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Explicit Calculation of Structural Commutation Relations for Stochastic and Dynamical Graph Grammar Rule Operators in Biological Morphodynamics

Eric Mjolsness

Front Syst Biol. Author manuscript; available in PMC 2023 Jan 26.

Published in final edited form as: Front Syst Biol. 2022 Sep; 2: 898858. Published online 2022 Sep 9. doi: 10.3389/fsysb.2022.898858

PMCID:: PMC9879069

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Graphical Models in Reconstructability Analysis and Bayesian Networks

Marcus Harris, Martin Zwick

Entropy (Basel) 2021 Aug; 23(8): 986. Published online 2021 Jul 30. doi: 10.3390/e23080986

PMCID:: PMC8393825

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Unsupervised Event Graph Representation and Similarity Learning on Biomedical Literature

Giacomo Frisoni, Gianluca Moro, Giulio Carlassare, Antonella Carbonaro

Sensors (Basel) 2022 Jan; 22(1): 3. Published online 2021 Dec 21. doi: 10.3390/s22010003

PMCID:: PMC8747118

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Metrics for graph comparison: A practitioner’s guide

Peter Wills, François G. Meyer

PLoS One. 2020; 15(2): e0228728. Published online 2020 Feb 12. doi: 10.1371/journal.pone.0228728

PMCID:: PMC7015405

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SCGG: A deep structure-conditioned graph generative model

Faezeh Faez, Negin Hashemi Dijujin, Mahdieh Soleymani Baghshah, Hamid R. Rabiee

PLoS One. 2022; 17(11): e0277887. Published online 2022 Nov 21. doi: 10.1371/journal.pone.0277887

PMCID:: PMC9678307

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Assessing portfolio diversification via two-sample graph kernel inference. A case study on the influence of ESG screening

Ragnar L. Gudmundarson, Gareth W. Peters

PLoS One. 2024; 19(4): e0301804. Published online 2024 Apr 16. doi: 10.1371/journal.pone.0301804

PMCID:: PMC11020627

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Molecular representations in AI-driven drug discovery: a review and practical guide

Laurianne David, Amol Thakkar, Rocío Mercado, Ola Engkvist

J Cheminform. 2020; 12: 56. Published online 2020 Sep 17. doi: 10.1186/s13321-020-00460-5

PMCID:: PMC7495975

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Getting new algorithmic results by extending distance-hereditary graphs via split composition

Serafino Cicerone, Gabriele Di Stefano

PeerJ Comput Sci. 2021; 7: e627. Published online 2021 Jul 7. doi: 10.7717/peerj-cs.627

PMCID:: PMC8279144

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An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás

Database (Oxford) 2021; 2021: baab026. Published online 2021 May 18. doi: 10.1093/database/baab026

PMCID:: PMC8130509

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Enhancing property and activity prediction and interpretation using multiple molecular graph representations with MMGX

Apakorn Kengkanna, Masahito Ohue

Commun Chem. 2024; 7: 74. Published online 2024 Apr 5. doi: 10.1038/s42004-024-01155-w

PMCID:: PMC10997661

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DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries

Jordan K. Matelsky, Elizabeth P. Reilly, Erik C. Johnson, Jennifer Stiso, Danielle S. Bassett, Brock A. Wester, William Gray-Roncal

Sci Rep. 2021; 11: 13045. Published online 2021 Jun 22. doi: 10.1038/s41598-021-91025-5

PMCID:: PMC8219732

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Graph reconstruction using covariance-based methods

Nurgazy Sulaimanov, Heinz Koeppl

EURASIP J Bioinform Syst Biol. 2016 Dec; 2016: 19. Published online 2016 Nov 23. doi: 10.1186/s13637-016-0052-y

PMCID:: PMC5121191

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Martingales and the fixation time of evolutionary graphs with arbitrary dimensionality

Travis Monk, André van Schaik

R Soc Open Sci. 2022 May; 9(5): 220011. Published online May 11, 2022. doi: 10.1098/rsos.220011

PMCID:: PMC9091843

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MSEDDI: Multi-Scale Embedding for Predicting Drug—Drug Interaction Events

Liyi Yu, Zhaochun Xu, Meiling Cheng, Weizhong Lin, Wangren Qiu, Xuan Xiao

Int J Mol Sci. 2023 Mar; 24(5): 4500. Published online 2023 Feb 24. doi: 10.3390/ijms24054500

PMCID:: PMC10002564

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Multiway p-spectral graph cuts on Grassmann manifolds

Dimosthenis Pasadakis, Christie Louis Alappat, Olaf Schenk, Gerhard Wellein

Mach Learn. 2022; 111(2): 791–829. Published online 2021 Nov 18. doi: 10.1007/s10994-021-06108-1

PMCID:: PMC8948154

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An analysis of the graph processing landscape

Miguel E. Coimbra, Alexandre P. Francisco, Luís Veiga

J Big Data. 2021; 8(1): 55. Published online 2021 Apr 9. doi: 10.1186/s40537-021-00443-9

PMCID:: PMC8033100

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Utility of a new notation to visualize flow cytometry analysis results: first preliminary comparison with immunohistochemistry to detect CD30 expression on T-cell lymphoma cells

Fumiyoshi Fujishima, Noriko Fukuhara, Hiroki Katsushima, Yasuhiro Nakamura, Hideo Harigae, Hironobu Sasano, Ryo Ichinohasama

BMC Cancer. 2021; 21: 1352. Published online 2021 Dec 20. doi: 10.1186/s12885-021-09098-4

PMCID:: PMC8690966

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Graph convolutional networks: a comprehensive review

Si Zhang, Hanghang Tong, Jiejun Xu, Ross Maciejewski

Comput Soc Netw. 2019; 6(1): 11. Published online 2019 Nov 10. doi: 10.1186/s40649-019-0069-y

PMCID:: PMC10615927

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Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome

Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks

PLoS Comput Biol. 2021 Jan; 17(1): e1008310. Published online 2021 Jan 28. doi: 10.1371/journal.pcbi.1008310

Correction in:: PLoS Comput Biol. 2022 Jun; 18(6): e1010224.

PMCID:: PMC7872285

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Quantum Secure Multi-Party Summation with Graph State

Yaohua Lu, Gangyi Ding

Entropy (Basel) 2024 Jan; 26(1): 80. Published online 2024 Jan 17. doi: 10.3390/e26010080

PMCID:: PMC10814682

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PMC Images search for graph notation

Figure 10

Graph of music notation recognition of English speech with LPC data analysis of original speech (partial).

A Deep Learning-Based Piano Music Notation Recognition Method

Comput Intell Neurosci. 2022;2022:2278683.
Figure 9

Graph of LPC data analysis of music notation recognition of piano pieces with original speech (partial).

A Deep Learning-Based Piano Music Notation Recognition Method

Comput Intell Neurosci. 2022;2022:2278683.
Figure 2

An excerpt from a music notation graph showing a group with a high frequency of interaction. This group had such a high frequency of interaction that the graph had to be plotted in one-hour blocks instead of the standard two-hour blocks.

Music notation: a new method for visualizing social interaction in animals and humans

Front Zool. 2006;3:18-18.
Figure 6

An excerpt from a graph raising questions about winner, loser, and bystander effects. This excerpt from a music notation graph of four hens illustrates the difficulties of clearly and unambiguously defining winner, loser, and bystander effects and which acts might represent particular effects during the formation of dominance hierarchies.

Music notation: a new method for visualizing social interaction in animals and humans

Front Zool. 2006;3:18-18.