arXiv subjects

James M. Shine

Publications and source records attributed to James M. Shine.

12 recordsLinked to original sources

arXiv2026

A Data-Driven Method to Map the Functional Organisation of Human Brain White Matter

The white matter of the brain is organised into axonal bundles that support long-range neural communication. Although diffusion MRI (dMRI) enables detailed mapping of these pathways through tractography, how white matter pathways directly facilitate large-scale neural synchronisation remains poorly understood. We developed a data-driven framework that integrates dMRI and functional MRI (fMRI) to model the dynamic coupling supported by white matter tracks. Specifically, we employed track dynamic functional connectivity (Track-DFC) to characterise functional coupling of remote grey matter connected by individual white matter tracks. Using independent component analysis followed by k-medoids clustering, we derived functionally-coherent clusters of white matter tracks from the Human Connectome Project young adult cohort. When applied to the HCP ageing cohort, these clusters exhibited widespread age-related declines in both functional coupling strength and temporal variability. Importantly, specific clusters encompassing pathways linking control, default mode, attention, and visual systems significantly mediated the relationship between age and cognitive performance. Together, these findings depict the functional organisation of white matter tracks and provide a powerful tool to study brain ageing and cognitive decline.

q-bio.NC↗

arXiv2026

Estimating measures of information processing during cognitive tasks using functional magnetic resonance imaging

Cognition is increasingly framed in terms of information processing, yet most fMRI analyses focus on activation or functional connectivity rather than quantifying how information is stored and transferred. To remedy this problem, we propose a framework for estimating measures of information processing: active information storage (AIS), transfer entropy (TE), and net synergy from task-based fMRI. AIS measures information maintained within a region, TE captures directed information flow, and net synergy contrasts higher-order synergistic to redundant interactions. Crucially, to enable this framework we utilised a recently developed approach for calculating information-theoretic measures: the cross mutual information. This approach combines resting-state and task data to address the challenges of limited sample size, non-stationarity and context in task-based fMRI. We applied this framework to the working memory (N-back) task from the Human Connectome Project (470 participants). Results show that AIS increases in fronto-parietal regions with working memory load, TE reveals enhanced directed information flows across control pathways, and net synergy indicates a global shift to redundancy. This work establishes a novel methodology for quantifying information processing in task-based fMRI.

q-bio.NC↗

arXiv2026

Unifying concepts in information-theoretic time-series analysis

Information theory is a powerful framework for quantifying complexity, uncertainty, and dynamical structure in time-series data, with widespread applicability across disciplines such as physics, finance, and neuroscience. However, the literature on these measures remains fragmented, with domain-specific terminologies, inconsistent mathematical notation, and disparate visualization conventions that hinder interdisciplinary integration. This work addresses these challenges by unifying key information-theoretic time-series measures through shared semantic definitions, standardized mathematical notation, and cohesive visual representations. We compare these measures in terms of their theoretical foundations, computational formulations, and practical interpretability -- mapping them onto a common conceptual space through an illustrative case study with functional magnetic resonance imaging time series in the brain. This case study exemplifies the complementary insights these measures offer in characterizing the dynamics of complex neural systems, such as signal complexity and information flow. By providing a structured synthesis, our work aims to enhance interdisciplinary dialogue and methodological adoption, which is particularly critical for reproducibility and interoperability in computational neuroscience. More broadly, our framework serves as a resource for researchers seeking to navigate and apply information-theoretic time-series measures to diverse complex systems.

cs.IT↗

arXiv2025

A Minimal Quantitative Model of Perceptual Suppression and Breakthrough in Visual Rivalry

When conflicting images are presented to either eye, binocular fusion is disrupted. Rather than experiencing a blend of both percepts, often only one eye's image is experienced, whilst the other is suppressed from awareness. Importantly, suppression is transient - the two rival images compete for dominance, with stochastic switches between mutually exclusive percepts occurring every few seconds with law-like regularity. From the perspective of dynamical systems theory, visual rivalry offers an experimentally tractable window into the dynamical mechanisms governing perceptual awareness. In a recently developed visual rivalry paradigm - tracking continuous flash suppression (tCFS) - it was shown that the transition between awareness and suppression is hysteretic, with a higher contrast threshold required for a stimulus to breakthrough suppression into awareness than to be suppressed from awareness. Here, we present an analytically-tractable model of visual rivalry that quantitatively explains the hysteretic transition between periods of awareness and suppression in tCFS. Grounded in the theory of neural dynamics, we derive closed-form expressions for the duration of perceptual dominance and suppression, and for the degree of hysteresis (i.e. the depth of perceptual suppression), as a function of model parameters. Finally, our model yields a series of novel behavioural predictions, the first of which - distributions of dominance and suppression durations during tCFS should be approximately equal - we empirically validate in human psychophysical data.

