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A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…

Quantitative Methods · Quantitative Biology 2010-11-24 Adam A. Margolin , Kai Wang , Andrea Califano , Ilya Nemenman

Accurately characterizing higher-order interactions of brain regions and extracting interpretable organizational patterns from Functional Magnetic Resonance Imaging data is crucial for brain disease diagnosis. Current graph-based deep…

Neurons and Cognition · Quantitative Biology 2026-03-16 Dengyi Zhao , Zhiheng Zhou , Guiying Yan , Dongxiao Yu , Xingqin Qi

One of the most well-established tools for modeling the brain as a complex system is the functional connectivity network, which examines the correlations between pairs of interacting brain regions. While powerful, the network model is…

Information Theory · Computer Science 2022-06-15 Thomas F. Varley , Maria Pope , Joshua Faskowitz , Olaf Sporns

To understand collective network behavior in the complex human brain, pairwise correlation networks alone are insufficient for capturing the high-order interactions that extend beyond pairwise interactions and play a crucial role in brain…

Neurons and Cognition · Quantitative Biology 2025-07-01 Qiang Li , Jingyu Liu , Vince D. Calhoun

Identifying dependency in multivariate data is a common inference task that arises in numerous applications. However, existing nonparametric independence tests typically require computation that scales at least quadratically with the sample…

Methodology · Statistics 2021-07-08 Shai Gorsky , Li Ma

The connectome, a map of the structural and/or functional connections in the brain, provides a complex representation of the neurobiological phenotypes on which it supervenes. This information-rich data modality has the potential to…

Traditional Topological Data Analysis (TDA) methods, such as Persistent Homology (PH), rely on distance measures (e.g., cross-correlation, partial correlation, coherence, and partial coherence) that are symmetric by definition. While useful…

Neurons and Cognition · Quantitative Biology 2024-07-19 Anass B. El-Yaagoubi , Moo K. Chung , Hernando Ombao

Several data-driven approaches based on information theory have been proposed for analyzing high-order interactions involving three or more components of a network system. Most of these methods are defined only in the time domain and rely…

Applications · Statistics 2025-03-18 Yuri Antonacci , Chiara Bara' , Laura Sparacino , Gorana Mijatovic , Ludovico Minati , Luca Faes

Functional brain networks exhibit topological structures that reflect neural organization; however, statistical comparison of these networks is challenging for several reasons. This paper introduces a topologically invariant permutation…

Neurons and Cognition · Quantitative Biology 2025-12-30 Sixtus Dakurah

Pairwise metrics are often employed to estimate statistical dependencies between brain regions, however they do not capture higher-order information interactions. It is critical to explore higher-order interactions that go beyond paired…

Neurons and Cognition · Quantitative Biology 2023-08-04 Qiang Li , Shujian Yu , Kristoffer H Madsen , Vince D Calhoun , Armin Iraji

In this paper, we focus on the problem of statistical dependence estimation using characteristic functions. We propose a statistical dependence measure, based on the maximum-norm of the difference between joint and product-marginal…

Machine Learning · Computer Science 2022-08-18 Povilas Daniušis , Shubham Juneja , Lukas Kuzma , Virginijus Marcinkevičius

Thresholding--the pruning of nodes or edges based on their properties or weights--is an essential preprocessing tool for extracting interpretable structure from complex network data, yet existing methods face several key limitations.…

Social and Information Networks · Computer Science 2025-10-07 Adam Schroeder , Russell Funk , Jingyi Guan , Taylor Okonek , Lori Ziegelmeier

The problem of measuring conditional dependence between two random phenomena arises when a third one (a confounder) has a potential influence on the amount of information between them. A typical issue in this challenging problem is the…

Machine Learning · Statistics 2025-03-12 Ferran de Cabrera , Marc Vilà-Insa , Jaume Riba

Poor data quality has become a pervasive issue due to the increasing complexity and size of modern datasets. Constraint based data cleaning techniques rely on integrity constraints as a benchmark to identify and correct errors. Data values…

Databases · Computer Science 2017-05-25 Sridevi Baskaran , Alexander Keller , Fei Chiang , Golab Lukasz , Jaroslaw Szlichta

Mild cognitive impairment (MCI) is characterized by subtle changes in cognitive functions, often associated with disruptions in brain connectivity. The present study introduces a novel fine-grained analysis to examine topological…

Computer Vision and Pattern Recognition · Computer Science 2024-08-29 Ninad Aithal , Debanjali Bhattacharya , Neelam Sinha , Thomas Gregor Issac

Battiston et al. (arXiv:2110.06023) provide a comprehensive overview of how investigations of complex systems should take into account interactions between more than two elements, which can be modelled by hypergraphs and studied via…

We propose the conditional predictive impact (CPI), a consistent and unbiased estimator of the association between one or several features and a given outcome, conditional on a reduced feature set. Building on the knockoff framework of…

Methodology · Statistics 2021-05-14 David S. Watson , Marvin N. Wright

Handling highly dependent data is crucial in clinical trials, particularly in fields related to ophthalmology. Incorrectly specifying the dependency structure can lead to biased inferences. Traditionally, models rely on three fixed…

Methodology · Statistics 2025-09-30 Shuyi Liang , Takeshi Emura , Chang-Xing Ma , Yijing Xin , Xin-Wei Huang

Dependency analysis is a technique to identify and determine data dependencies between service protocols. Protocols evolving concurrently in the service composition need to impose an order in their execution if there exist data…

Software Engineering · Computer Science 2010-07-30 Javier Cubo , Ernesto Pimentel , Gwen Salaün , Carlos Canal

In this paper, we leverage existing statistical methods to better understand feature learning from data. We tackle this by modifying the model-free variable selection method, Feature Ordering by Conditional Independence (FOCI), which is…

Machine Learning · Statistics 2025-02-14 Krunoslav Lehman Pavasovic , David Lopez-Paz , Giulio Biroli , Levent Sagun