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Modelling Highly Symmetrical Molecules: Linking Ontologies and Graphs [chapter]

Oliver Kutz, Janna Hastings, Till Mossakowski
2012 Lecture Notes in Computer Science  
However, classes of chemical entities which are highly symmetrical and contain large numbers of homogeneous parts (such as carbon atoms) are not straightforwardly classified in this fashion.  ...  To address these conflicting requirements, we introduce a novel framework in which we heterogeneously integrate standard ontological modelling with monadic second-order reasoning over chemical graphs,  ...  Some examples of highly symmetric molecules, constituted almost entirely by carbon atoms.  ... 
doi:10.1007/978-3-642-33185-5_11 fatcat:4zftzfldvvd33iaykoe3aindmq

Web-Based Visualization of Large Hierarchical Graphs Using Invisible Links in a Hyperbolic Space [chapter]

Ming C. Hao, Meichun Hsu, Umesh Dayal, Adrian Krug
2000 Advances in Visual Information Management  
This paper discusses a new invisible link technique for linking a large highly connected graph in a hyperbolic space without cluttering the display. Only the primary links are shown to the user.  ...  Many real-world data warehouse applications involve navigation of large highly connected hierarchies e.g. web pages, product catalogs, and document hot topics hierarchies.  ...  The others are non-tree/secondary links in a highly connected graph. A node can have one incoming primary link and many incoming nontree/secondary links, which are called invisible links.  ... 
doi:10.1007/978-0-387-35504-7_6 fatcat:qwbnzghpovfkdbsbdoec63n6se

GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs

T. Toyoda, Y. Mochizuki, A. Konagaya
2003 Bioinformatics  
A graphical tool to visualize highly complicated biomolecular network graphs is described.  ...  GSCope also helps us to find a molecule in the graphs by offering several searching functions. It is useful to publish biomolecular network graphs on the internet.  ...  In biomolecular networks, molecules are not always linked in a simple tree structure but sometimes in a multi-linked complex, where linked molecules are placed distantly.  ... 
doi:10.1093/bioinformatics/btg001 pmid:12584139 fatcat:enszsmn2qvd6xmos2ipyoovqqi

Novel Edge and Density Metrics for Link Cohesion [article]

Cetin Savkli, Catherine Schwartz, Amanda Galante, Jonathan Cohen
2020 arXiv   pre-print
We present a new metric of link cohesion for measuring the strength of edges in complex, highly connected graphs.  ...  Link cohesion and the density measure are employed to demonstrate community detection through graph sparsification by maximizing graph density.  ...  Conclusion We have developed a new link cohesion metric as well as a new graph densitybased pruning criteria that can be used to simplify highly connected graphs.  ... 
arXiv:2003.02999v1 fatcat:4to5pmnnfbbtbpia4ehvmhm7yq

LinkExplorer: Predicting, explaining and exploring links in large biomedical knowledge graphs [article]

Simon Ott, Adriano Barbosa-Silva, Matthias Samwald
2022 bioRxiv   pre-print
We present LinkExplorer, a software suite for predicting, explaining and exploring links in large biomedical knowledge graphs.  ...  Here, we demonstrate highly competitive evaluation results of our algorithm on multiple large biomedical knowledge graphs, and release a web interface that allows for interactive and intuitive exploration  ...  We also report highly competitive evaluation results of our explainable link prediction algorithm on several large-scale biomedical knowledge graphs.  ... 
doi:10.1101/2022.01.09.475537 fatcat:jjw2naog2bcrxa3sza3utjmjza

Benchmarking link analysis ranking methods in assistive environments

Konstantinos Georgatzis, Panagiotis Papapetrou
2012 Proceedings of the 5th International Conference on PErvasive Technologies Related to Assistive Environments - PETRA '12  
In this paper, we provide a benchmark of two graph ranking methods: pagerank and HITS.  ...  Our findings suggest that the quality of the ranking as well as the speed of convergence of both algorithms highly depends on the underlying network structure.  ...  SUMMARY We performed a qualitative and quantitative analysis of two link analysis ranking methods that are highly used in social networks.  ... 
doi:10.1145/2413097.2413154 dblp:conf/petra/GeorgatzisP12 fatcat:jn6ydwbl7jhivhhxt7szl4lr2i

Features of Mobile Diabetes Applications: Review of the Literature and Analysis of Current Applications Compared Against Evidence-Based Guidelines

Taridzo Chomutare, Luis Fernandez-Luque, Eirik Årsand, Gunnar Hartvigsen
2011 Journal of Medical Internet Research  
Varied motivational output graphs, smileys, etc. 1.4 Diet (self-monitoring) Food eaten, carbohydrate estimates Highly manual task.  ...  No seamless functional links. 5 Communication Email, import/export csv, pictures, graphs Most applications allowed exporting data to a spreadsheet or emailing data or pictures 6 PHR Personal  ... 
doi:10.2196/jmir.1874 pmid:21979293 pmcid:PMC3222161 fatcat:tw4spmtwsnf7to3kmff7djweei

