25 papers · ranked by Valyu relevance
Pierre Vandenhove
Representing the control flow of a computer program as a computation graph can bring many benefits in a broad variety of domains where performance is critical. This technique is a core component of most major numerical libraries (TensorFlow, PyTorch, Theano, MXNet,...) and is successfully used to speed up and optimise…
John M. Myers, Hadi Madjid
The accurate copying of nucleotides in DNA replication is arguably a digital computation. So are some cognitive capacities found in all organisms. In 2005 we proved that linking quantum calculations to evidence requires guesswork subject to revision (Madjid and Myers [9]). Based on this proof, we assume computations by…
Drew DeHaas, Ziqing Pan, Xinzhu Wei
Computational analysis of a large number of genomes requires a data structure that can represent the dataset compactly while also enabling efficient operations on variants and samples. Current practice is to store large-scale genetic polymorphism data using tabular data structures and file formats, where rows and…
Jordan Jalving, Yankai Cao, Víctor M. Zavala
We present graph-based modeling abstractions to represent cyber-physical dependencies arising in complex systems. Specifically, we propose an algebraic graph abstraction to capture physical connectivity in complex optimization models and a computing graph abstraction to capture communication connectivity in computing…
Nathanael Ackerman, Cameron E. Freer
We consider graph Turing machines, a model of parallel computation on a graph, in which each vertex is only capable of performing one of a finite number of operations. This model of computation is a natural generalization of several well-studied notions of computation, including ordinary Turing machines, cellular…
Marko A. Rodriguez
Gremlin is a graph traversal machine and language designed, developed, and distributed by the Apache TinkerPop project. Gremlin, as a graph traversal machine, is composed of three interacting components: a graph G, a traversal Ψ, and a set of traversers T . The traversers move about the graph according to the…
Authors not listed
Computational methods for predictive modeling have been increasingly utilized in the early stages of drug discovery to supplement high-throughput screening. The advent of highly efficient and complex machine learning architectures necessitates new methods of collating the plethora of topological, geometrical, and…
Amin Sahebi, Marco Barbone, Marco Procaccini, Wayne Luk + 2 more
'Georgi Gaydadjiev' 'Roberto Giorgi'] Processing large-scale graphs is challenging due to the nature of the computation that causes irregular memory access patterns. Managing such irregular accesses may cause significant performance degradation on both CPUs and GPUs. Thus, recent research trends propose graph…
Schaad, Philipp, Ben-Nun, Tal + 2 more
Control flow graphs (CFGs) are essential tools for understanding program behavior, yet the size of real-world CFGs makes them difficult to interpret. With thousands of nodes and edges, sophisticated graph drawing algorithms are required to present them on screens in ways that make them readable and understandable.…
Miguel E. Coimbra, Alexandre P. Francisco, Luís Veiga
The value of graph-based big data can be unlocked by exploring the topology and metrics of the networks they represent, and the computational approaches to this exploration take on many forms. For the use-case of performing global computations over a graph, it is first ingested into a graph processing system from one…
Tatsuya Akutsu, Hiroshi Nagamochi
Chemical compounds are usually represented as graph structured data in computers. In this review article, we overview several graph classes relevant to chemical compounds and the computational complexities of several fundamental problems for these graph classes. In particular, we consider the following problems…
Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani + 6 more
Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic data sets can be challenging to work at. These challenges have impeded…
Andrea Cracco, Alexandru I. Tomescu
Compacted de Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted graphs Bruijn graphs are a variant built on a collection of sequences, and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs…
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…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Subgraph isomorphism is a combinatorial problem that involves finding one or all occurrences of a pattern graph within a target graph. Subgraph isomorphism has numerous applications in fields such as biology, chemistry, social network analysis, and pattern recognition. Although subgraph isomorphism is generally…
Authors not listed
Identifying synthesis routes from knowledge graphs poses challenges beyond retrosynthesis, including path–finding artifacts and data issues. We introduce “SynGPS”, a novel algorithm that overcomes these limitations by identifying viable routes even with common artifacts. SynGPS can resolve nonsensical cycles…
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…
Bob Blakley, G. R. Blakley, Sean M. Blakley
A graph is a mathematical object consisting of a set of vertices and a set of edges connecting vertices. Graphs can be drawn on paper in various ways, but until recently all published methods of drawing graphs have had undesirable properties: (i) for graphs which are not plane embeddable, intersections between the…
Kavya Vaddadi, Naveen Sivadasan, Kshitij Tayal, Rajgopal Srinivasan
Genomic variations in a reference collection are naturally represented as genome variation graphs. Such graphs encode common subsequences as vertices and the variations are captured using additional vertices and directed edges. The resulting graphs are directed graphs possibly with cycles. Existing algorithms for…
Authors not listed
SynTemp is a framework designed to extract and hierarchically cluster reaction templates from large-scale reaction data repositories. Reaction templates are partial Imaginary Transition State graphs representing the reaction center as well as surrounding context. These graphs are equivalent to Double Pushout graph…
Venkatesh Kamaraj, Ayam Gupta, Karthik Raman, Manikandan Narayanan + 1 more
Genome graphs are reference structures appropriate for studying genetic diversity. By emphasising the polymorphic regions in a collection of genomes, their network layout can capture and compare the genetic diversity of different populations of interest. However, there are no existing methods to characterise and…
Authors not listed
Curried functions provide a systematic way of transforming multi-argument functions into nested singleargument functions. This transformation allows partial application and supports many central principles of functional programming. Their extension, called curried 𝑘-ary functions, naturally generalizes the familiar…
Siegfried Dubois, Matthias Zytnicki, Claire Lemaitre, Thomas Faraut
Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of…
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova + 5 more
RecGraph in recombination mode took from a few seconds to 3 min depending on the input graph size. We remind that our approach guarantees to find an optimal solution and that there are several heuristics that can be applied to speed up the computation-potentially forgoing this guarantee in a few cases. As expected…
Authors not listed
We present a unified, set–theoretic framework that extends molecular graphs to hypergraphs and superhypergraphs via iterated power sets. We define Molecular Graphs, Molecular HyperGraphs, and Molecular SuperHyperGraphs, and develop four complements over them: Weighted, Rough, Neural, and Multipolar frameworks. We prove…