Network NeurosciencePub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00422
Claudio Runfola, Matteo Neri, Daniele Schön, Benjamin Morillon, Agnès Trébuchon, Giovanni Rabuffo, Pierpaolo Sorrentino, Viktor Jirsa
{"title":"Complexity in speech and music listening via neural manifold flows.","authors":"Claudio Runfola, Matteo Neri, Daniele Schön, Benjamin Morillon, Agnès Trébuchon, Giovanni Rabuffo, Pierpaolo Sorrentino, Viktor Jirsa","doi":"10.1162/netn_a_00422","DOIUrl":"10.1162/netn_a_00422","url":null,"abstract":"<p><p>Understanding the complex neural mechanisms underlying speech and music perception remains a multifaceted challenge. In this study, we investigated neural dynamics using human intracranial recordings. Employing a novel approach based on low-dimensional reduction techniques, the Manifold Density Flow (MDF), we quantified the complexity of brain dynamics during naturalistic speech and music listening and during resting state. Our results reveal higher complexity in patterns of interdependence between different brain regions during speech and music listening compared with rest, suggesting that the cognitive demands of speech and music listening drive the brain dynamics toward states not observed during rest. Moreover, speech listening has more complexity than music, highlighting the nuanced differences in cognitive demands between these two auditory domains. Additionally, we validated the efficacy of the MDF method through experimentation on a toy model and compared its effectiveness in capturing the complexity of brain dynamics induced by cognitive tasks with another established technique in the literature. Overall, our findings provide a new method to quantify the complexity of brain activity by studying its temporal evolution on a low-dimensional manifold, suggesting insights that are invisible to traditional methodologies in the contexts of speech and music perception.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"146-158"},"PeriodicalIF":3.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Neural network embedding of functional microconnectome.","authors":"Arata Shirakami, Takeshi Hase, Yuki Yamaguchi, Masanori Shimono","doi":"10.1162/netn_a_00424","DOIUrl":"10.1162/netn_a_00424","url":null,"abstract":"<p><p>Our brains operate as a complex network of interconnected neurons. To gain a deeper understanding of this network architecture, it is essential to extract simple rules from its intricate structure. This study aimed to compress and simplify the architecture, with a particular focus on interpreting patterns of functional connectivity in 2.5 hr of electrical activity from a vast number of neurons in acutely sliced mouse brains. Here, we combined two distinct methods together: automatic compression and network analysis. Firstly, for automatic compression, we trained an artificial neural network named NNE (neural network embedding). This allowed us to reduce the connectivity to features, be represented only by 13% of the original neuron count. Secondly, to decipher the topology, we concentrated on the variability among the compressed features and compared them with 15 distinct network metrics. Specifically, we introduced new metrics that had not previously existed, termed as indirect-adjacent degree and neighbor hub ratio. Our results conclusively demonstrated that these new metrics could better explain approximately 40%-45% of the features. This finding highlighted the critical role of NNE in facilitating the development of innovative metrics, because some of the features extracted by NNE were not captured by the currently existed network metrics.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"159-180"},"PeriodicalIF":3.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00433
Rishikesan Maran, Eli J Müller, Ben D Fulcher
{"title":"Analyzing the brain's dynamic response to targeted stimulation using generative modeling.","authors":"Rishikesan Maran, Eli J Müller, Ben D Fulcher","doi":"10.1162/netn_a_00433","DOIUrl":"10.1162/netn_a_00433","url":null,"abstract":"<p><p>Generative models of brain activity have been instrumental in testing hypothesized mechanisms underlying brain dynamics against experimental datasets. Beyond capturing the key mechanisms underlying spontaneous brain dynamics, these models hold an exciting potential for understanding the mechanisms underlying the dynamics evoked by targeted brain stimulation techniques. This paper delves into this emerging application, using concepts from dynamical systems theory to argue that the stimulus-evoked dynamics in such experiments may be shaped by new types of mechanisms distinct from those that dominate spontaneous dynamics. We review and discuss (a) the targeted experimental techniques across spatial scales that can both perturb the brain to novel states and resolve its relaxation trajectory back to spontaneous dynamics and (b) how we can understand these dynamics in terms of mechanisms using physiological, phenomenological, and data-driven models. A tight integration of targeted stimulation experiments with generative quantitative modeling provides an important opportunity to uncover novel mechanisms of brain dynamics that are difficult to detect in spontaneous settings.