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The Graph Traversal Pattern [article]

Marko A. Rodriguez, Peter Neubauer
2010 arXiv   pre-print
In contrast to the index-intensive, set-theoretic operations of relational databases, graph databases make use of index-free, local traversals.  ...  The concept of a graph has been around since the late 19^th century, however, only in recent decades has there been a strong resurgence in both theoretical and applied graph research in mathematics, physics  ...  In stark contrast, graph databases do not store data in disparate tables. Instead there is a single data structure-the graph.  ... 
arXiv:1004.1001v1 fatcat:rwikvcbd2vc3vjdy3frberwpce

The quest for orthologs: finding the corresponding gene across genomes

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
2008 Trends in Genetics  
Review Trends in Genetics Vol. 24 No.11  ...  Acknowledgements The authors are grateful to Jack Franklin and Simon Fisher for their help in shaping the manuscript and to the anonymous reviewers for their valuable comments.  ...  In another case of a single gene loss, however, some graph-based methods (e.g.  ... 
doi:10.1016/j.tig.2008.08.009 pmid:18819722 fatcat:4w6qrixl7naw7aoqko73vruavq

Document Clustering based on Phrase and Single Term Similarity using Neo4j

2020 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
To find out shared phrases across the corpus the Document Index graph (DIG) representation model is used.  ...  Document similarity generally rely on single term similarity such as cosine similarity. To achieve better document similarity, along with single term phrase- more informative feature can be used.  ...  The method finds out dynamic length of shared phrases but it stores redundancies in the form of suffixes. In the DIG model the documents are stored into single graph sentence by sentence.  ... 
doi:10.35940/ijitee.c9050.109320 fatcat:t4a24pa3argxdecpi66t5sqchi

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA

Nur Syatila Ab Ghani, Reeki Emrizal, Sabrina Mohamed Moffit, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih
2022 Nucleic Acids Research  
The webserver interfaces the functions of five different graph theoretical algorithms – ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC – into a single substructure searching suite.  ...  provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB.  ...  As the user base for the servers increased, we revised the search and results examination functions for each program in addition to carrying out substantial updates to the databases that we present as  ... 
doi:10.1093/nar/gkac402 pmid:35639505 pmcid:PMC9252811 fatcat:x7ex6w75ajavlpt4xnxig5v2kq

Learning Kernels on Extended Reeb Graphs for 3D Shape Classification and Retrieval [article]

Vincent Barra, Silvia Biasotti
2013 Eurographics Workshop on 3D Object Retrieval, EG 3DOR  
For this purpose, 3D models are represented as bags of shortest paths defined over well chosen Extended Reeb graphs, while the similarity between pairs of Extended Reeb graphs is addressed through kernels  ...  This paper addresses 3D shape classification and retrieval in terms of supervised selection of the most significant features in a space of attributed graphs encoding different shape characteristics.  ...  that sufficient information is carried out in the graphs.  ... 
doi:10.2312/3dor/3dor13/025-032 fatcat:kidfcbdxqzaelkxope3yz3csaq

Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model

Yu-An Huang, Zhu-Hong You, Xing Chen, Zhi-An Huang, Shanwen Zhang, Gui-Ying Yan
2017 Journal of Translational Medicine  
Based on the assumption that functionally similar microbes tend to get involved in the mechanism of similar disease, we adopted neighbor-based collaborative filtering and a graphbased scoring method to  ...  Results: To evaluate the performance of the proposed model, we implemented leave-one-out and fivefold cross validations on the HMDAD database, which is recently built as the first database collecting experimentally-confirmed  ...  Considering the diseases Neighbor-based single model with symptom-based similarity 0.8935 ± 0.0041 Neighbor-based single model without symptom-based similarity 0.8834 ± 0.0034 recorded in HMDAD database  ... 
doi:10.1186/s12967-017-1304-7 pmid:29037244 pmcid:PMC5644104 fatcat:rhfs5p6f7rg53bvlaht3l436ea

Predicting binding motifs of complex adsorbates using machine learning with a physics-inspired graph representation [article]

Wenbin Xu, Karsten Reuter, Mie Andersen
2022 arXiv   pre-print
Furthermore, incorporation of minimal new training data allows for predicting an out-of-domain TM.  ...  We believe the model may be useful in active learning approaches, for which we present an ensemble uncertainty estimation approach.  ...  The graph similarity is calculated from the WWL graph kernel and input to a GPR model.  ... 
arXiv:2202.11866v1 fatcat:y5x6q7bgtzfkngycndxgbbyz2m

Automatic visual object formation using image fragment matching

M Paradowski, A Sluzek
2010 Proceedings of the International Multiconference on Computer Science and Information Technology  
Such vision approaches are used to build a learning system capable to form meaningful visual objects out of unlabelled collections of images.  ...  This leads to formation of visual objects, which (typically) represent specific underlying physical objects in a form of automatically extracted multiple template images.  ...  ., q} is represented by a single graph node (note that prototypes are groups of image fragments from the same image). Each image fragment is matched with a similar fragment in another database image.  ... 
doi:10.1109/imcsit.2010.5679732 fatcat:zkaxtcg4jzdvzpb3kqn6xoq7ay

