13 papers · ranked by Valyu relevance
Yun-Fei Liu, Marina Bedny
Programming is a cornerstone of modern society, yet its cognitive and neural basis remains poorly understood. In this study, we test the hypothesis that programming “recycles” pre-existing neural mechanisms and representations in fronto-parietal reasoning networks. Using fMRI, we scanned programming-naïve…
Ragnar Groot Koerkamp, Igor Martayan
Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular…
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…
Koichi Miyamoto, Naoki Yamamoto, Yasubumi Sakakibara
We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the minimal k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the smallest k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Patrick Kunzmann
Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k-mer decomposition: listing all…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Arseny Shur, Ido Tziony, Yaron Orenstein
Minimizers are sampling schemes which are ubiquitous in almost any high-throughput sequencing analysis. Assuming a fixed alphabet of size σ, a minimizer is defined by two positive integers k, w and a linear order ρ on k-mers. A sequence is processed by a sliding window algorithm that chooses in each window of length w…
Florian Ingels, Lucas Robidou, Igor Martayan, Camille Marchet + 1 more
High-throughput sequence analysis commonly relies on k-mers (words of fixed length k) to remain tractable at modern scales. These k-mer-based pipelines can employ a sampling step, which in turn allows grouping consecutive k-mers into larger strings to improve data locality. Although other sampling strategies exist…
Jianshu Zhao, Xiaofei Zhao, Jean Pierre-Both, Konstantinos T. Konstantinidis
Comparing large number of genomes in term of their genomic distance is becoming more and more challenging because there is an increasing number of microbial genomes deposited in public databases. Nowadays, we may need to estimate pairwise distances between millions or even billions of genomes. Few softwares can perform…
Bastian Wiederhold, Martin Stemmler, Andreas V.M. Herz
While our senses transmit information at rates exceeding 10^6^ bit/s, high-level cognitive processing is thought to be much slower, on the order of 10 bit/s regardless of the task^1^. It is unclear, though, whether this limit holds when the human mind is challenged. To test how fast one can process abstract…
Jia Lu, Ryan Tsoi, Nan Luo, Yuanchi Ha + 8 more
Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the essence of information encoding and decoding. Here, we demonstrate the use of self-organized patterns, combined with machine…