25 papers · ranked by Valyu relevance
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…
Amirmohammad Farzaneh, Justin P. Coon, Mihai-Alin Badiu, Narsis A. Kiani + 2 more
'Narsis A. Kiani' 'Hector Zenil' 'Jesper Tegnér'] Throughout the years, measuring the complexity of networks and graphs has been of great interest to scientists. The Kolmogorov complexity is known as one of the most important tools to measure the complexity of an object. We formalized a method to calculate an upper…
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…
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…
Bafna, Mehul, Amirian, Shaghik
Graph polynomials encode fundamental combinatorial invariants of graphs. Their computation is investigated using tree and path decomposition frameworks, with formal definitions of treewidth, k-trees, and pathwidth establishing the structural basis for algorithmic efficiency. Explicit algorithms are constructed for each…
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.…
Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr + 7 more
'Tiffany J. Callahan' 'Carlos Cano' 'Marcin P. Joachimiak' 'Christopher J. Mungall' 'Peter N. Robinson' 'Justin Reese' 'Giorgio Valentini'] Graph representation learning methods opened new avenues for addressing complex, real-world problems represented by graphs. However, many graphs used in these applications comprise…
Jack Liell-Cock, Tom Schrijvers
Approach We present a novel data type for edge graphs, based on total and recursive definitions, that prevents usage errors from partial APIs and promotes structurally recursive computations. We follow an algebraic approach and provide a set of primitive constructors and combinators, along with equational laws that…
Tobias Røikjer, Asger Hobolth, Kasper Munch
Phase-type distributions model the time until absorption in continuous or discrete-time Markov chains on a finite state space. The multivariate phase-type distributions have diverse and important applications by modeling rewards accumulated at visited states. However, even moderately-sized state spaces make the…
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…
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…
Alun Thomas
We describe the implementation of the Giudici-Green Metropolis sampling method for decomposable graphs using a variety of structures to represent the graph. These comprise the graph itself, the Junction tree, the Almond tree and the Ibarra clique-separator graph. For each structure, we describe the process for…
Ziad Ismaili Alaoui, Detlef Plump
Algorithms Authors: ['Ziad Ismaili Alaoui' 'Detlef Plump'] > Abstract. We report on a recent breakthrough in rule-based graph programming, which allows us to match the time complexity of some fundamental imperative graph algorithms. In general, achieving the complexity of graph algorithms in conventional languages…
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…
Paul Merrell
This is a companion piece to my paper on "Example-Based Procedural Modeling Using Graph Grammars." This paper examines some of the theoretical issues in more detail. This paper discusses some more complex parts of the implementation, why certain algorithmic decisions were made, proves the algorithm can solve certain…
Tom Claassen, Joris M. Mooij
We present a new, efficient procedure to establish Markov equivalence between directed graphs that may or may not contain cycles under the dseparation criterion. It is based on the Cyclic Equivalence Theorem (CET) in the seminal works on cyclic models by Thomas Richardson in the mid '90s, but now rephrased from an…
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…
Tom Davot, Annie Chateau, Rohan Fossé, Rodolphe Giroudeau + 1 more
Background Scaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem of a particular graph called the “scaffold graph”. Results We provide some NP-hardness and…