and strategies to efficiently find these regions of high importance to advance brain research. Exploring the high dimensional parameter space using numerical simulations has been a frequently used technique in the last years in many areas of computational neuroscience. Today, high performance computing (HPC) can provide a powerful infrastructure to speed up explorations and increase our general understanding of the behavior of the model in reasonable times. Learning to learn (L2L) is a well-known concept in machine learning (ML) and a specific method for acquiring constraints to improve learning performance. This concept can be decomposed into a two loop optimization process where the target of optimization can consist of any program such as an artificial neural network, a spiking network, a single cell model, or a whole brain simulation. In this work, we present L2L as an easy to use and flexible framework to perform parameter and hyper-parameter space exploration of neuroscience models on HPC infrastructure. Learning to learn is an implementation of the L2L concept written in Python. This open-source software allows several instances of an optimization target to be executed with different parameters in an embarrassingly parallel fashion on HPC. L2L provides a set of built-in optimizer algorithms, which make adaptive and efficient exploration of parameter spaces possible. Different from other optimization toolboxes, L2L provides maximum flexibility for the way the optimization target can be executed. In this paper, we show a variety of examples of neuroscience models being optimized within the L2L framework to execute different types of tasks. The tasks used to illustrate the concept go from reproducing empirical data to learning how to solve a problem in a dynamic environment. We particularly focus on simulations with models ranging from the single cell to the whole brain and using a variety of simulation engines like NEST, Arbor, TVB, OpenAIGym, and NetLogo.

Local structure-function relationships in human brain networks across the lifespan

A growing number of studies have used stylized network models of communication to predict brain function from structure. Most have focused on a small set of models applied globally. Here, we compare a large number of models at both global and regional levels. We find that globally most predictors perform poorly. At the regional level, performance improves but heterogeneously, both in terms of variance explained and the optimal model. Next, we expose synergies among predictors by using pairs to jointly predict FC. Finally, we assess age-related differences in global and regional coupling across the human lifespan. We find global decreases in the magnitude of structure-function coupling with age. We find that these decreases are driven by reduced coupling in sensorimotor regions, while higher-order cognitive systems preserve local coupling with age. Our results describe patterns of structure-function coupling across the cortex and how this may change with age.

Effects of virtual lesions on temporal dynamics in cortical networks based on personalized dynamic models

The human brain dynamically shifts between a predominantly integrated state and a predominantly segregated state, each with different roles in supporting cognition and behavior. However, no studies to date have investigated lesions placed in different regions of the cerebral cortex to determine the effects on the temporal balance of integration and segregation. Here, we used the integrated state occurrence rate to measure the temporal balance of integration and segregation in the resting brain. Based on dynamic mean-field models coupled through the individual's structural white matter connections, neural activity was modeled. By lesioning different individual nodes from the model, our results implied that the impact of lesions reaches far beyond focal damage and could impair cognition by affecting system-level dynamics. Lesions in a portion of the nodes in the visual, somatomotor, limbic, and default networks significantly compromised the temporal balance of integration and segregation. Crucially, the effects of lesions in different regions could be predicted based on the hierarchical axis inferred from the T1w/T2w map and specific graph measures of structural brain networks. Taken together, our findings indicate the possibility of significant contributions of anatomical heterogeneity to the dynamics of functional network topology. Although still in its infancy, computational modeling may provide an entry point for understanding brain disorders at a causal mechanistic level, possibly leading to novel, more effective therapeutic interventions.

Directed functional and structural connectivity in a large-scale model for the mouse cortex

Inferring the structural connectivity from electrophysiological measurements is a fundamental challenge in systems neuroscience. Directed functional connectivity measures, such as the generalized partial directed coherence (GPDC), provide estimates of the causal influence between areas. However, the relation between causality estimates and structural connectivity is still not clear. We analyzed this problem by evaluating the effectiveness of GPDC to estimate the connectivity of a ground-truth, data-constrained computational model of a large-scale network model of the mouse cortex. The model contains 19 cortical areas composed of spiking neurons, with areas connected by long-range projections with weights obtained from a tract-tracing cortical connectome. We show that GPDC values provide a reasonable estimate of structural connectivity, with an average Pearson correlation over simulations of 0.74. Moreover, even in a typical electrophysiological recording scenario containing five areas, the mean correlation was above 0.6. These results suggest that it may be possible to empirically estimate structural connectivity from functional connectivity even when detailed whole-brain recordings are not achievable.