q-bio.NC↗

arXiv2025

Cross Mutual Information

Mutual information (MI) is a useful information-theoretic measure to quantify the statistical dependence between two random variables: $X$ and $Y$. Often, we are interested in understanding how the dependence between $X$ and $Y$ in one set of samples compares to another. Although the dependence between $X$ and $Y$ in each set of samples can be measured separately using MI, these estimates cannot be compared directly if they are based on samples from a non-stationary distribution. Here, we propose an alternative measure for characterising how the dependence between $X$ and $Y$ as defined by one set of samples is expressed in another, \textit{cross mutual information}. We present a comprehensive set of simulation studies sampling data with $X$-$Y$ dependencies to explore this measure. Finally, we discuss how this relates to measures of model fit in linear regression, and some future applications in neuroimaging data analysis.

cs.IT↗

arXiv2025

The role of gain neuromodulation in layer-5 pyramidal neurons

Biological and artificial learning systems alike confront the plasticity-stability dilemma. In the brain, neuromodulators such as acetylcholine and noradrenaline relieve this tension by tuning neuronal gain and inhibitory gating, balancing segregation and integration of circuits. Fed by dense cholinergic and noradrenergic projections from the ascending arousal system, layer-5 pyramidal neurons in the cerebral cortex offer a relevant substrate for understanding these dynamics. When distal dendritic signals coincide with back-propagating action potentials, calcium plateaus turn a single somatic spike into a high-gain burst, and interneuron inhibition sculpts the output. These properties make layer-5 cells gain-tunable amplifiers that translate neuromodulatory cues into flexible cortical activity. To capture this mechanism we developed a two-compartment Izhikevich model for pyramidal neurons and single-compartment somatostatin (SOM) and parvalbumin (PV) interneurons, linked by Gaussian connectivity and spike-timing-dependent plasticity (STDP). The soma and apical dendrite are so coupled that somatic spikes back-propagate, while dendritic plateaus can switch the soma from regular firing to bursting by shifting reset and adaptation variables. We show that stronger dendritic drive or tighter coupling raise gain by increasing the likelihood of calcium-triggered somatic bursts. In contrast, dendritic-targeted inhibition suppresses gain, while somatic-targeted inhibition raises the firing threshold of neighboring neurons, thus gating neurons output. Notably, bursting accelerates STDP, supporting rapid synaptic reconfiguration and flexibility. This suggests that brief gain pulses driven by neuromodulators could serve as an adaptive two-timescale optimization mechanism, effectively modulating the synaptic weight updates.

q-bio.NC↗

arXiv2023

The feasibility of artificial consciousness through the lens of neuroscience

Interactions with large language models have led to the suggestion that these models may soon be conscious. From the perspective of neuroscience, this position is difficult to defend. For one, the inputs to large language models lack the embodied, embedded information content characteristic of our sensory contact with the world around us. Secondly, the architecture of large language models is missing key features of the thalamocortical system that have been linked to conscious awareness in mammals. Finally, the evolutionary and developmental trajectories that led to the emergence of living conscious organisms arguably have no parallels in artificial systems as envisioned today. The existence of living organisms depends on their actions, and their survival is intricately linked to multi-level cellular, inter-cellular, and organismal processes culminating in agency and consciousness.

q-bio.NC↗

arXiv2023

On the information-theoretic formulation of network participation

The participation coefficient is a widely used metric of the diversity of a node's connections with respect to a modular partition of a network. An information-theoretic formulation of this concept of connection diversity, referred to here as participation entropy, has been introduced as the Shannon entropy of the distribution of module labels across a node's connected neighbors. While diversity metrics have been studied theoretically in other literatures, including to index species diversity in ecology, many of these results have not previously been applied to networks. Here we show that the participation coefficient is a first-order approximation to participation entropy and use the desirable additive properties of entropy to develop new metrics of connection diversity with respect to multiple labelings of nodes in a network, as joint and conditional participation entropies. The information-theoretic formalism developed here allows new and more subtle types of nodal connection patterns in complex networks to be studied.