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"237-258"},"PeriodicalIF":3.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00428
Anastasiya Salova, István A Kovács
{"title":"Combined topological and spatial constraints are required to capture the structure of neural connectomes.","authors":"Anastasiya Salova, István A Kovács","doi":"10.1162/netn_a_00428","DOIUrl":"10.1162/netn_a_00428","url":null,"abstract":"<p><p>Volumetric brain reconstructions provide an unprecedented opportunity to gain insights into the complex connectivity patterns of neurons in an increasing number of organisms. Here, we model and quantify the complexity of the resulting neural connectomes in the fruit fly, mouse, and human and unveil a simple set of shared organizing principles across these organisms. To put the connectomes in a physical context, we also construct contactomes, the network of neurons in physical contact in each organism. With these, we establish that physical constraints-either given by pairwise distances or the contactome-play a crucial role in shaping the network structure. For example, neuron positions are highly optimal in terms of distance from their neighbors. Yet, spatial constraints alone cannot capture the network topology, including the broad degree distribution. Conversely, the degree sequence alone is insufficient to recover the spatial structure. We resolve this apparent mismatch by formulating scalable maximum entropy models, incorporating both types of constraints. The resulting generative models have predictive power beyond the input data, as they capture several additional biological and network characteristics, like synaptic weights and graphlet statistics.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"181-206"},"PeriodicalIF":3.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00418
Mihai Dragos Maliia, Elif Köksal-Ersöz, Adrien Benard, Tristan Calas, Anca Nica, Yves Denoyer, Maxime Yochum, Fabrice Wendling, Pascal Benquet
{"title":"Localization of the epileptogenic network from scalp EEG using a patient-specific whole-brain model.","authors":"Mihai Dragos Maliia, Elif Köksal-Ersöz, Adrien Benard, Tristan Calas, Anca Nica, Yves Denoyer, Maxime Yochum, Fabrice Wendling, Pascal Benquet","doi":"10.1162/netn_a_00418","DOIUrl":"10.1162/netn_a_00418","url":null,"abstract":"<p><p>Computational modeling is a key tool for elucidating the neuronal mechanisms underlying epileptic activity. Despite considerable progress, existing models often lack realistic accuracy in representing electrophysiological epileptic activity. In this study, we used a comprehensive human brain model based on a neural mass model, which is tailored to the layered structure of the neocortex and incorporates patient-specific imaging data. This approach allowed the simulation of scalp EEGs in an epileptic patient suffering from type 2 focal cortical dysplasia (FCD). The simulation specifically addressed epileptic activity induced by FCD, faithfully reproducing intracranial interictal epileptiform discharges (IEDs) recorded with electrocorticography. For constructing the patient-specific scalp EEG, we carefully defined a clear delineation of the epileptogenic zone by numerical simulations to ensure fidelity to the topography, polarity, and diffusion characteristics of IEDs. This nuanced approach improves the accuracy of the simulated EEG signal, provides a more accurate representation of epileptic activity, and enhances our understanding of the mechanism behind the epileptogenic networks. The accuracy of the model was confirmed by a postoperative reevaluation with a secondary EEG simulation that was consistent with the lesion's removal. Ultimately, this personalized approach may prove instrumental in optimizing and tailoring epilepsy treatment strategies.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"18-37"},"PeriodicalIF":3.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00419
Mahdi Moghaddam, Mario Dzemidzic, Daniel Guerrero, Mintao Liu, Jonathan Alessi, Martin H Plawecki, Jaroslaw Harezlak, David A Kareken, Joaquín Goñi
