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A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021.
The euclidean travelling salesman problem is np-complete
Christos H Papadimitriou · 1977
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A fast and high quality multilevel scheme for partitioning irregular graphs
George Karypis and Vipin Kumar · 1998
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The pagerank citation ranking: Bringing order to the web
Lawrence Page, Sergey Brin, Rajeev Motwani, and Terry Winograd · 1999
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Initial sequencing and analysis of the human genome
Eric S Lander, Lauren M Linton, Bruce Birren, Chad Nusbaum, Michael C Zody, Jennifer Baldwin, Keri Devon, Ken Dewar, Michael Doyle, William FitzHugh, et al · 2001
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The graph neural network model
Franco Scarselli, Marco Gori, Ah Chung Tsoi, Markus Hagenbuchner, and Gabriele Monfardini · 2008
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Quast: quality assessment tool for genome assemblies
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, and Glenn Tesler · 2013
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Adam: A method for stochastic optimization
Diederik P Kingma and Jimmy Ba · 2014
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Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Heng Li · 2016
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Xavier Bresson and Thomas Laurent · 2017
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Medaka, 2018
Oxford Nanopore Technologies Ltd · 2018
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Minimap2: pairwise alignment for nucleotide sequences
Heng Li · 2018
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D-genies: dot plot large genomes in an interactive, efficient and simple way
Floréal Cabanettes and Christophe Klopp · 2018
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Performance of neural network basecalling tools for oxford nanopore sequencing
Ryan R Wick, Louise M Judd, and Kathryn E Holt · 2019
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An efficient graph convolutional network technique for the travelling salesman problem
Chaitanya K Joshi, Thomas Laurent, and Xavier Bresson · 2019
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On learning paradigms for the travelling salesman problem
Chaitanya K Joshi, Thomas Laurent, and Xavier Bresson · 2019
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Relational pooling for graph representations
Ryan Murphy, Balasubramaniam Srinivasan, Vinayak Rao, and Bruno Ribeiro · 2019
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A two-step graph convolutional decoder for molecule generation
Xavier Bresson and Thomas Laurent · 2019
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Time-and memory-efficient genome assembly with raven
Robert Vaser and Mile Šikić · 2021
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Deepconsensus: Gap-aware sequence transformers for sequence correction
Gunjan Baid, Daniel E Cook, Kishwar Shafin, Taedong Yun, Felipe Llinares-Lopez, Quentin Berthet, Aaron M Wenger, William J Rowell, Maria Nattestad, Howard Yang, et al · 2021
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Predicting anticancer hyperfoods with graph convolutional networks
Guadalupe Gonzalez, Shunwang Gong, Ivan Laponogov, Michael Bronstein, and Kirill Veselkov · 2021
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The transformer network for the traveling salesman problem
Xavier Bresson and Thomas Laurent · 2021
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, and Heng Li · 2021
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A step towards neural genome assembly
Lovro Vrček, Petar Veličković, and Mile Šikić · 2020
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A deep learning approach to antibiotic discovery
Jonathan M Stokes, Kevin Yang, Kyle Swanson, Wengong Jin, Andres Cubillos-Ruiz, Nina M Donghia, Craig R MacNair, Shawn French, Lindsey A Carfrae, Zohar Bloom-Ackermann, et al · 2020
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Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Pablo Gainza, Freyr Sverrisson, Frederico Monti, Emanuele Rodola, D Boscaini, MM Bronstein, and BE Correia · 2020
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Hicanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, and Sergey Koren · 2020
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Benchmarking graph neural networks
Vijay Prakash Dwivedi, Chaitanya K Joshi, Thomas Laurent, Yoshua Bengio, and Xavier Bresson · 2020
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What graph neural networks cannot learn: depth vs width
Andreas Loukas · 2020
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Can graph neural networks count substructures?
Zhengdao Chen, Lei Chen, Soledad Villar, and Joan Bruna · 2020
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A generalization of transformer networks to graphs
Vijay Prakash Dwivedi and Xavier Bresson · 2021
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Do transformers really perform badly for graph representation?
Chengxuan Ying, Tianle Cai, Shengjie Luo, Shuxin Zheng, Guolin Ke, Di He, Yanming Shen, and Tie-Yan Liu · 2021
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Minimizer-space de bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
Barış Ekim, Bonnie Berger, and Rayan Chikhi · 2021
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The complete sequence of a human genome
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, et al · 2022
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Sign and basis invariant networks for spectral graph representation learning
Derek Lim, Joshua David Robinson, Lingxiao Zhao, Tess Smidt, Suvrit Sra, Haggai Maron, and Stefanie Jegelka · 2022
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Graph neural networks with learnable structural and positional representations
Vijay Prakash Dwivedi, Anh Tuan Luu, Thomas Laurent, Yoshua Bengio, and Xavier Bresson · 2022
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Multiplex de bruijn graphs enable genome assembly from long, high-fidelity reads
Anton Bankevich, Andrey V Bzikadze, Mikhail Kolmogorov, Dmitry Antipov, and Pavel A Pevzner · 2022
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