We analyzed the relationship between structural and directed functional connectivity by evaluating the effectiveness of generalized partial directed coherence (GPDC) to estimate the connectivity of a ground-truth, data-constrained computational model of a large-scale network model of the mouse cortex. We show that GPDC values provide a reasonable estimate of structural connectivity even in a typical electrophysiological recording scenario containing few areas. These results suggest that it may be possible to empirically estimate structural connectivity from functional connectivity even when detailed whole-brain recordings are not achievable.

RateML: A Code Generation Tool for Brain Network Models

Whole brain network models are now an established tool in scientific and clinical research, however their use in a larger workflow still adds significant informatics complexity. We propose a tool, RateML, that enables users to generate such models from a succinct declarative description, in which the mathematics of the model are described without specifying how their simulation should be implemented. RateML builds on NeuroML's Low Entropy Model Specification (LEMS), an XML based language for specifying models of dynamical systems, allowing descriptions of neural mass and discretized neural field models, as implemented by the Virtual Brain (TVB) simulator: the end user describes their model's mathematics once and generates and runs code for different languages, targeting both CPUs for fast single simulations and GPUs for parallel ensemble simulations. High performance parallel simulations are crucial for tuning many parameters of a model to empirical data such as functional magnetic resonance imaging (fMRI), with reasonable execution times on small or modest hardware resources. Specifically, while RateML can generate Python model code, it enables generation of Compute Unified Device Architecture C++ code for NVIDIA GPUs. When a CUDA implementation of a model is generated, a tailored model driver class is produced, enabling the user to tweak the driver by hand and perform the parameter sweep. The model and driver can be executed on any compute capable NVIDIA GPU with a high degree of parallelization, either locally or in a compute cluster environment. The results reported in this manuscript show that with the CUDA code generated by RateML, it is possible to explore thousands of parameter combinations with a single Graphics Processing Unit for different models, substantially reducing parameter exploration times and resource usage for the brain network models, in turn accelerating the research workflow itself. This provides a new tool to create efficient and broader parameter fitting workflows, support studies on larger cohorts, and derive more robust and statistically relevant conclusions about brain dynamics.

Parcellation-induced variation of empirical and simulated brain connectomes at group and subject levels

Recent developments of whole-brain models have demonstrated their potential when investigating resting-state brain activity. However, it has not been systematically investigated how alternating derivations of the empirical structural and functional connectivity, serving as the model input, from MRI data influence modeling results. Here, we study the influence from one major element: the brain parcellation scheme that reduces the dimensionality of brain networks by grouping thousands of voxels into a few hundred brain regions. We show graph-theoretical statistics derived from the empirical data and modeling results exhibiting a high heterogeneity across parcellations. Furthermore, the network properties of empirical brain connectomes explain the lion’s share of the variance in the modeling results with respect to the parcellation variation. Such a clear-cut relationship is not observed at the subject-resolved level per parcellation. Finally, the graph-theoretical statistics of the simulated connectome correlate with those of the empirical functional connectivity across parcellations. However, this relation is not one-to-one, and its precision can vary between models. Our results imply that network properties of both empirical connectomes can explain the goodness-of-fit of whole-brain models to empirical data at a global group level but not at a single-subject level, which provides further insights into the personalization of whole-brain models.

The structural and functional connectivities of the brain, which reflect the anatomical connections of axonal bundles and the amount of coactivation between brain regions, respectively, only weakly correlate with each other. In order to enhance and investigate this relationship, large-scale whole-brain dynamical models were involved in this branch of research. However, how the definitions of the brain regions parcellated according to a so-called brain atlas influence these models has so far not been systematically assessed. In this article, we show that this influence can be large, and link group-averaged, atlas-induced deviations to network properties extracted from both types of connectivity. Additionally, we demonstrate that the same association does not apply to subject-specific variations. These results may contribute to the further personalization of the whole-brain models.

