26 papers · ranked by Valyu relevance
François Caron, Emily B. Fox
Title: Summary Statistical network modelling has focused on representing the graph as a discrete structure, namely the adjacency matrix. When assuming exchangeability of this array-which can aid in modelling, computations and theoretical analysis-the Aldous-Hoover theorem informs us that the graph is necessarily either…
Adithya Gungi, Pradyumna Sepúlveda Delgado, Ines F. Aitsahalia, Marta Blanco-Pozo + 1 more
Flexible, goal-directed behavior depends on learning predictive relationships, yet how reward shapes learned transition structure remains incompletely understood. Here we introduce the Sparse Cognitive Graph, a reinforcement-learning framework in which a continuously updated transition representation is sparsified into…
Martin Rektoris, Milan Papež, Václav Šmídl, Tomáš Pevný
Deep generative models (DGMs) for graphs achieve impressively high expressive power thanks to very efficient and scalable neural networks. However, these networks contain non-linearities that prevent analytical computation of many standard probabilistic inference queries, i.e., these DGMs are considered intractable.…
Svante Janson
We study a recent model for edge exchangeable random graphs introduced by Crane and Dempsey; in particular we study asymptotic properties of the random simple graph obtained by merging multiple edges. We study a number of examples, and show that the model can produce dense, sparse and extremely sparse random graphs.…
Anton Tsitsulin, Bryan Perozzi
In this work, we introduce the Graph Lottery Ticket (GLT) Hypothesis – that there is an extremely sparse backbone for every graph, and that graph learning algorithms attain comparable performance when trained on that subgraph as on the full graph. We identify and systematically study 8 key metrics of interest that…
Mikko Rautiainen, Tobias Marschall
De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally long read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided a combination of long read length and low error rate, which enables…
Peter Wills, François G. Meyer
Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience [1], cyber security [2], social network analysis [3], and bioinformatics [4], among others. Discovery and comparison of structures such as modular communities, rich clubs…
Swati Goswami, Asit Kumar Das, Subhas C. Nandy
A majority of real-life networks are weighted and sparse. The present article aims at characterization of weighted networks based on sparsity, as an indicator of inherent diversity of different network parameters. The measure called sparsity index defined on ordered degree sequence of simple networks is extended and…
Sevvandi Kandanaarachchi, Cheng Soon Ong
We consider the problem of estimating graph limits, known as graphons, from observations of sequences of sparse finite graphs. In this paper we show a simple method that can shed light on a subset of sparse graphs. The method involves mapping the original graphs to their line graphs. We show that graphs satisfying a…
Tomokaze Shiratori, Yuichi Takano, Jianchao Bai
Sparse estimation of a Gaussian graphical model (GGM) is an important technique for making relationships between observed variables more interpretable. Various methods have been proposed for sparse GGM estimation, including the graphical lasso that uses the ℓ1 norm regularization term, and other methods that use…
Kazumitsu Maehara, Yasuyuki Ohkawa
Single-cell analysis is a powerful technique used to identify a specific cell population of interest during differentiation, aging, or oncogenesis. Individual cells occupy a particular transient state in the cell cycle, circadian rhythm, or during cell death. An appealing concept of pseudo-time trajectory analysis of…
Heli Sun, Xuechun Liu, Miaomiao Sun, Ruichen Cao + 4 more
The Sparse Subgraph Finding (SGF) problem addresses the challenge of identifying sub-graphs with weak social interactions and sparse connections within a graph, which can be effectively modeled as discovering sparse subsystems in intelligent sensor networks. Traditional methods often rely on manually designed…
Harsh Shrivastava
There is a considerable body of work in the field of computer science on the topic of sparse graph recovery, particularly with regards to the innovative deep learning approaches that have been recently introduced. Despite this abundance of research, however, these methods are often not applied to the recovery of Gene…
Runze Chen, Kaibiao Lin, Binsheng Hong, Shandan Zhang + 1 more
In previous research, the prevailing assumption was that Graph Neural Networks (GNNs) precisely depicted the interconnections among nodes within the graph's architecture. Nonetheless, real-world graph datasets are often rife with noise, elements that can disseminate through the network and ultimately affect the outcome…
Aric Hagberg, Nathan Lemons, Wen-Bo Du
The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse…
Ryan Wickman, Xiaofei Zhang, Weizi Li
—The interconnectedness and interdependence of modern graphs are growing ever more complex, causing enormous resources for processing, storage, communication, and decision-making of these graphs. In this work, we focus on the task graph sparsification: an edge-reduced graph of a similar structure to the original graph…
Peter Eades, Quan Nguyen, Seok-Hee Hong
Spectral sparsification is a general technique developed by Spielman et al. to reduce the number of edges in a graph while retaining its structural properties. We investigate the use of spectral sparsification to produce good visual representations of big graphs. We evaluate spectral sparsification approaches on…
Lionel Zoubritzky, François-Xavier Coudert
We present here an open-source Julia library for the topological identification of crystalline materials, with algorithmic and computational improvements over the previously available software in the field, resulting in a speed increase of one order of magnitude. This new algorithm and implementation can therefore be…
Aristides Gionis, Polina Rozenshtein, Nikolaj Tatti, Evimaria Terzi
In this paper, we consider a novel formulation of the network-sparsification problem. In addition to the network, we also consider as input a set of communities. The goal is to sparsify the network so as to preserve the network structure with respect to the given communities. We introduce two variants of the…
Laura Eslava, Sayle Sigarreta Ricardo, Arno Siri-Jégousse
We prove that the generalized Randić index over graphs following the Erdos-Rényi model, for both the sparse and dense regimes, is concentrated around its mean when the number of vertices tends to infinity.
Jianshu Zhao, Jean Pierre Both, Rob Knight
Graph/network representation learning (or graph/network embedding) is a widely used machine learning technique in industry recommending systems and has recently been applied in computational biology. Popular network representation learning algorithms include random walk and matrix factorization methods, but they do not…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Subgraph isomorphism is a fundamental combinatorial problem that involves finding one or more occurrences of a pattern graph within a target graph. It arises in a wide range of application domains, including biology, chemistry, social network analysis, and pattern recognition. Although subgraph isomorphism is…
Sanjar Adilov
Machine learning models for molecular-property prediction typically work with molecular representations in the form of fingerprints, descriptors, or graphs. In case of fingerprints and descriptors, molecular representations usually comprise thousands of features, which causes the curse of dimensionality for many…
David Buterez, Jon Paul Janet, Steven Kiddle, Pietro Liò
We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property ofinterest. This problem arises in discovery processes…
Trevor Gokey, David L. Mobley
Molecular mechanics force fields require a chemical perception model to assign parameters to molecules. A recent advancement in force fields is the use of the SMARTS substructure query language as the perception model. Although it is straightforward to write SMARTS patterns to define new force field parameters, it is…
Authors not listed
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…