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Networks are ubiquitous in biology where they encode connectivity patterns at all scales of organization, from molecular to the biome. However, biological networks are noisy due to the limitations of measurement technology and inherent…

Molecular Networks · Quantitative Biology 2018-08-16 Bo Wang , Armin Pourshafeie , Marinka Zitnik , Junjie Zhu , Carlos D. Bustamante , Serafim Batzoglou , Jure Leskovec

Global and national efforts to deliver high-quality nuclear data to users have a broad impact across applications such as national security, reactor operation, basic science, medical fields, and more. Cross section evaluation is a large…

Computational Physics · Physics 2025-05-08 Noah A. W. Walton , Oleksii Zivenko , William Fritsch , Jacob Forbes , Amanda Lewis , Jesse Brown , Vlad Sobes

There is a growing literature on the statistical analysis of multiple networks in which the network is the fundamental data object. However, most of this work requires networks on a shared set of labeled vertices. In this work, we consider…

Methodology · Statistics 2022-03-21 Nathaniel Josephs , Wenrui Li , Eric D. Kolaczyk

A reliable method for characterizing quantum operations that is suitable for improving and validating their accuracies is indispensable for realizing a practical quantum computer. Known methods are still not sufficient because they lack…

Quantum Physics · Physics 2021-06-25 Takanori Sugiyama , Shinpei Imori , Fuyuhiko Tanaka

Network structure is growing popular for capturing the intrinsic relationship between large-scale variables. In the paper we propose to improve the estimation accuracy for large-dimensional factor model when a network structure between…

Methodology · Statistics 2020-01-30 Long Yu , Yong He , Xinsheng Zhang , Ji Zhu

Algebraic neural networks (AlgNNs) are composed of a cascade of layers each one associated to and algebraic signal model, and information is mapped between layers by means of a nonlinearity function. AlgNNs provide a generalization of…

Machine Learning · Computer Science 2020-10-23 Alejandro Parada-Mayorga , Alejandro Ribeiro

Traditional algorithms for compressive sensing recovery are computationally expensive and are ineffective at low measurement rates. In this work, we propose a data driven non-iterative algorithm to overcome the shortcomings of earlier…

Computer Vision and Pattern Recognition · Computer Science 2017-08-18 Suhas Lohit , Kuldeep Kulkarni , Ronan Kerviche , Pavan Turaga , Amit Ashok

The number of algorithms available to reconstruct a biological network from a dataset of high-throughput measurements is nowadays overwhelming, but evaluating their performance when the gold standard is unknown is a difficult task. Here we…

Molecular Networks · Quantitative Biology 2012-09-11 Giuseppe Jurman , Michele Filosi , Roberto Visintainer , Samantha Riccadonna , Cesare Furlanello

Reconstructing complex networks from measurable data is a fundamental problem for understanding and controlling collective dynamics of complex networked systems. However, a significant challenge arises when we attempt to decode structural…

Physics and Society · Physics 2015-11-20 Xiao Han , Zhesi Shen , Wen-Xu Wang , Zengru Di

The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…

Computational Engineering, Finance, and Science · Computer Science 2015-01-19 Mirco Giacobbe , Calin C. Guet , Ashutosh Gupta , Thomas A. Henzinger , Tiago Paixao , Tatjana Petrov

Neuroscientists are actively pursuing high-precision maps, or graphs, consisting of networks of neurons and connecting synapses in mammalian and non-mammalian brains. Such graphs, when coupled with physiological and behavioral data, are…

We study online robust matrix completion on graphs. At each iteration a vector with some entries missing is revealed and our goal is to reconstruct it by identifying the underlying low-dimensional subspace from which the vectors are drawn.…

Information Theory · Computer Science 2016-05-16 Symeon Chouvardas , Mohammed Amin Abdullah , Lucas Claude , Moez Draief

Designing mechanically efficient geometry for architectural structures like shells, towers, and bridges, is an expensive iterative process. Existing techniques for solving such inverse problems rely on traditional optimization methods,…

Computational Engineering, Finance, and Science · Computer Science 2025-03-18 Rafael Pastrana , Eder Medina , Isabel M. de Oliveira , Sigrid Adriaenssens , Ryan P. Adams

Previous preliminary results on the application of knowledge networks to noise reduction in stationary harmonic and weakly chaotic signals are extended to more general cases. The formalism gives a novel algorithm from which statistical…

Data Analysis, Statistics and Probability · Physics 2007-05-23 Arturo Berrones

Researchers have developed neural network verification algorithms motivated by the need to characterize the robustness of deep neural networks. The verifiers aspire to answer whether a neural network guarantees certain properties with…

Machine Learning · Computer Science 2021-10-04 Kai Jia , Martin Rinard

Traditional artificial neural networks consist of nodes with non-oscillatory dynamics. Biological neural networks, on the other hand, consist of oscillatory components embedded in an oscillatory environment. Motivated by this feature of…

Neurons and Cognition · Quantitative Biology 2026-03-17 Mark A. Kramer

Discovering and characterizing the large-scale topological features in empirical networks are crucial steps in understanding how complex systems function. However, most existing methods used to obtain the modular structure of networks…

Data Analysis, Statistics and Probability · Physics 2014-03-26 Tiago P. Peixoto

As it is getting increasingly difficult to achieve gains in the density and power efficiency of microelectronic computing devices because of lithographic techniques reaching fundamental physical limits, new approaches are required to…

Emerging Technologies · Computer Science 2017-07-05 Jean C. Coulombe , Mark C. A. York , Julien Sylvestre

The identification of states and parameters from noisy measurements of a dynamical system is of great practical significance and has received a lot of attention. Classically, this problem is expressed as optimization over a class of models.…

Deep neural networks unlocked a vast range of new applications by solving tasks of which many were previously deemed as reserved to higher human intelligence. One of the developments enabling this success was a boost in computing power…

Neural and Evolutionary Computing · Computer Science 2021-12-17 Nadezhda Semenova , Laurent Larger , Daniel Brunner
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