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MotifMiner: Efficient discovery of common substructures in biochemical molecules

Matt Coatney, Srinivasan Parthasarathy
2005 Knowledge and Information Systems  
Previous automated substructure discovery approaches have each introduced variations of similar underlying techniques and have embedded domain knowledge.  ...  We describe both the framework and several algorithms as well as demonstrate the flexibility of our system by analyzing protein and drug biochemical datasets.  ...  Substructure discovery in pharmaceutical compounds The pharmaceutical domain is one of the most heavily studied regarding structural patterns.  ... 
doi:10.1007/s10115-003-0119-4 fatcat:qaydlmilkvgpvi4o2m4myt73fi

Graph-based data mining

D.J. Cook, L.B. Holder
2000 IEEE Intelligent Systems and their Applications  
In this experiment, Subdue generated substructures in three ways: using no background knowledge, using background knowledge in the form of graph match rules customized for this domain, and using both graph  ...  An earlier article provides the derivation of this expression. 7 Discovery system applications We have successfully applied Subdue, with and without domain knowledge, to databases in domains including  ... 
doi:10.1109/5254.850825 fatcat:uhmbej7osncgndxkc7rbyvvtmi

Approaches to Parallel Graph-Based Knowledge Discovery

Diane J. Cook, Lawrence B. Holder, Gehad Galal, Ron Maglothin
2001 Journal of Parallel and Distributed Computing  
In particular, scientific discovery systems focus on the utilization of richer data representation, sometimes without regard for scalability.  ...  Subdue has been used to discover interesting and repetitive concepts in graph-based databases from a variety of domains, but requires a substantial amount of processing time.  ...  In this paper, we analyze the ability of Subdue to scale to large databases.  ... 
doi:10.1006/jpdc.2000.1696 fatcat:vme4ebokxzakrksexggd7l7aem

Structural mining of molecular biology data

D.J. Cook, L.B. Holder, S. Su, R. Maglothin, I. Jonyer
2001 IEEE Engineering in Medicine and Biology Magazine  
The results obtained in this study indicate that SUBDUE is suitable for knowledge discovery in molecular structural databases.  ...  Application of Unsupervised SUBDUE to Molecular Biology The SUBDUE discovery system has been applied to databases in a number of domains.  ...  Holder is currently an associate professor in the Department of Computer S c i e n c e a n d E n g ineering at the Univer- Istvan Jonyer is a Ph.D. student in the Computer Science and Engineering Department  ... 
doi:10.1109/51.940050 pmid:11494772 fatcat:mprzjt3csvhhtli2py6nnoaige


2001 International journal on artificial intelligence tools  
A graph-based representation of structural information combined with a substructure discovery technique has been shown to be successful in knowledge discovery.  ...  The SUBDUE substructure discovery system provides one such combination of approaches. This work presents SUBDUE and the development of its clustering functionalities.  ...  Acknowledgements This research was supported by National Science Foundation grants IRI-9615272 and IIS-0097517, and the State of Texas Higher Education Coordinating Board Advanced Technology Program grant  ... 
doi:10.1142/s0218213001000441 fatcat:je4d57a2bjbaldhsiiqvskhjcy

Guest Editors' Introduction: Special Issue on Mining Biological Data

Wei Wang, Jiong Yang
2005 IEEE Transactions on Knowledge and Data Engineering  
Case-based reasoning (CBR) is a suitable paradigm for class discovery in molecular biology, where the rules that define the domain knowledge are difficult to obtain and the number and the complexity of  ...  substructures present in the data set.  ... 
doi:10.1109/tkde.2005.128 fatcat:o3vmjyzy3ncplknsce52diieo4

Applying graph-based anomaly detection approaches to the discovery of insider threats

William Eberle, Lawrence Holder
2009 2009 IEEE International Conference on Intelligence and Security Informatics  
The ability to mine data represented as a graph has become important in several domains for detecting various structural patterns.  ...  One important area of data mining is anomaly detection, but little work has been done in terms of detecting anomalies in graph-based data.  ...  GBAD (Graph-Based Anomaly Detection) [2] is an unsupervised approach, based upon the SUBDUE graph-based knowledge discovery method [1] .  ... 
doi:10.1109/isi.2009.5137304 dblp:conf/isi/EberleH09 fatcat:hq3zpi56mrevxd326mwmfplyte

Graph-based data mining: A new tool for the analysis and comparison of scientific domains represented as scientograms