Optimization of epilepsy surgery through virtual resections on individual structural brain networks

The success of epilepsy surgery in patients with refractory epilepsy depends upon correct identification of the epileptogenic zone (EZ) and an optimal choice of the resection area. In this study we developed individualized computational models based upon structural brain networks to explore the impact of different virtual resections on the propagation of seizures. The propagation of seizures was modelled as an epidemic process [susceptible-infected-recovered (SIR) model] on individual structural networks derived from presurgical diffusion tensor imaging in 19 patients. The candidate connections for the virtual resection were all connections from the clinically hypothesized EZ, from which the seizures were modelled to start, to other brain areas. As a computationally feasible surrogate for the SIR model, we also removed the connections that maximally reduced the eigenvector centrality (EC) (large values indicate network hubs) of the hypothesized EZ, with a large reduction meaning a large effect. The optimal combination of connections to be removed for a maximal effect were found using simulated annealing. For comparison, the same number of connections were removed randomly, or based on measures that quantify the importance of a node or connection within the network. We found that 90% of the effect (defined as reduction of EC of the hypothesized EZ) could already be obtained by removing substantially less than 90% of the connections. Thus, a smaller, optimized, virtual resection achieved almost the same effect as the actual surgery yet at a considerably smaller cost, sparing on average 27.49% (standard deviation: 4.65%) of the connections. Furthermore, the maximally effective connections linked the hypothesized EZ to hubs. Finally, the optimized resection was equally or more effective than removal based on structural network characteristics both regarding reducing the EC of the hypothesized EZ and seizure spreading. The approach of using reduced EC as a surrogate for simulating seizure propagation can suggest more restrictive resection strategies, whilst obtaining an almost optimal effect on reducing seizure propagation, by taking into account the unique topology of individual structural brain networks of patients.

Data-driven computational modeling predicts "superhubs" play key role in epileptic dynamics

How individual neurons influence epileptic networks remains an open question. In this issue of Neuron, Hadjiabadi et al. (2021) use data-driven, computational models to predict the presence of "superhubs": highly connected neurons that drive network activity through feedforward motifs.

On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread

Individualized anatomical information has been used as prior knowledge in Bayesian inference paradigms of whole-brain network models. However, the actual sensitivity to such personalized information in priors is still unknown. In this study, we introduce the use of fully Bayesian information criteria and leave-one-out cross-validation technique on the subject-specific information to assess different epileptogenicity hypotheses regarding the location of pathological brain areas based on a priori knowledge from dynamical system properties. The Bayesian Virtual Epileptic Patient (BVEP) model, which relies on the fusion of structural data of individuals, a generative model of epileptiform discharges, and a self-tuning Monte Carlo sampling algorithm, is used to infer the spatial map of epileptogenicity across different brain areas. Our results indicate that measuring the out-of-sample prediction accuracy of the BVEP model with informative priors enables reliable and efficient evaluation of potential hypotheses regarding the degree of epileptogenicity across different brain regions. In contrast, while using uninformative priors, the information criteria are unable to provide strong evidence about the epileptogenicity of brain areas. We also show that the fully Bayesian criteria correctly assess different hypotheses about both structural and functional components of whole-brain models that differ across individuals. The fully Bayesian information-theory based approach used in this study suggests a patient-specific strategy for epileptogenicity hypothesis testing in generative brain network models of epilepsy to improve surgical outcomes.

Brain functional network modeling and analysis based on fMRI: a systematic review

In recent years, the number of patients with neurodegenerative diseases (i.e., Alzheimer's disease, Parkinson's disease, mild cognitive impairment) and mental disorders (i.e., depression, anxiety and schizophrenia) have increased dramatically. Researchers have found that complex network analysis can reveal the topology of brain functional networks, such as small-world, scale-free, etc. In the study of brain diseases, it has been found that these topologies have undergoed abnormal changes in different degrees. Therefore, the research of brain functional networks can not only provide a new perspective for understanding the pathological mechanism of neurological and psychiatric diseases, but also provide assistance for the early diagnosis. Focusing on the study of human brain functional networks, this paper reviews the research results in recent years. First, this paper introduces the background of the study of brain functional networks under complex network theory and the important role of topological properties in the study of brain diseases. Second, the paper describes how to construct a brain functional network using neural image data. Third, the common methods of functional network analysis, including network structure analysis and disease classification, are introduced. Fourth, the role of brain functional networks in pathological study, analysis and diagnosis of brain functional diseases is studied. Finally, the paper summarizes the existing studies of brain functional networks and points out the problems and future research directions.

Functional Weight of Somatic and Cognitive Networks and Asymmetry of Compensatory Mechanisms: Collaboration or Divergency among Hemispheres after Cerebrovascular Accident?

