arXiv subjects

Farnaz Zamani Esfahlani

Publications and source records attributed to Farnaz Zamani Esfahlani.

5 recordsLinked to original sources

arXiv2026

Structurally Constrained Brain Network Dynamics Reveal Reduced Functional Flexibility in Cocaine Use Disorder

Cocaine Use Disorder (CUD) is associated with widespread alterations in large-scale functional brain networks, yet the mechanisms contributing to these changes and their relationship to clinical and cognitive outcomes remain poorly understood. To address this gap, we introduce a framework to extract structurally informed dynamic functional connectivity patterns. We then leverage these connectivity patterns to characterize differences in functional brain network organization associated with CUD and to examine their relationship with clinical measures. Specifically, we applied Laplacian spectral smoothing to each participant's functional connectivity matrix using individualized structural priors derived from diffusion imaging. These structurally informed connectivity features were subsequently used to examine cross-network interactions and characterize dynamic community organization across functional brain states. Our findings indicate that individuals with cocaine use disorder exhibit increased integration and recruitment accompanied by reduced flexibility in the functional brain networks, with the most pronounced alterations in visual, attentional, and control systems. In addition, structurally informed functional connectivity features were predictive of weekly cocaine use within the CUD cohort. Overall, these results highlight the value of structurally informed dynamic connectivity measures for characterizing network-level alterations associated with cocaine addiction and for linking these alterations to clinically meaningful measures of cocaine use severity.

q-bio.NC↗

arXiv2026

Beyond Activation Alignment: The Geometry of Neural Sensitivity

Activation-alignment measures such as Representational Similarity Analysis (RSA), Canonical Correlation Analysis (CCA), and Centered Kernel Alignment (CKA) are widely used to compare biological and artificial neural representations. Recent theoretical work interprets many of these methods as assessing agreement between optimal linear readouts over broad families of global tasks. However, agreement at the level of global readouts does not determine how a system uses local stimulus evidence. Specifically, representations may align in activation space yet differ in their sensitivity to small perturbations. To address this challenge, we introduce a complementary framework based on local decodable information, which focuses on a representation's ability, under noise, to discriminate small perturbations within a specified stimulus-coordinate subspace. Building on Fisher information and local representation geometry, we summarize each representation using the expected projected pullback/Fisher metric over that subspace. This formulation induces a second-moment family of local discrimination tasks, for which the resulting operator provides a minimal, complete dataset-level summary of expected discriminability. We compare these regularized signatures using a log-spectral distance on the manifold of symmetric positive definite (SPD) matrices, yielding the Spectral Riemannian Alignment Score (S-RAS) and a uniform multiplicative certificate over the corresponding family of lifted task values. Empirically, this framework enables the recovery of corresponding layers across independently trained artificial neural networks, supports transferable class-conditional probes, reveals controlled dissociations between standard and robust training, and uncovers stimulus-coordinate family effects across mouse visual cortex using the Allen Brain Observatory static gratings dataset.

cs.LG↗

arXiv2021

Modularity maximization as a flexible and generic framework for brain network exploratory analysis

The modular structure of brain networks supports specialized information processing, complex dynamics, and cost-efficient spatial embedding. Inter-individual variation in modular structure has been linked to differences in performance, disease, and development. There exist many data-driven methods for detecting and comparing modular structure, the most popular of which is modularity maximization. Although modularity maximization is a general framework that can be modified and reparamaterized to address domain-specific research questions, its application to neuroscientific datasets has, thus far, been narrow. Here, we highlight several strategies in which the ``out-of-the-box'' version of modularity maximization can be extended to address questions specific to neuroscience. First, we present approaches for detecting ``space-independent'' modules and for applying modularity maximization to signed matrices. Next, we show that the modularity maximization frame is well-suited for detecting task- and condition-specific modules. Finally, we highlight the role of multi-layer models in detecting and tracking modules across time, tasks, subjects, and modalities. In summary, modularity maximization is a flexible and general framework that can be adapted to detect modular structure resulting from a wide range of hypotheses. This article highlights opens multiple frontiers for future research and applications.

q-bio.NC↗

arXiv2017

A Percolation-based Thresholding Method with Applications in Functional Connectivity Analysis

Despite the recent advances in developing more effective thresholding methods to convert weighted networks to unweighted counterparts, there are still several limitations that need to be addressed. One such limitation is the inability of the most existing thresholding methods to take into account the topological properties of the original weighted networks during the binarization process, which could ultimately result in unweighted networks that have drastically different topological properties than the original weighted networks. In this study, we propose a new thresholding method based on the percolation theory to address this limitation. The performance of the proposed method was validated and compared to the existing thresholding methods using simulated and real-world functional connectivity networks in the brain. Comparison of macroscopic and microscopic properties of the resulted unweighted networks to the original weighted networks suggest that the proposed thresholding method can successfully maintain the topological properties of the original weighted networks.

q-bio.QM↗

arXiv2017

Robust Tracking and Behavioral Modeling of Movements of Biological Collectives from Ordinary Video Recordings

We propose a novel computational method to extract information about interactions among individuals with different behavioral states in a biological collective from ordinary video recordings. Assuming that individuals are acting as finite state machines, our method first detects discrete behavioral states of those individuals and then constructs a model of their state transitions, taking into account the positions and states of other individuals in the vicinity. We have tested the proposed method through applications to two real-world biological collectives: termites in an experimental setting and human pedestrians in a university campus. For each application, a robust tracking system was developed in-house, utilizing interactive human intervention (for termite tracking) or online agent-based simulation (for pedestrian tracking). In both cases, significant interactions were detected between nearby individuals with different states, demonstrating the effectiveness of the proposed method.

cs.MA↗