Tensor-based document retrieval over Neo4j with an application to PubMed mining

PubMed mining is currently at the epicenter of intense interdisciplinary research. Text mining methodologies provide a way to retrieve and analyze emotionally charged words, punctuation, and syntax. Moreover, they can analyze scientific literature and process document collections. Moving beyond traditional document-term matrix representation, an architecture for content based retrieval from PubMed is proposed whose core is a document-term-author third order tensor. This methodology has been implemented in Python over Neo4j and has been applied to a PubMed document article collection.

[1]  Onofrio Panzarino,et al.  Learning Cypher , 2014 .

[2]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[3]  Fabien L. Gandon,et al.  Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy , 2009, BMC Bioinformatics.

[4]  Ioannis Hatzilygeroudis,et al.  Modeling ReTweet Diffusion Using Emotional Content , 2014, AIAI.

[5]  Wendy Hall,et al.  The Semantic Web Revisited , 2006, IEEE Intelligent Systems.

[6]  Tamara G. Kolda,et al.  Tensor Decompositions and Applications , 2009, SIAM Rev..

[7]  Sophia Ananiadou,et al.  Enhancing Search: Events and Their Discourse Context , 2013, CICLing.

[8]  Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource , 2003 .

[9]  Ioannis Hatzilygeroudis,et al.  Conversation Emotional Modeling in Social Networks , 2014, 2014 IEEE 26th International Conference on Tools with Artificial Intelligence.

[10]  Kevin W. Boyack,et al.  Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches , 2011, PloS one.

[11]  Torulf Mollestad,et al.  Additional Gene Ontology structure for improved biological reasoning , 2006, Bioinform..

[12]  James S. Duncan,et al.  Synthesis of Research: Medical Image Databases: A Content-based Retrieval Approach , 1997, J. Am. Medical Informatics Assoc..

[13]  Xiaohua Hu,et al.  Biomedical Ontology MeSH Improves Document Clustering Qualify on MEDLINE Articles: A Comparison Study , 2006, 19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06).

[14]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[15]  Doina Caragea,et al.  Graph Databases , 2019, Encyclopedia of Big Data Technologies.

[16]  P. Cochat,et al.  Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.

[17]  Mark E. J. Newman,et al.  Ego-centered networks and the ripple effect , 2001, Soc. Networks.

[18]  Robert Stevens,et al.  Using reasoning to guide annotation with gene ontology terms in GOAT , 2004, SGMD.

[19]  Vasileios Megalooikonomou,et al.  On the weight sparsity of multilayer perceptrons , 2015, 2015 6th International Conference on Information, Intelligence, Systems and Applications (IISA).

[20]  Ioannis Hatzilygeroudis,et al.  Integrating User's Emotional Behavior for Community Detection in Social Networks , 2016, WEBIST.

[21]  Sampo Pyysalo,et al.  BioCause: Annotating and analysing causality in the biomedical domain , 2013, BMC Bioinformatics.

[22]  Zhiyong Lu,et al.  Recommending MeSH terms for annotating biomedical articles , 2011, J. Am. Medical Informatics Assoc..

[23]  Leticia I. Gómez,et al.  A generic data model and query language for spatiotemporal OLAP cube analysis , 2012, EDBT '12.

[24]  Evangelos Theodoridis,et al.  Topic Categorization of Biomedical Abstracts , 2015, Int. J. Artif. Intell. Tools.

[25]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[26]  Gang Feng,et al.  Disease Ontology: a backbone for disease semantic integration , 2011, Nucleic Acids Res..

[27]  Alan R. Aronson,et al.  Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program , 2001, AMIA.

[28]  Evangelos Theodoridis,et al.  On Topic Categorization of PubMed Query Results , 2012, AIAI.

[29]  Evangelos Theodoridis,et al.  A PubMed Meta Search Engine Based on Biomedical Entity Mining , 2014, 2014 25th International Workshop on Database and Expert Systems Applications.

[30]  J R Scherrer,et al.  Natural Language Processing and Semantical Representation of Medical Texts , 1992, Methods of Information in Medicine.

[31]  Lefteris Angelis,et al.  PuReD-MCL: a graph-based PubMed document clustering methodology , 2008, Bioinform..

[32]  Chang-Tsun Li,et al.  A Content-Based Approach to Medical Image Database Retrieval , 2009, Database Technologies: Concepts, Methodologies, Tools, and Applications.

[33]  Martha Palmer,et al.  Verb Semantics and Lexical Selection , 1994, ACL.

[34]  A. Ortony,et al.  What's basic about basic emotions? , 1990, Psychological review.