Arnaud Quirin, Oscar Cordón, Benjamín Vargas-Quesada, Félix de Moya-Anegón
2010 Journal of Informetrics  
in the world, and the comparison of scientific domains between different countries.  ...  This algorithm has been customized to deal with three different scientogram analysis tasks regarding the evolution of a scientific domain over time, the extraction of the common research categories substructures  ...  We would like to thank Elsevier for its permission to use the SCOPUS-SJR data in order to build and compare the scientograms.  ... 
doi:10.1016/j.joi.2010.01.004 fatcat:ch344ki5fvafjd3sd4wldxvk6i

Underdeveloped territories of bioinformatics

John C. Wootton
1996 Nature Biotechnology  
However, one increasingly important domain for many of these methodologies is not empha-sized in this book, namely, the association of knowledge of complex biological functions such as metabolism, signal  ...  The author has a talent for capturing in a nutshell the essentials of a methodology together with concise views of its domain of applicability and its strengths and limitations.  ... 
doi:10.1038/nbt1096-1303a fatcat:cpsaetv2brcohpesr24slief5i

Graph-Based Analysis of Nuclear Smuggling Data

Diane Cook, Lawrence Holder, Sandy Thompson, Paul Whitney, Lawrence Chilton
2009 Journal of Applied Security Research  
This ability to analyze structural data has become a particular challenge in many security-related domains.  ...  In these domains, focusing on the relationships between entities in the data is critical to detect important underlying patterns.  ...  Analyzing nuclear smuggling incidents requires analyzing the structure of the incidents.  ... 
doi:10.1080/19361610903176310 fatcat:5xwperzyobeqjbjjntpeclfwne


2006 International journal on artificial intelligence tools  
Our research is particularly applicable to domains in which the data is event driven, such as counter-terrorism intelligence analysis.  ...  We contrast two formulations of the change detection process and demonstrate the ability to identify salient changes along meaningful dimensions and recognize trends in a relational data stream.  ...  The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of AFRL or the  ... 
doi:10.1142/s0218213006003041 fatcat:wyxzrgrvd5g7fgold7z7w5t3iq

Comparison of graph-based and logic-based multi-relational data mining

Nikhil S. Ketkar, Lawrence B. Holder, Diane J. Cook
2005 SIGKDD Explorations  
An analysis of the results indicates that the differences in the performance of the systems are a result of the difference in the expressiveness of the logic-based and the graph-based representations.  ...  The use of this weaker representation is advantageous while learning structurally large concepts but it limits the learning of semantically complicated concepts and the utilization background knowledge  ...  The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of AFRL or the  ... 
doi:10.1145/1117454.1117463 fatcat:f7b2t5rw2naozalv7g4bhxsrry

Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer

Anthony W. Goering, Ryan A. McClure, James R. Doroghazi, Jessica C. Albright, Nicole A. Haverland, Yongbo Zhang, Kou-San Ju, Regan J. Thomson, William W. Metcalf, Neil L. Kelleher
2016 ACS Central Science  
The discovery of tambromycin via large-scale correlation of gene clusters with metabolites (a.k.a. metabologenomics) illuminates a path for structure-based discovery of natural products at a sharply increased  ...  We sought a strategy to reinvigorate the discovery of natural products with distinctive structures using bacterial genome sequencing combined with metabolomics.  ...  We also thank the Agricultural Research Service of the United States Department of Agriculture for providing the bacterial strains used in this publication.  ... 
doi:10.1021/acscentsci.5b00331 pmid:27163034 pmcid:PMC4827660 fatcat:zzvi5qauarcblgbpbwpik6moom

Structure-based classification and ontology in chemistry

Janna Hastings, Despoina Magka, Colin Batchelor, Lian Duan, Robert Stevens, Marcus Ennis, Christoph Steinbeck
2012 Journal of Cheminformatics  
Recent years have seen an explosion in the availability of data in the chemistry domain.  ...  Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI.  ...  Acknowledgements The authors wish to thank Peter Ertl from Novartis for generating the scaffolds illustrated, and ChemAxon for providing the software used to generate the hierarchy by MCS, in Figure 2  ... 
doi:10.1186/1758-2946-4-8 pmid:22480202 pmcid:PMC3361486 fatcat:54c73jnc6jgmjlbdob2vzyupi4

A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications [article]

Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
2022 arXiv   pre-print
The knowledge implicitly encoded in model parameters can benefit various downstream tasks and help to alleviate several fundamental issues of learning on graphs.  ...  Next, we present the applications of PGMs in social recommendation and drug discovery. Finally, we outline several promising research directions that can serve as a guideline for future research.  ...  To incorporate the domain knowledge into pre-training more explicitly, MoCL [Sun et al., 2021] proposed a new augmentation operator called substructure substitution, in which a valid substructure in  ... 
arXiv:2202.07893v2 fatcat:vidcathokrfibe53yuc3xaihzy
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