{"title":"Tangent space functional reconfigurations in individuals at risk for alcohol use disorder.","authors":"Mahdi Moghaddam, Mario Dzemidzic, Daniel Guerrero, Mintao Liu, Jonathan Alessi, Martin H Plawecki, Jaroslaw Harezlak, David A Kareken, Joaquín Goñi","doi":"10.1162/netn_a_00419","DOIUrl":"10.1162/netn_a_00419","url":null,"abstract":"<p><p>Human brain function dynamically adjusts to ever-changing stimuli from the external environment. Studies characterizing brain functional reconfiguration are, nevertheless, scarce. Here, we present a principled mathematical framework to quantify brain functional reconfiguration when engaging and disengaging from a stop signal task (SST). We apply tangent space projection (a Riemannian geometry mapping technique) to transform the functional connectomes (FCs) of 54 participants and quantify functional reconfiguration using the correlation distance of the resulting tangent-FCs. Our goal was to compare functional reconfigurations in individuals at risk for alcohol use disorder (AUD). We hypothesized that functional reconfigurations when transitioning to/from a task would be influenced by family history of AUD (FHA) and other AUD risk factors. Multilinear regression models showed that engaging and disengaging functional reconfiguration were associated with FHA and recent drinking. When <i>engaging</i> in the SST after a rest condition, functional reconfiguration was negatively associated with recent drinking, while functional reconfiguration when <i>disengaging</i> from the SST was negatively associated with FHA. In both models, several other factors contributed to the functional reconfiguration. This study demonstrates that tangent-FCs can characterize task-induced functional reconfiguration and that it is related to AUD risk.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"38-60"},"PeriodicalIF":3.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00427
Spandan Sengupta, Afroditi Talidou, Jeremie Lefebvre, Frances K Skinner
{"title":"Cell-type-specific contributions to theta-gamma coupled rhythms in the hippocampus.","authors":"Spandan Sengupta, Afroditi Talidou, Jeremie Lefebvre, Frances K Skinner","doi":"10.1162/netn_a_00427","DOIUrl":"10.1162/netn_a_00427","url":null,"abstract":"<p><p>Distinct inhibitory cell types participate in cognitively relevant nested brain rhythms, and particular changes in such rhythms are known to occur in disease states. Specifically, the coexpression of theta and gamma rhythms in the hippocampus is believed to represent a general coding scheme, but cellular-based generation mechanisms for these coupled rhythms are currently unclear. We develop a population rate model of the CA1 hippocampus that encompasses circuits of three inhibitory cell types (bistratified cells and parvalbumin [PV]-expressing and cholecystokinin [CCK]-expressing basket cells) and pyramidal cells to examine this. We constrain parameters and perform numerical and theoretical analyses. The theory, in combination with the numerical explorations, predicts circuit motifs and specific cell-type mechanisms that are essential for the coexistence of theta and gamma oscillations. We find that CCK-expressing basket cells initiate the coupled rhythms and regularize theta, and PV-expressing basket cells enhance both theta and gamma rhythms. Pyramidal and bistratified cells govern the generation of theta rhythms, and PV-expressing basket and pyramidal cells play dominant roles in controlling theta frequencies. Our circuit motifs for the theta-gamma coupled rhythm generation could be applicable to other brain regions.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"100-124"},"PeriodicalIF":3.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00432
Isaac N Treves, Winson F Z Yang, Terje Sparby, Matthew D Sacchet
{"title":"Dynamic brain states underlying advanced concentrative absorption meditation: A 7-T fMRI-intensive case study.","authors":"Isaac N Treves, Winson F Z Yang, Terje Sparby, Matthew D Sacchet","doi":"10.1162/netn_a_00432","DOIUrl":"10.1162/netn_a_00432","url":null,"abstract":"<p><p>Advanced meditation consists of states and stages of practice that unfold with mastery and time. Dynamic functional connectivity (DFC) analysis of fMRI could identify brain states underlying advanced meditation. We conducted an intensive DFC case study of a meditator who completed 27 runs of <i>jhāna</i> advanced absorptive concentration meditation (ACAM-J), concurrently with 7-T fMRI and phenomenological reporting. We identified three brain states that marked differences between ACAM-J and nonmeditative control conditions. These states were characterized as