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We present a topological framework for analysing neural time series that integrates Transfer Entropy (TE) with directed Persistent Homology (PH) to characterize information flow in spiking neural systems. TE quantifies directional influence…

Neurons and Cognition · Quantitative Biology 2025-08-27 Dylan Peek , Siddharth Pritam , Matthew P. Skerritt , Stephan Chalup

Hypergraphs and simplical complexes both capture the higher-order interactions of complex systems, ranging from higher-order collaboration networks to brain networks. One open problem in the field is what should drive the choice of the…

Physics and Society · Physics 2022-09-28 Federica Baccini , Filippo Geraci , Ginestra Bianconi

Brain networks, graphical models such as those constructed from MRI, have been widely used in pathological prediction and analysis of brain functions. Within the complex brain system, differences in neuronal connection strengths parcellate…

Machine Learning · Computer Science 2023-05-09 Wei Dai , Hejie Cui , Xuan Kan , Ying Guo , Sanne van Rooij , Carl Yang

The main goal of this study is to extract a set of brain networks in multiple time-resolutions to analyze the connectivity patterns among the anatomic regions for a given cognitive task. We suggest a deep architecture which learns the…

Machine Learning · Statistics 2017-08-16 Arash Rahnama , Abdullah Alchihabi , Vijay Gupta , Panos Antsaklis , Fatos T. Yarman Vural

Recent advances in neuroimaging along with algorithmic innovations in statistical learning from network data offer a unique pathway to integrate brain structure and function, and thus facilitate revealing some of the brain's organizing…

Signal Processing · Electrical Eng. & Systems 2021-12-21 Yang Li , Gonzalo Mateos , Zhengwu Zhang

The study of hierarchy in networks of the human brain has been of significant interest among the researchers as numerous studies have pointed out towards a functional hierarchical organization of the human brain. This paper provides a novel…

Neurons and Cognition · Quantitative Biology 2021-03-02 Dushyant Sahoo , Theodore D. Satterthwaite , Christos Davatzikos

Data-driven graph learning models a network by determining the strength of connections between its nodes. The data refers to a graph signal which associates a value with each graph node. Existing graph learning methods either use simplified…

Machine Learning · Computer Science 2020-11-05 Nafiseh Ghoroghchian , David M. Groppe , Roman Genov , Taufik A. Valiante , Stark C. Draper

Large-scale electrophysiological recordings now allow simultaneous monitoring of thousands of neurons across multiple brain regions, revealing structured variability in neural population activity. Understanding how these collective patterns…

Neurons and Cognition · Quantitative Biology 2026-03-12 Nicolas Béreux , Giovanni Catania , Aurélien Decelle , Francesca Mignacco , Alfonso de Jesús Navas Gómez , Beatriz Seoane

In brain network analysis using resting-state fMRI, there is growing interest in modeling higher-order interactions beyond simple pairwise connectivity via persistent homology. Despite the promise of these advanced topological tools, robust…

Neurons and Cognition · Quantitative Biology 2025-03-20 Moo K. Chung , Anass B. El-Yaagoubi , Anqi Qiu , Hernando Ombao

Understanding how neural systems efficiently process information through distributed representations is a fundamental challenge at the interface of neuroscience and machine learning. Recent approaches analyze the statistical and geometrical…

Neurons and Cognition · Quantitative Biology 2025-04-01 Francesca Mignacco , Chi-Ning Chou , SueYeon Chung

Computer-aided diagnosis (CAD) systems play a crucial role in analyzing neuroimaging data for neurological and psychiatric disorders. However, small-sample studies suffer from low reproducibility, while large-scale datasets introduce…

Machine Learning · Computer Science 2025-08-12 Xinglin Zhao , Yanwen Wang , Xiaobo Liu , Yanrong Hao , Rui Cao , Xin Wen

Object rearrangement is a challenge for embodied agents because solving these tasks requires generalizing across a combinatorially large set of configurations of entities and their locations. Worse, the representations of these entities are…

Machine Learning · Computer Science 2023-03-22 Michael Chang , Alyssa L. Dayan , Franziska Meier , Thomas L. Griffiths , Sergey Levine , Amy Zhang

This study focuses on the problem of user satisfaction classification and proposes a framework based on graph neural networks to address the limitations of traditional methods in handling complex interaction relationships and…

Human-Computer Interaction · Computer Science 2025-11-07 Rui Liu , Runsheng Zhang , Shixiao Wang

Brain networks/graphs derived from resting-state functional MRI (fMRI) help study underlying pathophysiology of neurocognitive disorders by measuring neuronal activities in the brain. Some studies utilize learning-based methods for brain…

Image and Video Processing · Electrical Eng. & Systems 2024-11-05 Qianqian Wang , Wei Wang , Yuqi Fang , Hong-Jun Li , Andrea Bozoki , Mingxia Liu

Graph Neural Networks (GNNs) draw their strength from explicitly modeling the topological information of structured data. However, existing GNNs suffer from limited capability in capturing the hierarchical graph representation which plays…

Machine Learning · Computer Science 2021-03-30 Jinyu Yang , Peilin Zhao , Yu Rong , Chaochao Yan , Chunyuan Li , Hehuan Ma , Junzhou Huang

Graphs can represent relational information among entities and graph structures are widely used in many intelligent tasks such as search, recommendation, and question answering. However, most of the graph-structured data in practice suffers…

Information Retrieval · Computer Science 2021-12-30 Hanxiong Chen , Yunqi Li , Shaoyun Shi , Shuchang Liu , He Zhu , Yongfeng Zhang

We introduce the hierarchical compositional network (HCN), a directed generative model able to discover and disentangle, without supervision, the building blocks of a set of binary images. The building blocks are binary features defined…

Machine Learning · Computer Science 2017-10-27 Miguel Lázaro-Gredilla , Yi Liu , D. Scott Phoenix , Dileep George

We propose a Bayesian framework for uncertainty quantification and comparison in brain connectivity graph analysis. Standard graph-based approaches typically rely on point estimates of correlation matrices, overlooking the uncertainty…

Methodology · Statistics 2026-05-29 Alice Chevaux , Julyan Arbel , Guillaume Kon Kam King , Sophie Achard

Most humans have the good fortune to live their lives embedded in richly structured social groups. Yet, it remains unclear how humans acquire knowledge about these social structures to successfully navigate social relationships. Here we…

Neurons and Cognition · Quantitative Biology 2019-04-23 Steven H. Tompson , Ari E. Kahn , Emily B. Falk , Jean M. Vettel , Danielle S. Bassett

The Hopfield network model and its generalizations were introduced as a model of associative, or content-addressable, memory. They were widely investigated both as an unsupervised learning method in artificial intelligence and as a model of…

Neurons and Cognition · Quantitative Biology 2024-12-10 Marco Cafiso , Paolo Paradisi