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Network Unfolding Map by Vertex-Edge Dynamics Modeling

Filipe Alves Neto Verri, Paulo Roberto Urio, Liang Zhao
2018 IEEE Transactions on Neural Networks and Learning Systems  

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2016 pre-print arXiv:1603.01182v1 fatcat:l7gz3dszwrgbnbyd5vn5xcfysq

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2018 accepted
arXiv:1603.01182v2 fatcat:ftiaal2njrb7hgqdu4y5pv3aie
Furthermore, the edge domination process corresponds to an unfolding map in such way that edges "stretch" and "shrink" according to the vertex-edge dynamics.  ...  Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles.  ...  Furthermore, the edge domination process corresponds to an unfolding map. Intuitively, edges "stretch" and "shrink" according to edge dynamics.  ... 
doi:10.1109/tnnls.2016.2626341 pmid:27913359 fatcat:3ivzwmewofcq5chh6dqcrzmfbq
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Filipe Alves Neto Verri, Paulo Roberto Urio, Liang Zhao. "Network Unfolding Map by Vertex-Edge Dynamics Modeling." IEEE Transactions on Neural Networks and Learning Systems 29.2 (2018) 405-418

Weisfeiler–Lehman goes Dynamic: An Analysis of the Expressive Power of Graph Neural Networks for Attributed and Dynamic Graphs [article]

Silvia Beddar-Wiesing, Giuseppe Alessio D'Inverno, Caterina Graziani, Veronica Lachi, Alice Moallemy-Oureh, Franco Scarselli, Josephine Maria Thomas
2022 arXiv   pre-print

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Graph Neural Networks (GNNs) are a large class of relational models for graph processing. Recent theoretical studies on the expressive power of GNNs have focused on two issues.  ...  Moreover, it has been shown that the equivalence enforced by 1-WL equals unfolding equivalence.  ...  Acknowledgments This work was partially supported by the Ministry of Education and Research Germany (BMBF, grant number 01IS20047A) and partially by INdAM GNCS group.  ... 
arXiv:2210.03990v1 fatcat:sjm3byq74zdvbhkyauyf2epltm
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Silvia Beddar-Wiesing, Giuseppe Alessio D'Inverno, Caterina Graziani, Veronica Lachi, Alice Moallemy-Oureh, Franco Scarselli, Josephine Maria Thomas. "Weisfeiler–Lehman goes Dynamic: An Analysis of the Expressive Power of Graph Neural Networks for Attributed and Dynamic Graphs." arXiv (2022)

Inference of dynamic networks using time-course data

Y. Kim, S. Han, S. Choi, D. Hwang
2013 Briefings in Bioinformatics  

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He has been studying design principles of biological networks via mathematical modeling approaches.  ...  Dynamic networks delineate the operation of biological networks in terms of temporal changes of abundances or activities of nodes (proteins and RNAs), as well as formation of new edges and disappearance  ...  of network characteristics and (iv) modeling kinetic behaviors represented by dynamic networks.  ... 
doi:10.1093/bib/bbt028 pmid:23698724 fatcat:4l2wxcy3bnhrjhd345tiuhigxm
Citation

Y. Kim, S. Han, S. Choi, D. Hwang. "Inference of dynamic networks using time-course data." Briefings in Bioinformatics 15.2 (2013) 212-228

Memory and betweenness preference in temporal networks induced from time series

Tongfeng Weng, Jie Zhang, Michael Small, Rui Zheng, Pan Hui
2017 Scientific Reports  

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lifetime" of edges.  ...  us to better understand the dynamical variation of real systems deviating significantly from what one would expect from static network models.  ...  Based on time-stamped edges (υ, ω; t) ∈ E, we construct a temporal network from time series by unfolding temporal information t into an additional topological dimension.  ... 
doi:10.1038/srep41951 pmid:28157194 pmcid:PMC5291220 fatcat:a7gi4zdlonegjbfiezychurbye
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Tongfeng Weng, Jie Zhang, Michael Small, Rui Zheng, Pan Hui. "Memory and betweenness preference in temporal networks induced from time series." Scientific Reports 7.1 (2017)

Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone

Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker, Fatah Kashanchi
2017 PLoS ONE  

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Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies  ...  By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK  ...  Ensemble-based residue interaction networks and modeling of communication pathways A graph-based model of protein structure considers residues as network nodes while inter-residue edges represent residue  ... 
doi:10.1371/journal.pone.0186089 pmid:29095844 pmcid:PMC5667858 fatcat:ksxbywam4fcvrf65plftwrwkt4
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Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker, Fatah Kashanchi. "Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone." PLoS ONE 12.11 (2017) e0186089