The human brain holds highly sophisticated compensatory mechanisms relying on neuroplasticity. Neuronal degeneracy, redundancy, and brain network organization make the human nervous system more robust and evolvable to continuously guarantee an optimal environmental-related homeostasis. Nevertheless, after injury, restitution processes appear dissimilar, depending on the pathology. Following a cerebrovascular accident, asymmetry, within- and across-network compensation and interhemispheric inhibition are key features to functional recovery. In moderate-to-severe stroke, neurological outcome is often poor, and little is known about the paths that enable either an efficient collaboration among hemispheres or, on the contrary, an antagonism of adaptative responses. In this review, we aim to decipher key issues of ipsilesional and contralesional hemispheric functioning allowing the foundations of effective neurorehabilitation strategies.

Computational Models in Electroencephalography

Computational models lie at the intersection of basic neuroscience and healthcare applications because they allow researchers to test hypotheses in silico and predict the outcome of experiments and interactions that are very hard to test in reality. Yet, what is meant by “computational model” is understood in many different ways by researchers in different fields of neuroscience and psychology, hindering communication and collaboration. In this review, we point out the state of the art of computational modeling in Electroencephalography (EEG) and outline how these models can be used to integrate findings from electrophysiology, network-level models, and behavior. On the one hand, computational models serve to investigate the mechanisms that generate brain activity, for example measured with EEG, such as the transient emergence of oscillations at different frequency bands and/or with different spatial topographies. On the other hand, computational models serve to design experiments and test hypotheses in silico. The final purpose of computational models of EEG is to obtain a comprehensive understanding of the mechanisms that underlie the EEG signal. This is crucial for an accurate interpretation of EEG measurements that may ultimately serve in the development of novel clinical applications.

Quantitative systems pharmacology in neuroscience: Novel methodologies and technologies

The development and application of quantitative systems pharmacology models in neuroscience have been modest relative to other fields, such as oncology and immunology, which may reflect the complexity of the brain. Technological and methodological advancements have enhanced the quantitative understanding of brain physiology and pathophysiology and the effects of pharmacological interventions. To maximize the knowledge gained from these novel data types, pharmacometrics modelers may need to expand their toolbox to include additional mathematical and statistical frameworks. A session was held at the 10th annual American Conference on Pharmacometrics (ACoP10) to highlight several recent advancements in quantitative and systems neuroscience. In this mini‐review, we provide a brief overview of technological and methodological advancements in the neuroscience therapeutic area that were discussed during the session and how these can be leveraged with quantitative systems pharmacology modeling to enhance our understanding of neurological diseases. Microphysiological systems using human induced pluripotent stem cells (IPSCs), digital biomarkers, and large‐scale imaging offer more clinically relevant experimental datasets, enhanced granularity, and a plethora of data to potentially improve the preclinical‐to‐clinical translation of therapeutics. Network neuroscience methodologies combined with quantitative systems models of neurodegenerative disease could help bridge the gap between cellular and molecular alterations and clinical end points through the integration of information on neural connectomics. Additional topics, such as the neuroimmune system, microbiome, single‐cell transcriptomic technologies, and digital device biomarkers, are discussed in brief.

Path-dependent connectivity, not modularity, consistently predicts controllability of structural brain networks

The human brain displays rich communication dynamics that are thought to be particularly well-reflected in its marked community structure. Yet, the precise relationship between community structure in structural brain networks and the communication dynamics that can emerge therefrom is not well understood. In addition to offering insight into the structure-function relationship of networked systems, such an understanding is a critical step toward the ability to manipulate the brain's large-scale dynamical activity in a targeted manner. We investigate the role of community structure in the controllability of structural brain networks. At the region level, we find that certain network measures of community structure are sometimes statistically correlated with measures of linear controllability. However, we then demonstrate that this relationship depends on the distribution of network edge weights. We highlight the complexity of the relationship between community structure and controllability by performing numerical simulations using canonical graph models with varying mesoscale architectures and edge weight distributions. Finally, we demonstrate that weighted subgraph centrality, a measure rooted in the graph spectrum, and which captures higher order graph architecture, is a stronger and more consistent predictor of controllability. Our study contributes to an understanding of how the brain's diverse mesoscale structure supports transient communication dynamics.

