Low-dimensional representation of genomic sequences

DOI10.1007/s00285-019-01348-1zbMath1417.92121OpenAlexW2929682486WikidataQ92721054 ScholiaQ92721054MaRDI QIDQ2311893

Manuel E. Lladser, Richard C. Tillquist

Publication date: 4 July 2019

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s00285-019-01348-1

zbMATH Keywords

Hamming graphfeature extractiongraph embeddingsresolving setmetric dimensionreads

Mathematics Subject Classification ID

Applications of graph theory (05C90) Protein sequences, DNA sequences (92D20)

Related Items (8)

Truncated metric dimension for finite graphs ⋮ On mixed metric dimension in subdivision, middle, and total graphs ⋮ Getting the Lay of the Land in Discrete Space: A Survey of Metric Dimension and Its Applications ⋮ Metric Dimension Parameterized by Feedback Vertex Set and Other Structural Parameters ⋮ Graphs whose mixed metric dimension is equal to their order ⋮ Resolvability and convexity properties in the Sierpiński product of graphs ⋮ Levenshtein graphs: resolvability, automorphisms \& determining sets ⋮ Resolvability of Hamming Graphs

Uses Software

• Scikit
• AUGUSTUS
• word2vec
• dna2vec
• t-SNE
• node2vec
• pSLIP
• DeepWalk
• SVM-Prot

Cites Work

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• Approximation complexity of metric dimension problem
• Mastermind
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• Resolvability in graphs and the metric dimension of a graph
• Support-vector networks
• Variable neighborhood search for metric dimension and minimal doubly resolving set problems
• Tight approximability results for test set problems in bioinformatics
• Landmarks in graphs
• Discriminatory Analysis. Nonparametric Discrimination: Consistency Properties
• Automorphisms group of generalized Hamming Graphs
• On the Metric Dimension of Cartesian Products of Graphs
• Error Detecting and Error Correcting Codes
• Reducibility among Combinatorial Problems
• Statistical Inference for Probabilistic Functions of Finite State Markov Chains
• The complexity of theorem-proving procedures
• The Number of Transitivity Sets of Boolean Functions

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