FAULT DIAGNOSIS FOR DISTRIBUTED ASYNCHRONOUS DYNAMICALLY RECONFIGURED DISCRETE EVENT SYSTEMS

S. Haar, A. Benveniste, E. Fabre, C. Jard
2005 IFAC Proceedings Volumes  

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The use of Petri net unfoldings allows to formalize diagnosis using partial order semantics, a generalization from the global state model imposed by the use of automata.  ...  If, in addition to asynchronicity and distribution, the network topology itself is subject to dynamic changes, all static models, including Petri nets, reach their limits.  ...  Section 3 introduces graph grammars as a model for dynamicity, and their unfoldings.  ... 
doi:10.3182/20050703-6-cz-1902.00299 fatcat:j27kutmyhrcifavo4o3gyfgr6q
Citation

S. Haar, A. Benveniste, E. Fabre, C. Jard. "FAULT DIAGNOSIS FOR DISTRIBUTED ASYNCHRONOUS DYNAMICALLY RECONFIGURED DISCRETE EVENT SYSTEMS." IFAC Proceedings Volumes 38.1 (2005) 85-90

Edges in Brain Networks: Contributions to Models of Structure and Function [article]

Joshua Faskowitz, Richard F. Betzel, Olaf Sporns
2021 arXiv   pre-print

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Network models describe the brain as sets of nodes and edges that represent its distributed organization.  ...  Importantly, these functional contributions are determined and expressed by the web of their interrelationships, formed by network edges.  ...  ; one way to approach this question is to model how communication processes, guided by certain algorithmic rules, might unfold over the structural edges.  ... 
arXiv:2105.07069v1 fatcat:lw4o54si55fe5d5brxebuewwky
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Joshua Faskowitz, Richard F. Betzel, Olaf Sporns. "Edges in Brain Networks: Contributions to Models of Structure and Function." arXiv (2021)

Automated Analysis of the Interactions Between Sustainable Development Goals Extracted from Models and Texts of Sustainability Science

Gyula Dorgo, Gergely Honti, Janos Abonyi
2018 Chemical Engineering Transactions  

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These key aspects and their connections can be represented by a network structure and compared to the subsystems of the dynamic models of sustainability to explore the deficiencies of the models or the  ...  In the present work, the proposed methodology through the analysis of five strategical documents is demonstrated and the determined aspects with the structure of the famous World3 system dynamics model  ...  Gyula Dörgő was supported by the ÚNKP-17-3 New National Excellence Program of the Ministry of Human Capacities.  ... 
doi:10.3303/cet1870131 doaj:8fbbd68ed79e49c49b128f197900e2b8 fatcat:mplos2n2nbdyjj6tixmszbpmoy
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Citation

Gyula Dorgo, Gergely Honti, Janos Abonyi. "Automated Analysis of the Interactions Between Sustainable Development Goals Extracted from Models and Texts of Sustainability Science." Chemical Engineering Transactions (2018)

Multi-Projection Fusion and Refinement Network for Salient Object Detection in 360 Omnidirectional Image [article]

Runmin Cong, Ke Huang, Jianjun Lei, Yao Zhao, Qingming Huang, Sam Kwong
2022 arXiv   pre-print

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Different from the existing methods, the equirectangular projection image and four corresponding cube-unfolding images are embedded into the network simultaneously as inputs, where the cube-unfolding images  ...  In order to make full use of these two projection modes, a Dynamic Weighting Fusion (DWF) module is designed to adaptively integrate the features of different projections in a complementary and dynamic  ...  [71] mapped an omnidirectional image into six patches and obtained saliency maps respectively through a CNN network, which are combined together by postprocessing technique to deal with the heavy distortion  ... 
arXiv:2212.12378v1 fatcat:jr6jvmeyp5hqxkv6fmyx6stpli
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Runmin Cong, Ke Huang, Jianjun Lei, Yao Zhao, Qingming Huang, Sam Kwong. "Multi-Projection Fusion and Refinement Network for Salient Object Detection in 360 Omnidirectional Image." arXiv (2022)

Edges in brain networks: contributions to models of structure and function

Joshua Faskowitz, Richard F Betzel, Olaf Sporns
2021 Network Neuroscience  

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Network models describe the brain as sets of nodes and edges that represent its distributed organization.  ...  Importantly, these functional contributions are determined and expressed by the web of their interrelationships, formed by network edges.  ...  ; one way to approach this question is to model how communication processes, guided by certain algorithmic rules, might unfold over the structural edges.  ... 
doi:10.1162/netn_a_00204 pmid:35350585 pmcid:PMC8942607 fatcat:oitbjtkgm5crlpm27o7fwrnpji
DOAJ
Citation

Joshua Faskowitz, Richard F Betzel, Olaf Sporns. "Edges in brain networks: contributions to models of structure and function." Network Neuroscience 6.1 (2021) 1-63

