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Analysis of word co-occurrence in human literature for supporting semantic correspondence discovery

Jorge Martinez-Gil, Mario Pichler
2014 Proceedings of the 14th International Conference on Knowledge Technologies and Data-driven Business - i-KNOW '14  
Our research work has revealed that appropriately analyzing the co-occurrence of words in some periods of human literature can help us to determine the semantic similarity between these words by means  ...  In this work, we describe the way to exploit broad cultural trends for identifying semantic similarity.  ...  Acknowledgments We thank in advance the anonymous reviewers for their help to improve our work.  ... 
doi:10.1145/2637748.2638422 dblp:conf/iknow/GilP14 fatcat:kwo5qmdvzje4nmffayduo3nqbm

Towards extracting supporting information about predicted protein-protein interactions [article]

Adam Roth, Sandeep Subramanian, Madhavi Ganapathiraju
2015 bioRxiv   pre-print
We describe UPSITE, a text mining tool for extracting evidence in support of a hypothesized interaction.  ...  similarity of the two proteins to provide evidential support for the predicted PPI.  ...  Analysis of co-occurrence networks has shown that proteins and genes co-mentioned in the same article can reasonably be assumed to be related in some way [30] [31] .  ... 
doi:10.1101/031591 fatcat:azxblwzvijcwjph2yhcgav26ee

Text Based Knowledge Discovery with Information Flow Analysis [chapter]

Dawei Song, Peter Bruza
2006 Lecture Notes in Computer Science  
The potential of information flow analysis in text based knowledge discovery has been demonstrated by two case studies: literature-based scientific discovery by attempting to simulate Swanson's Raynaud-fish  ...  Concepts are represented as vectors in a high dimensional semantic space automatically derived from a text corpus.  ...  After traversing the corpus, an accumulated co-occurrence matrix for all the words in a target vocabulary is produced.  ... 
doi:10.1007/11610113_60 fatcat:7adnnynzfbhovddsnmwc73teia

Exploring relation types for literature-based discovery

Judita Preiss, Mark Stevenson, Robert Gaizauskas
2015 JAMIA Journal of the American Medical Informatics Association  
co-occurrence or linguistic analysis.  ...  Many LBD approaches use simple techniques to identify semantically weak relations between concepts, for example, document co-occurrence.  ...  This contrasts with the term co-occurrence based approaches where the sheer volume of hidden knowledge produced exceeds human capacity to review it.  ... 
doi:10.1093/jamia/ocv002 pmid:25971437 pmcid:PMC4986660 fatcat:zlu6idzu6bdk3jqgrba4lpar3i

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year.  ...  Acknowledgements DDF was supported by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM) and Lister Hill National Center for Biomedical Communication  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy

Using concepts in literature-based discovery: Simulating Swanson's Raynaud-fish oil and migraine-magnesium discoveries

Marc Weeber, Henny Klein, Lolkje T.W. de Jong-van den Berg, Rein Vos
2001 Journal of the American Society for Information Science and Technology  
Literature-based discovery has resulted in new knowledge. In the biomedical context, Don R.  ...  In this paper, we propose a two-step model of the discovery process in which hypotheses are generated and subsequently tested.  ...  Mork of the National Library of Medicine, Bethesda, Maryland for their generous help and efforts in providing the MetaMap program to us.  ... 
doi:10.1002/asi.1104 fatcat:oxhbusz6efe4fn4j3muwd33nwa

Towards Operational Abduction from a Cognitive Perspective

Peter Bruza, Richard Cole, Dawei Song, Zeeniya Bari
2006 Logic Journal of the IGPL  
Thanks to Marc Weeber for the Arrowsmith stop word list.  ...  Acknowledgments The work reported in this paper has been funded in part by the Co-operative Research Centre for Enterprise Distributed Systems Technology (DSTC) through the Australian Federal Government's  ...  ) term co-occurrence.  ... 
doi:10.1093/jigpal/jzk012 fatcat:ixkannx7ivbtln2dornpxft7ai

TechNet: Technology Semantic Network Based on Patent Data

Serhad Sarica, Jianxi Luo, Kristin L. Wood
2019 Expert systems with applications  
The growing developments in general semantic networks, knowledge graphs and ontology databases have motivated us to build a large-scale comprehensive semantic network of technology-related data for engineering  ...  The TechNet may serve as an infrastructure to support a wide range of applications, e.g., technical text summaries, search query predictions, relational knowledge discovery, and design ideation support  ...  co-occurrence counts of words.  ... 
doi:10.1016/j.eswa.2019.112995 fatcat:mrc6a2ujynezzd2hk2t5zs6xvi