Discovering highly reliable subgraphs in uncertain graphs

Ruoming Jin, Lin Liu, Charu C. Aggarwal
2011 Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '11  
In this paper, we investigate the highly reliable subgraph problem, which arises in the context of uncertain graphs.  ...  Furthermore, we transform the core mining task into a new frequent cohesive set problem in deterministic graphs.  ...  it is a linked set in at least θ · N graphs.  ... 
doi:10.1145/2020408.2020569 dblp:conf/kdd/JinLA11 fatcat:zgnrpk4qgvfc3ffpfkfpjzjkem

Recent research provides new picture of router-level Internet

S. Robinson
2006 Computing in science & engineering (Print)  
The researchers note that within the large class of heavy-tailed graphs, most have the highly connected, highly trafficked, vulnerable hub nodes described by Barabási , yet a few have an altogether different  ...  To explain why this structure, highly unlikely in random graphs, is likely to reflect the actual Internet, the researchers came up with an alternative mechanism for generating a heavytailed Internet graph  ... 
doi:10.1109/mcse.2006.31 fatcat:hlckmcc6pfhtdlqknxczbud4my

Study on the Characteristics of the Korea Internet AS-Level Topology Using Node Degree and Node Connectivity Metrics

Dong Ik Oh, Kang Won Lee
2013 The Journal of Korean Institute of Communications and Information Sciences  
It has 685 nodes and 1,428 links. The Korea Internet AS-level topology is a small regional subgraph of the massive global one.  ...  These power-laws capture concisely the highly skewed distributions of the graph properties.  ...  Even though the graphs built by generators follow power-laws, they cannot represent the highly skewed characteristic of the Korea AS graph.  ... 
doi:10.7840/kics.2013.38b.6.417 fatcat:v5baam26zvg7vlaqfvi2virxk4

TeleGraph: A Benchmark Dataset for Hierarchical Link Prediction [article]

Min Zhou, Bisheng Li, Menglin Yang, Lujia Pan
2022 arXiv   pre-print
To bridge this gap, we present a new benchmark dataset TeleGraph, a highly sparse and hierarchical telecommunication network associated with rich node attributes, for assessing and fostering the link inference  ...  Their performance on sparse or highly hierarchical networks has not been well studied.  ...  Hence, TeleGraph is a suitable benchmark to assess and foster link prediction techniques. However, inferring the missing links in a highly sparse and tree-like graph is challenging.  ... 
arXiv:2204.07703v1 fatcat:llfytdp77vhfxemn4o3jqquxma

OpenBioLink: A benchmarking framework for large-scale biomedical link prediction [article]

Anna Breit, Simon Ott, Asan Agibetov, Matthias Samwald
2020 arXiv   pre-print
With OpenBioLink, we introduce a large-scale, high-quality and highly challenging biomedical link prediction benchmark to transparently and reproducibly evaluate such algorithms.  ...  SUMMARY: Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks.  ...  A dedicated, high-quality and highly challenging benchmark optimized for the task of evaluating link prediction methods in large, heterogeneous biomedical knowledge bases has not yet been established.  ... 
arXiv:1912.04616v2 fatcat:rm374omamnbf3cwnodnlmkk5cm

Inferring Molecular Interactions Pathways from eQTL Data [chapter]

Imran Rashid, Jason McDermott, Ram Samudrala
2009 Msphere  
Here we describe a series of techniques for finding explanatory pathways by exploring the graphs of molecular interactions.  ...  Importance of the interaction graph. All of the methods mentioned here are highly sensitive to the edges, which are in the interaction graph.  ...  Finding Pathways Between Differentially Expressed Genes and Linked Loci With a set of differentially expressed genes and their linked loci, as well as an interaction graph, we can formulate our problem  ... 
doi:10.1007/978-1-59745-243-4_10 pmid:19381546 fatcat:jaafv57zv5eevk7ahr3gbmxeui

Scale-Free Behavior in Protein Domain Networks

Stefan Wuchty
2001 Molecular biology and evolution  
Several technical, social, and biological networks were recently found to demonstrate scale-free and small-world behavior instead of random graph characteristics.  ...  A small-world graph is formally defined as a sparse graph which is much more highly clustered than an equally sparse random graph.  ...  Thus, highly linked domains represent functional centers in various different cellular aspects.  ... 
doi:10.1093/oxfordjournals.molbev.a003957 pmid:11504849 fatcat:c4ggq5u355fczfzotrv2u3th3u

Graph Search and Beyond

Omar Alonso, Marti A. Hearst, Jaap Kamps
2015 Proceedings of the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval - SIGIR '15  
This goes beyond the traditional two-term queries and ten blue links results that users are familiar with, requiring a highly interactive session covering both query formulation and result exploration.  ...  We view the notion of "graph search" as searching information from your personal point of view (you are the query) over a highly structured and curated information space.  ...  [9] investigate captioning or summarizing results in highly curated graph data.  ... 
doi:10.1145/2766462.2767855 dblp:conf/sigir/AlonsoHK15 fatcat:7ejwifwngzejhhxtsakbnvxtf4
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