Models of communication and control for brain networks: distinctions, convergence, and future outlook

Recent advances in computational models of signal propagation and routing in the human brain have underscored the critical role of white-matter structure. A complementary approach has utilized the framework of network control theory to better understand how white matter constrains the manner in which a region or set of regions can direct or control the activity of other regions. Despite the potential for both of these approaches to enhance our understanding of the role of network structure in brain function, little work has sought to understand the relations between them. Here, we seek to explicitly bridge computational models of communication and principles of network control in a conceptual review of the current literature. By drawing comparisons between communication and control models in terms of the level of abstraction, the dynamical complexity, the dependence on network attributes, and the interplay of multiple spatiotemporal scales, we highlight the convergence of and distinctions between the two frameworks. Based on the understanding of the intertwined nature of communication and control in human brain networks, this work provides an integrative perspective for the field and outlines exciting directions for future work.

Focused attention meditation changes the boundary and configuration of functional networks in the brain

Research has shown that focused attention meditation not only improves our cognitive and motivational functioning (e.g., attention, mental health), it influences the way our brain networks [e.g., default mode network (DMN), fronto-parietal network (FPN), and sensory-motor network (SMN)] function and operate. However, surprisingly little attention has been paid to the possibility that meditation alters the architecture (composition) of these functional brain networks. Here, using a single-case experimental design with intensive longitudinal data, we examined the effect of mediation practice on intra-individual changes in the composition of whole-brain networks. The results showed that meditation (1) changed the community size (with a number of regions in the FPN being merged into the DMN after meditation) and (2) led to instability in the community allegiance of the regions in the FPN. These results suggest that, in addition to altering specific functional connectivity, meditation leads to reconfiguration of whole-brain network architecture. The reconfiguration of community architecture in the brain provides fruitful information about the neural mechanisms of meditation.

Whole-Brain Models to Explore Altered States of Consciousness from the Bottom Up

The scope of human consciousness includes states departing from what most of us experience as ordinary wakefulness. These altered states of consciousness constitute a prime opportunity to study how global changes in brain activity relate to different varieties of subjective experience. We consider the problem of explaining how global signatures of altered consciousness arise from the interplay between large-scale connectivity and local dynamical rules that can be traced to known properties of neural tissue. For this purpose, we advocate a research program aimed at bridging the gap between bottom-up generative models of whole-brain activity and the top-down signatures proposed by theories of consciousness. Throughout this paper, we define altered states of consciousness, discuss relevant signatures of consciousness observed in brain activity, and introduce whole-brain models to explore the biophysics of altered consciousness from the bottom-up. We discuss the potential of our proposal in view of the current state of the art, give specific examples of how this research agenda might play out, and emphasize how a systematic investigation of altered states of consciousness via bottom-up modeling may help us better understand the biophysical, informational, and dynamical underpinnings of consciousness.

Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state

At the macroscale, the brain operates as a network of interconnected neuronal populations, which display coordinated rhythmic dynamics that support interareal communication. Understanding how stimulation of different brain areas impacts such activity is important for gaining basic insights into brain function and for further developing therapeutic neurmodulation. However, the complexity of brain structure and dynamics hinders predictions regarding the downstream effects of focal stimulation. More specifically, little is known about how the collective oscillatory regime of brain network activity—in concert with network structure—affects the outcomes of perturbations. Here, we combine human connectome data and biophysical modeling to begin filling these gaps. By tuning parameters that control collective system dynamics, we identify distinct states of simulated brain activity and investigate how the distributed effects of stimulation manifest at different dynamical working points. When baseline oscillations are weak, the stimulated area exhibits enhanced power and frequency, and due to network interactions, activity in this excited frequency band propagates to nearby regions. Notably, beyond these linear effects, we further find that focal stimulation causes more distributed modifications to interareal coherence in a band containing regions’ baseline oscillation frequencies. Importantly, depending on the dynamical state of the system, these broadband effects can be better predicted by functional rather than structural connectivity, emphasizing a complex interplay between anatomical organization, dynamics, and response to perturbation. In contrast, when the network operates in a regime of strong regional oscillations, stimulation causes only slight shifts in power and frequency, and structural connectivity becomes most predictive of stimulation-induced changes in network activity patterns. In sum, this work builds upon and extends previous computational studies investigating the impacts of stimulation, and underscores the fact that both the stimulation site, and, crucially, the regime of brain network dynamics, can influence the network-wide responses to local perturbations.