Literature-based discovery for Oceanographic climate science

Elias Aamot
2014 Proceedings of the Student Research Workshop at the 14th Conference of the European Chapter of the Association for Computational Linguistics  
This paper presents an overview of the field of literature-based discovery, as originally applied in biomedicine.  ...  Furthermore it identifies some of the challenges to employing the results of the field in a new domain, namely oceanographic climate science, and elaborates on some of the research that needs to be conducted  ...  Acknowledgements This paper is a part of an ongoing master's thesis under the supervision of PinarÖztürk, with Erwin Marsi as co-supervisor. I am extremely grateful for their feedback and support.  ... 
doi:10.3115/v1/e14-3001 dblp:conf/eacl/Aamot14 fatcat:hj6ngptzwngnvpaujja7dy6qxe

Enriching plausible new hypothesis generation in PubMed

Seung Han Baek, Dahee Lee, Minjoo Kim, Jong Ho Lee, Min Song, Neil R. Smalheiser
2017 PLoS ONE  
Most of earlier studies in the field of literature-based discovery have adopted Swanson's ABC model that links pieces of knowledge entailed in disjoint literatures.  ...  Applying the proposed method to other cases, it would be helpful for biologists to support the existing hypothesis and easily expect the logical process within it.  ...  Semantic relatedness in the field of computing refers to how two words are contextually associated with each other, namely the degree of statistically significant co-occurrence of two words.  ... 
doi:10.1371/journal.pone.0180539 pmid:28678852 pmcid:PMC5498031 fatcat:6y3ue4yqavhmdmoezjan526v3q

Using literature-based discovery to identify disease candidate genes

Dimitar Hristovski, Borut Peterlin, Joyce A. Mitchell, Susanne M. Humphrey
2005 International Journal of Medical Informatics  
We present BITOLA, an interactive literature-based biomedical discovery support system.  ...  To make the system more suitable for disease candidate gene discovery and to decrease the number of candidate relations, we integrate background knowledge about the chromosomal location of the starting  ...  Dimitar Hristovski thanks NLM and the ORISE program for support. In addition, we would like to thank Tom Rindflesch and Neil Smalheiser for providing valuable comments and insights.  ... 
doi:10.1016/j.ijmedinf.2004.04.024 pmid:15694635 fatcat:gaxffooxwnbjxaycy5y74ebjmm

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Martin Krallinger, Alfonso Valencia, Lynette Hirschman
2008 Genome Biology  
Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the  ...  The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases.  ...  Part of this work was financially supported by the EU Framework programme for research, contract number LSHG-CT-2004-512143.  ... 
doi:10.1186/gb-2008-9-s2-s8 pmid:18834499 pmcid:PMC2559992 fatcat:oeqr7ctzgjeo5nnw53fimelwxa

Reflective Random Indexing and indirect inference: A scalable method for discovery of implicit connections

Trevor Cohen, Roger Schvaneveldt, Dominic Widdows
2010 Journal of Biomedical Informatics  
Corpus-derived statistical models of semantic distance such as Latent Semantic Analysis (LSA) have been evaluated previously as methods for the discovery of such implicit connections.  ...  The discovery of implicit connections between terms that do not occur together in any scientific document underlies the model of literature-based knowledge discovery first proposed by Swanson.  ...  We would like to thank Tom Landauer for providing the TASA corpus, and to acknowledge Google Inc. for their support of author DW's ongoing research on the subject.  ... 
doi:10.1016/j.jbi.2009.09.003 pmid:19761870 fatcat:vzlnntofhfc6tbvbwwcusgld2y

Effective use of latent semantic indexing and computational linguistics in biological and biomedical applications

Hongyu Chen, Bronwen Martin, Caitlin M. Daimon, Stuart Maudsley
2013 Frontiers in Physiology  
In this review, we will focus on Latent Semantic Indexing (LSI), a computational linguistics technique increasingly used for a variety of biological purposes.  ...  analysis and integration of literature with associated metadata.  ...  ACKNOWLEDGMENTS This research was supported by the Intramural Research Program of the National Institute on Aging, National Institutes of Health.  ... 
doi:10.3389/fphys.2013.00008 pmid:23386833 pmcid:PMC3558626 fatcat:476phl67nngrvkp6naon4qx2qa

From Distributional Semantics to Conceptual Spaces: A Novel Computational Method for Concept Creation

Stephen McGregor, Kat Agres, Matthew Purver, Geraint A. Wiggins
2015 Journal of Artificial General Intelligence  
We define a computational method for discovering members of concepts based on semantic spaces: starting with a standard distributional model derived from corpus co-occurrence statistics, we dynamically  ...  This approach performs as well as, and in some cases better than, leading distributional semantic models on a WordNet-based concept discovery task, while also providing a model of concepts as convex regions  ...  co-occurrence of both the morphological forms of words and the syntactical dependencies between words, achieving marginal improvements over purely semantic models in correlation with human responses to  ... 
doi:10.1515/jagi-2015-0004 fatcat:tzlwuogvnjchxd6dufotsw6rhy
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