physics.soc-ph↗

arXiv2023

Noradrenergic neuromodulation of nonlinear bursting neurons controls critical dynamics

In order to remain adaptable to a dynamic environment, neural activity must be simultaneously both sensitive and stable. To solve this problem, the brain has been hypothesised to sit near a critical boundary. Yet, precisely how criticality and these opposing information processing modes are implemented in the brain remains elusive. A potential solution to this problem involves modulating intrinsically nonlinear neurons within the cerebral cortex with neuromodulatory neurotransmitters such as noradrenaline, a highly-conserved chemical released from the pontine locus coeruleus. Here we confirm that neuronal spiking in mice is poised close to the critical point of a branching process and that time-varying signatures of criticality fluctuate with neuromodulatory tone, as assessed by dynamic alterations in pupil diameter. We explore these results theoretically by creating a dual-compartment model of non-linear pyramidal neurons - capable of both regular spike and bursting modes - that replicates our main empirical findings of slightly subcritical dynamics. We then probe our model at a resolution impossible in vivo to demonstrate that noradrenaline differentially alters spiking- and bursting-criticality to facilitate sensitive and stable dynamics following an inverted-U profile that peaks at intermediate noradrenergic tone. Finally, we demonstrate that this intermediate noradrenergic regime displays burst avalanches with power-law size and duration distributions and scaling relationship belonging to the universality class of self-organized criticality. Our results confirm that the noradrenergic ascending arousal system acts as a control parameter for emergent critical dynamics in the brain. This methodology could be extended to explore other neuromodulators as control parameters of the brain.

q-bio.NC↗

arXiv2021

Assessing the Significance of Directed and Multivariate Measures of Linear Dependence Between Time Series

Inferring linear dependence between time series is central to our understanding of natural and artificial systems. Unfortunately, the hypothesis tests that are used to determine statistically significant directed or multivariate relationships from time-series data often yield spurious associations (Type I errors) or omit causal relationships (Type II errors). This is due to the autocorrelation present in the analysed time series -- a property that is ubiquitous across diverse applications, from brain dynamics to climate change. Here we show that, for limited data, this issue cannot be mediated by fitting a time-series model alone (e.g., in Granger causality or prewhitening approaches), and instead that the degrees of freedom in statistical tests should be altered to account for the effective sample size induced by cross-correlations in the observations. This insight enabled us to derive modified hypothesis tests for any multivariate correlation-based measures of linear dependence between covariance-stationary time series, including Granger causality and mutual information with Gaussian marginals. We use both numerical simulations (generated by autoregressive models and digital filtering) as well as recorded fMRI-neuroimaging data to show that our tests are unbiased for a variety of stationary time series. Our experiments demonstrate that the commonly used $F$- and $χ^2$-tests can induce significant false-positive rates of up to $100\%$ for both measures, with and without prewhitening of the signals. These findings suggest that many dependencies reported in the scientific literature may have been, and may continue to be, spuriously reported or missed if modified hypothesis tests are not used when analysing time series.

stat.ME↗

arXiv2016

Temporal meta-states are associated with differential patterns of dynamic connectivity, network topology and attention

Little is currently known about the coordination of neural activity over longitudinal time-scales and how these changes relate to behavior. To investigate this issue, we used resting-state fMRI data from a single individual to identify the presence of two distinct temporal states that fluctuated over the course of 18 months. We then demonstrated that these temporal states were associated with distinct neural dynamics within individual scanning sessions. In addition, the temporal states were also related to significant alterations in global efficiency, as well as differences in self-reported attention. These patterns were replicated in a separate longitudinal dataset, providing further supportive evidence for the presence of fluctuations in functional network topology over time. Together, our results underscore the importance of longitudinal phenotyping in cognitive neuroscience.

q-bio.NC↗

arXiv2016

The Dynamics of Functional Brain Networks: Integrated Network States during Cognitive Function

Higher brain function relies upon the ability to flexibly integrate information across specialized communities of brain regions, however it is unclear how this mechanism manifests over time. In this study, we use time-resolved network analysis of functional magnetic resonance imaging data to demonstrate that the human brain traverses between two functional states that maximize either segregation into tight-knit communities or integration across otherwise disparate neural regions. The integrated state enables faster and more accurate performance on a cognitive task, and is associated with dilations in pupil diameter, suggesting that ascending neuromodulatory systems may govern the transition between these alternative modes of brain function. Our data confirm a direct link between cognitive performance and the dynamic reorganization of the network structure of the brain.

q-bio.NC↗