BİYOLOJİK AĞLARDA AĞ MOTİFLERİ VE İNDEKSLEME TEKNİKLERİ

Yusuf KAVURUCU
2012 Journal of Naval Science and Engineering  
Given a query graph, SAGA enumerates the fragments in the query in a similar way to database graphs. It probes FragmentIndex for each query fragment. Then, it filters out unmatched index entries.  ...  Thus, eliminating or altering a single entity does not only affect the function of that entity, it may affect the function of other entities.  ... 
doaj:c81ffb12cbc84be8aa755aff59415c16 fatcat:53o2jtwuijfvxgvx3w4wj3guiq

Netlist Decompilation Workflow for Recovered Design Verification, Validation, and Assurance [article]

Katie Liszewski, Tim McDonley, Josh Delozier, Andrew Elliott, Dylan Jones, Matthew Sutter, Adam G. Kimura
2021 IACR Cryptology ePrint Archive  
ACKNOWLEDGMENT All of the research presented in this paper was funded by Wright-Patterson Air Force Research Lab in Dayton, OH.  ...  In this similarity graph, flip-flops in the original netlist are represented as nodes, with edges between them indicating a similarity score greater than zero and the edge weight relating to the similarity  ...  Nodes going out of or into flip-flops always form roots or leaves respectively in the combinational graph.  ... 
dblp:journals/iacr/LiszewskiMDEJSK21 fatcat:3egaqqr4dbd4bkdud45z4nqmfm

Using Term Lists and Inverted Files to Improve Search Speed for Metabolic Pathway Databases [chapter]

Greeshma Neglur, Robert L. Grossman, Natalia Maltsev, Clement Yu
2006 Lecture Notes in Computer Science  
By maintaining an inverted file that indexes all pathways in a database on their edges, our algorithm finds and ranks all pathways similar to the user input query pathway in time, which is linear in the  ...  Similarity between two graphs can be computed using a metric based on Maximal Common Subgraph (MCS).  ...  We are also currently integrating additional pathway databases so that similarity searching can be done across multiple distributed pathway databases.  ... 
doi:10.1007/11799511_15 fatcat:mdlvnpt3g5gffehpcshsfz7gia

GA-PPI-Net Approach vs Analytical Approaches for Community Detection in PPI Networks

Marwa Ben M'barek, Sana Ben Hmida, Amel Borgi, Marta Rukoz
2021 Procedia Computer Science  
In the computational tests carried out in this work, the proposed genetic algorithm achieved excellent results to detect existing or even new communities from PPI networks.  ...  Prediction of communities from Protein-Protein Interaction (PPI) networks is important problem in system biology as they control different cellular functions.  ...  Single objective optimization identifies a single best solution that gives insights on the graph organization.  ... 
doi:10.1016/j.procs.2021.08.093 fatcat:z26z37ov2vahnio4yn5bfk2emi

BioScout

Anastasios Kementsietsidis, Frank Neven, Dieter Van de Craen
2008 Proceedings of the 11th international conference on Extending database technology Advances in database technology - EDBT '08  
In more detail, we demonstrate the following functionality: (i) in BioScout, scientists draw their queries graphically, resulting in a query graph.  ...  Given the query graph, the system is able to generate, as a first step, an optimal query plan for the submitted query; (ii) BioScout uses four different strategies to combine the optimal query plans of  ...  is associated with which functional description in Go.  ... 
doi:10.1145/1352431.1352525 fatcat:3issdee3cndrfggoqonnapgppa

BioScout

Anastasios Kementsietsidis, Frank Neven, Dieter Van de Craen
2008 Proceedings of the 11th international conference on Extending database technology Advances in database technology - EDBT '08  
In more detail, we demonstrate the following functionality: (i) in BioScout, scientists draw their queries graphically, resulting in a query graph.  ...  Given the query graph, the system is able to generate, as a first step, an optimal query plan for the submitted query; (ii) BioScout uses four different strategies to combine the optimal query plans of  ...  is associated with which functional description in Go.  ... 
doi:10.1145/1353343.1353437 dblp:conf/edbt/KementsietsidisNC08 fatcat:ojjylqsb7bfk5i4kzvd2rtcfwq

ELISA: a unified, multidimensional view of the protein domain universe

Boris E Shakhnovich, John Max Harvey, Charles Delisi
2004 Genome Informatics Series  
In this database we introduce and employ a novel method of functional annotation and comparison. For each protein domain we create a probabilistic functional annotation tree using GO.  ...  Thus, the database is useful in defining structural and functional links between related protein domains and by extension sequences that encode them.  ...  Conclusion ELISA is a database that is created to solve a long-standing problem in the domain evolution community of consolidation of different types of comparisons for a single dataset.  ... 
pmid:15712123 fatcat:puehxmgbivdvbawtpntlgfsa44
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