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…
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…
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…
Yu-Hsueh Fang, He-Zhe Lin, Jie-Jyun Liu, Chih-Jen Lin
Automatic differentiation is a key component in deep learning. This topic is well studied and excellent surveys such as Baydin et al. (2018) have been available to clearly describe the basic concepts. Further, sophisticated implementations of automatic differentiation are now an important part of popular deep learning…
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…
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…
Shumei Yang, Jianhang Tang, Yang Zhang, Shaobo Li + 1 more
Cloud-assisted Internet of Things (IoT) has become the core infrastructure of smart society since it solves the computational power, storage, and collaboration bottlenecks of traditional IoT through resource decoupling and capability complementarity. The development of a graph database and cloud-assisted IoT promotes…
Danilo Numeroso
The development of artificial intelligence systems with advanced reasoning capabilities represents a persistent and long-standing research question. Traditionally, the primary strategy to address this challenge involved the adoption of symbolic approaches, where knowledge was explicitly represented by means of symbols…
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…
Nafiseh Jafarzadeh, Jordan M Eizenga, Benedict Paten
In this paper, we present diploid sequence graphs, graphs whose paths encode pairs of haplotypes. We describe an efficient algorithm for creating a diploid graph from a directed acyclic (haploid) sequence graph, such that the diploid graph represents all the possible pairings of haplotypes present in the sequence graph…
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…
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…
Lukas Schmidbauer, Elisabeth Lobe, Ina Schaefer, Wolfgang Mauerer
Many of the envisioned use-cases for quantum computers involve optimisation processes. While there are many algorithmic primitives to perform the required calculations, all eventually lead to quantum gates operating on quantum bits, with an order as determined by the structure of the objective function and the…
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…
Michael Statt, Brian Rohr, Dan Guevarra, Ja'Nya Breeden + 2 more
Materials knowledge is inherently hierarchical. While high-level descriptors such as composition and structure are valuable for contextualizing materials data, the data must ultimately be considered in the context of its low-level acquisition details. Graph databases offer an opportunity to represent hierarchical…
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…
Joseph Bond, Cristina David, Minh Tho Nguyen, Dominic Orchard + 1 more
'Roly Perera'] Charts, figures, and text derived from data play an important role in decision making, from data-driven policy development to day-to-day choices informed by online articles. Making sense of, or fact-checking, outputs means understanding how they relate to the underlying data. Even for domain experts with…
Authors not listed
A directed graph (or digraph) consists of a finite vertex set 𝑉 and a set of ordered edges 𝐸 ⊆ 𝑉 × 𝑉, each edge (𝑢, 𝑣) indicating a one-way connection from 𝑢 (source) to 𝑣 (target). A bidirected graph is a generalization of an undirected graph where each edge is assigned a direction at each of its endpoints…
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…
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…
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…
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…