Stimulation can be used to alter brain activity and is a therapeutic option for certain neurological conditions. However, predicting the distributed effects of local perturbations is difficult. Previous studies show that responses to stimulation depend on anatomical (or structural) coupling. In addition to structure, here we consider how stimulation effects also depend on the brain’s collective dynamical (or functional) state, arising from the coordination of rhythmic activity across large-scale networks. In a whole-brain computational model, we show that global responses to regional stimulation can indeed be contingent upon and differ across various dynamical working points. Notably, depending on the network’s oscillatory regime, stimulation can accelerate the activity of the stimulated site, and lead to widespread effects at both the new, excited frequency, as well as in a much broader frequency range including areas’ baseline frequencies. While structural connectivity is a good predictor of “excited band” changes, in some states “baseline band” effects can be better predicted by functional connectivity, which depends upon the system’s oscillatory regime. By integrating and extending past efforts, our results thus indicate that dynamical—in additional to structural—brain organization plays a role in governing how focal stimulation modulates interactions between distributed network elements.

Dynamic representations in networked neural systems

A group of neurons can generate patterns of activity that represent information about stimuli; subsequently, the group can transform and transmit activity patterns across synapses to spatially distributed areas. Recent studies in neuroscience have begun to independently address the two components of information processing: the representation of stimuli in neural activity and the transmission of information in networks that model neural interactions. Yet only recently are studies seeking to link these two types of approaches. Here we briefly review the two separate bodies of literature; we then review the recent strides made to address this gap. We continue with a discussion of how patterns of activity evolve from one representation to another, forming dynamic representations that unfold on the underlying network. Our goal is to offer a holistic framework for understanding and describing neural information representation and transmission while revealing exciting frontiers for future research.

Control of brain network dynamics across diverse scales of space and time

The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow timescales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast timescales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure.

The Bayesian Virtual Epileptic Patient: A probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread

Despite the importance and frequent use of Bayesian frameworks in brain network modeling for parameter inference and model prediction, the advanced sampling algorithms implemented in probabilistic programming languages to overcome the inference difficulties have received relatively little attention in this context. In this technical note, we propose a probabilistic framework, namely the Bayesian Virtual Epileptic Patient (BVEP), which relies on the fusion of structural data of individuals to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread. To invert the individualized whole-brain model employed in this study, we use the recently developed algorithms known as No-U-Turn Sampler (NUTS) as well as Automatic Differentiation Variational Inference (ADVI). Our results indicate that NUTS and ADVI accurately estimate the degree of epileptogenicity of brain regions, therefore, the hypothetical brain areas responsible for the seizure initiation and propagation, while the convergence diagnostics and posterior behavior analysis validate the reliability of the estimations. Moreover, we illustrate the efficiency of the transformed non-centered parameters in comparison to centered form of parameterization. The Bayesian framework used in this work proposes an appropriate patient-specific strategy for estimating the epileptogenicity of the brain regions to improve outcome after epilepsy surgery.

The road ahead in clinical network neuroscience

Clinical network neuroscience, the study of brain network topology in neurological and psychiatric diseases, has become a mainstay field within clinical neuroscience. Being a multidisciplinary group of clinical network neuroscience experts based in The Netherlands, we often discuss the current state of the art and possible avenues for future investigations. These discussions revolve around questions like "How do dynamic processes alter the underlying structural network?" and "Can we use network neuroscience for disease classification?" This opinion paper is an incomplete overview of these discussions and expands on ten questions that may potentially advance the field. By no means intended as a review of the current state of the field, it is instead meant as a conversation starter and source of inspiration to others.

Cognitive effort decreases beta, alpha, and theta coherence and ends afterdischarges in human brain

OBJECTIVE

Mental activation has been reported to modify the occurrence of epileptiform activity. We studied its effect on afterdischarges.

METHOD

In 15 patients with implanted electrodes we presented cognitive tasks when afterdischarges occurred. We developed a wavelet cross-coherence function to analyze the electrocorticography before and after the tasks and compared findings when cognitive tasks did or did not result in afterdischarge termination. Six patients returned for functional MRI (fMRI) testing, using similar tasks.

RESULTS

Cognitive tasks often could terminate afterdischarges when direct abortive stimulation could not. Wavelet cross-coherence analysis showed that, when afterdischarges stopped, there was decreased coherence throughout the brain in the 7.13-22.53 Hz frequency ranges (p values 0.008-0.034). This occurred a) regardless of whether an area activated on fMRI and b) regardless of whether there were afterdischarges in the area.

CONCLUSIONS

It is known that cognitive tasks can alter localized or network synchronization. Our results show that they can change activity throughout the brain. These changes in turn can terminate localized epileptiform activity.