a DMN-anticorrelated brain state, a hyperconnected brain state, and a sparsely connected brain state. Our analyses indicate higher prevalence of the DMN-anticorrelated brain state during ACAM-J than control states, and the prevalence increased significantly with deeper ACAM-J states. The hyperconnected brain state was also more common during ACAM-J and was characterized by elevated thalamocortical connectivity and somatomotor network connectivity. The hyperconnected brain state significantly decreased over the course of ACAM-J, associating with self-reports of wider attention and diminished physical sensations. This brain state may be related to sensory awareness. Advanced meditators have developed well-honed abilities to move in and out of different altered states of consciousness, and this study provides initial evidence that functional neuroimaging can objectively track their dynamics.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"125-145"},"PeriodicalIF":3.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00425
Eric G Ceballos, Andrea I Luppi, Gabriel Castrillon, Manish Saggar, Bratislav Misic, Valentin Riedl
{"title":"The control costs of human brain dynamics.","authors":"Eric G Ceballos, Andrea I Luppi, Gabriel Castrillon, Manish Saggar, Bratislav Misic, Valentin Riedl","doi":"10.1162/netn_a_00425","DOIUrl":"10.1162/netn_a_00425","url":null,"abstract":"<p><p>The human brain is a complex system with high metabolic demands and extensive connectivity that requires control to balance energy consumption and functional efficiency over time. How this control is manifested on a whole-brain scale is largely unexplored, particularly what the associated costs are. Using the network control theory, here, we introduce a novel concept, time-averaged control energy (TCE), to quantify the cost of controlling human brain dynamics at rest, as measured from functional and diffusion MRI. Importantly, TCE spatially correlates with oxygen metabolism measures from the positron emission tomography, providing insight into the bioenergetic footing of resting-state control. Examining the temporal dimension of control costs, we find that brain state transitions along a hierarchical axis from sensory to association areas are more efficient in terms of control costs and more frequent within hierarchical groups than between. This inverse correlation between temporal control costs and state visits suggests a mechanism for maintaining functional diversity while minimizing energy expenditure. By unpacking the temporal dimension of control costs, we contribute to the neuroscientific understanding of how the brain governs its functionality while managing energy expenses.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"77-99"},"PeriodicalIF":3.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Network NeurosciencePub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.1162/netn_a_00421
Shiva Mirzaeian, Ashkan Faghiri, Vince D Calhoun, Armin Iraji
{"title":"A telescopic independent component analysis on functional magnetic resonance imaging dataset.","authors":"Shiva Mirzaeian, Ashkan Faghiri, Vince D Calhoun, Armin Iraji","doi":"10.1162/netn_a_00421","DOIUrl":"10.1162/netn_a_00421","url":null,"abstract":"<p><p>Brain function can be modeled as dynamic interactions between functional sources at different spatial scales, and each spatial scale can contain its functional sources with unique information, thus using a single scale may provide an incomplete view of brain function. This paper introduces a novel approach, termed \"telescopic independent component analysis (TICA),\" designed to construct spatial functional hierarchies and estimate functional sources across multiple spatial scales using fMRI data. The method employs a recursive independent component analysis (ICA) strategy, leveraging information from a larger network to guide the extraction of information about smaller networks. We apply our model to the default mode network (DMN), visual network (VN), and right frontoparietal network (RFPN). We investigate further on the DMN by evaluating the difference between healthy people and individuals with schizophrenia. We show that the TICA approach can detect the spatial hierarchy of the DMN, VN, and RFPN. In addition, the TICA revealed DMN-associated group differences between cohorts that may not be captured if we focus on a single-scale ICA. In sum, our proposed approach represents a promising new tool for studying functional sources.</p>","PeriodicalId":48520,"journal":{"name":"Network Neuroscience","volume":"9 1","pages":"61-76"},"PeriodicalIF":3.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}