Long-range Regulation of Partially Folded Amyloidogenic Peptides

Shayon Bhattacharya, Liang Xu, Damien Thompson
2020 Scientific Reports  

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Our computed free energies, population shifts, and dynamic cross-correlation network analyses reveal a common feature of long-range intra-peptide modulation of partial helical folds of the amyloidogenic  ...  The absence of such inter-domain fluctuations in both fully helical and completely unfolded (disordered) states suggests that long-range coupling regulates the dynamicity of partially folded helices, in  ...  Acknowledgements This work was financially supported by Science Foundation Ireland (SFI) under Grant Number 15/CDA/3491 and through the "Mis_ing Link" EU Joint Programme -Neurodegenerative Disease Research  ... 
doi:10.1038/s41598-020-64303-x pmid:32371882 fatcat:5fpdls4x3relrnl65qdm3otmoa
DOAJ
Citation

Shayon Bhattacharya, Liang Xu, Damien Thompson. "Long-range Regulation of Partially Folded Amyloidogenic Peptides." Scientific Reports 10.1 (2020) 7597

Predicting partially observed processes on temporal networks by Dynamics-Aware Node Embeddings (DyANE)

Koya Sato, Mizuki Oka, Alain Barrat, Ciro Cattuto
2021 EPJ Data Science  

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We achieve this by using a lossless modified supra-adjacency representation of temporal networks and building on standard embedding techniques for static graphs based on random walks.  ...  Here, we present a node embedding technique aimed at providing low-dimensional feature vectors that are informative of dynamical processes occurring over temporal networks – rather than of the network  ...  Since dynamical processes unfold over time-respecting paths determined by the underlying network and by its evolution over time, we argue that the sought embeddings should be informative of these paths  ... 
doi:10.1140/epjds/s13688-021-00277-8 doaj:98a05955517141bc8d9d413d1a726ce8 fatcat:kig3otolenbkxhzsd7gjpkapnm
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Koya Sato, Mizuki Oka, Alain Barrat, Ciro Cattuto. "Predicting partially observed processes on temporal networks by Dynamics-Aware Node Embeddings (DyANE)." EPJ Data Science 10.1 (2021)

CTformer: Convolution-free Token2Token Dilated Vision Transformer for Low-dose CT Denoising [article]

Dayang Wang, Fenglei Fan, Zhan Wu, Rui Liu, Fei Wang, Hengyong Yu
2022 arXiv   pre-print

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We interpret the CTformer by statically inspecting patterns of its internal attention maps and dynamically tracing the hierarchical attention flow with an explanatory graph.  ...  It also dilates and shifts feature maps to capture longer-range interaction.  ...  Edge: To construct edges among nodes, we propose to forward a masked feature map.  ... 
arXiv:2202.13517v1 fatcat:hdzvqexrinanjdqfn3ynom7qju
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Citation

Dayang Wang, Fenglei Fan, Zhan Wu, Rui Liu, Fei Wang, Hengyong Yu. "CTformer: Convolution-free Token2Token Dilated Vision Transformer for Low-dose CT Denoising." arXiv (2022)

Annular Computational Imaging: Capture Clear Panoramic Images through Simple Lens [article]

Qi Jiang, Hao Shi, Lei Sun, Shaohua Gao, Kailun Yang, Kaiwei Wang
2022 arXiv   pre-print

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2022 pre-print
arXiv:2206.06070v1 fatcat:gzgo66zcsbatrck4apt52hr6la
Furthermore, we design the Physics Informed Image Restoration Network (PI2RNet) considering the physical priors of panoramic imaging and single-pass physics-informed engine.  ...  At the dataset level, we create the DIVPano dataset and the extensive experiments on it illustrate that our proposed network sets the new state of the art in the panoramic image restoration under spatially-variant  ...  We map the annular image into unfolded one for the similar data distribution of perspective image by which our network is trained with.  ... 
arXiv:2206.06070v2 fatcat:p47yogdq75dtldh57fzu6slfda
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Qi Jiang, Hao Shi, Lei Sun, Shaohua Gao, Kailun Yang, Kaiwei Wang. "Annular Computational Imaging: Capture Clear Panoramic Images through Simple Lens." arXiv (2022)

Temporal networks in collaborative learning: A case study

Mohammed Saqr, Ward Peeters
2022 British Journal of Educational Technology  

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By using temporal networks, we show how to analyse the longitudinal evolution of a collaborative network visually and quantitatively.  ...  Compressing a temporal process by discarding time, however, may result in reductionist oversimplifications.  ...  Dynamic GL measures calculated at each time point: (1) dynamic density (ie, the sum of edges divided by the maximum possible edges) as an indication of the activity and distribution of interactions among  ... 
doi:10.1111/bjet.13187 fatcat:ec32ullmkzdnfkb26e4hbejxrm
Open Access
Citation

Mohammed Saqr, Ward Peeters. "Temporal networks in collaborative learning: A case study." British Journal of Educational Technology (2022)
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