SIGNIFICANCE

Cognitive tasks result in diffuse brain changes that can modify focal brain activity. Combined with a seizure detection device, cognitive activation might provide a non-invasive method of terminating or modifying seizures.

The role that choice of model plays in predictions for epilepsy surgery

Mathematical modelling has been widely used to predict the effects of perturbations to brain networks. An important example is epilepsy surgery, where the perturbation in question is the removal of brain tissue in order to render the patient free of seizures. Different dynamical models have been proposed to represent transitions to ictal states in this context. However, our choice of which mathematical model to use to address this question relies on making assumptions regarding the mechanism that defines the transition from background to the seizure state. Since these mechanisms are unknown, it is important to understand how predictions from alternative dynamical descriptions compare. Herein we evaluate to what extent three different dynamical models provide consistent predictions for the effect of removing nodes from networks. We show that for small, directed, connected networks the three considered models provide consistent predictions. For larger networks, predictions are shown to be less consistent. However consistency is higher in networks that have sufficiently large differences in ictogenicity between nodes. We further demonstrate that heterogeneity in ictogenicity across nodes correlates with variability in the number of connections for each node.

Cognitive chimera states in human brain networks

The human brain is a complex dynamical system, and how cognition emerges from spatiotemporal patterns of regional brain activity remains an open question. As different regions dynamically interact to perform cognitive tasks, variable patterns of partial synchrony can be observed, forming chimera states. We propose that the spatial patterning of these states plays a fundamental role in the cognitive organization of the brain and present a cognitively informed, chimera-based framework to explore how large-scale brain architecture affects brain dynamics and function. Using personalized brain network models, we systematically study how regional brain stimulation produces different patterns of synchronization across predefined cognitive systems. We analyze these emergent patterns within our framework to understand the impact of subject-specific and region-specific structural variability on brain dynamics. Our results suggest a classification of cognitive systems into four groups with differing levels of subject and regional variability that reflect their different functional roles.

Homeostatic plasticity and emergence of functional networks in a whole-brain model at criticality

Understanding the relationship between large-scale structural and functional brain networks remains a crucial issue in modern neuroscience. Recently, there has been growing interest in investigating the role of homeostatic plasticity mechanisms, across different spatiotemporal scales, in regulating network activity and brain functioning against a wide range of environmental conditions and brain states (e.g., during learning, development, ageing, neurological diseases). In the present study, we investigate how the inclusion of homeostatic plasticity in a stochastic whole-brain model, implemented as a normalization of the incoming node's excitatory input, affects the macroscopic activity during rest and the formation of functional networks. Importantly, we address the structure-function relationship both at the group and individual-based levels. In this work, we show that normalization of the node's excitatory input improves the correspondence between simulated neural patterns of the model and various brain functional data. Indeed, we find that the best match is achieved when the model control parameter is in its critical value and that normalization minimizes both the variability of the critical points and neuronal activity patterns among subjects. Therefore, our results suggest that the inclusion of homeostatic principles lead to more realistic brain activity consistent with the hallmarks of criticality. Our theoretical framework open new perspectives in personalized brain modeling with potential applications to investigate the deviation from criticality due to structural lesions (e.g. stroke) or brain disorders.

Data-driven brain network models differentiate variability across language tasks

The relationship between brain structure and function has been probed using a variety of approaches, but how the underlying structural connectivity of the human brain drives behavior is far from understood. To investigate the effect of anatomical brain organization on human task performance, we use a data-driven computational modeling approach and explore the functional effects of naturally occurring structural differences in brain networks. We construct personalized brain network models by combining anatomical connectivity estimated from diffusion spectrum imaging of individual subjects with a nonlinear model of brain dynamics. By performing computational experiments in which we measure the excitability of the global brain network and spread of synchronization following a targeted computational stimulation, we quantify how individual variation in the underlying connectivity impacts both local and global brain dynamics. We further relate the computational results to individual variability in the subjects' performance of three language-demanding tasks both before and after transcranial magnetic stimulation to the left-inferior frontal gyrus. Our results show that task performance correlates with either local or global measures of functional activity, depending on the complexity of the task. By emphasizing differences in the underlying structural connectivity, our model serves as a powerful tool to assess individual differences in task performances, to dissociate the effect of targeted stimulation in tasks that differ in cognitive demand, and to pave the way for the development of personalized therapeutics.