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Literature-Based Discovery beyond the ABC paradigm: a contrastive approach [article]

Erwan Moreau, Orla Hardiman, Mark Heverin, Declan O'Sullivan
2021 bioRxiv   pre-print
Literature-Based Discovery (LBD) aims to help researchers to identify relations between concepts which are worthy of further investigation by text-mining the biomedical literature.  ...  The study emphasizes the impact of the choice of source data and extraction method on the resulting knowledge base: different "views" of the biomedical literature offer different levels of accuracy and  ...  Acknowledgements This work was conducted with the financial support of Irish Health Research Board (HRB) BRAINMend project (grant number HRB-JPI-JPND-2017-1) and with the support of the Science Foundation  ... 
doi:10.1101/2021.09.22.461375 fatcat:43e32dfhnrhmvab4y627ymimxe

Literature-Based Discovery? The Very Idea [chapter]

D. R. Swanson
2008 Literature-based Discovery  
The purpose of this introduction is to outline goals, concepts, problems, and literature structures that offer one approach to understanding the potential and limitations of literature-based discovery  ...  In that sense, the two articles are complementary, a relationship based on the scientific problems, findings, and arguments presented.  ...  Sutton's paper holds at least two important lessons for literature-based discovery.  ... 
doi:10.1007/978-3-540-68690-3_1 fatcat:jl4ugklkfbdlbeo3ouxqdc2st4

Towards Open Domain Literature Based Discovery

Oliver Bensch, Tobias Hecking
2021 Zenodo  
Based on the ABC model two search approaches can be used to generate new hypotheses from literature corpora (illustrated in 1. In open discovery, the search term "A" is given.  ...  RELATED WORK Although literature-based discovery has a long research history originating in the 80's [1] , it is still mainly focused on variations of the classical ABC model with applications in biomedicine  ... 
doi:10.5281/zenodo.6144571 fatcat:oyvlxetwaraz3eyzqwemctps2e

Neural networks for open and closed Literature-based Discovery

Gamal Crichton, Simon Baker, Yufan Guo, Anna Korhonen, Francisco J. Esteban
2020 PLoS ONE  
Literature-based Discovery (LBD) aims to discover new knowledge automatically from large collections of literature.  ...  In the first experiments, our best methods performed 2-4 times better than the baselines in closed discovery and 2-3 times better in open discovery.  ...  Acknowledgments We wish to thank all the implementers of LINE and the creators and contributors of the 2 datasets used for making them freely available.  ... 
doi:10.1371/journal.pone.0232891 pmid:32413059 fatcat:p4tvtm7ymfgv5p6azckb5zijki

A systematic review on literature-based discovery workflow

Menasha Thilakaratne, Katrina Falkner, Thushari Atapattu
2019 PeerJ Computer Science  
Literature-Based Discovery (LBD), supporting automated knowledge discovery, helps facilitate this process by eliciting novel knowledge by analysing existing scientific literature.  ...  With regards to the input component, we discuss the data types and data sources used in the literature.  ...  a ''literature based discovery'' OR ''literature based discoveries'' b ''literature based knowledge discovery'' OR ''literature based knowledge discoveries''.  ... 
doi:10.7717/peerj-cs.235 pmid:33816888 pmcid:PMC7924697 fatcat:w3gat4llvfarhbjo2gpfgt4smi

Beyond the ABCs: Higher Education and Developing Countries

Devesh Kapur, Megan Crowley
2008 Social Science Research Network  
Three, with the state unable to meet growing demand pressures, what should be the proper role of the state to ensure not just quality but also equity and access?  ...  Two, how does the impact of higher education depend on the type of education and its beneficiaries?  ...  and beyond the student's innate abilities.  ... 
doi:10.2139/ssrn.1099934 fatcat:xmncqadcfbc75khenmlk6gcxcy

Bisociative Literature-Based Discovery: Lessons Learned and New Prospects

Nada Lavrac, Matej Martinc, Senja Pollak, Bojan Cestnik
2020 International Conference on Computational Creativity  
The field of bisociative literature-based discovery aims at exploring scientific literature to reveal new discoveries based on yet uncovered relations between knowledge from different, relatively isolated  ...  Finally, the paper addresses new prospects in bisociative literaturebased discovery, emphasizing the use of advanced embeddings technology for cross-domain literature mining.  ...  Acknowledgements This work was supported by Slovenian Research Agency grant P-0103 and the European Unions Horizon 2020 research and innovation programme under grant agreement No 825153, project EMBEDDIA  ... 
dblp:conf/icccrea/LavracMPC20 fatcat:x4uazdmgobdhvan24u4szhkajq

Scientometric analysis and knowledge mapping of literature-based discovery (1986-2020) [article]

Andrej Kastrin, Dimitar Hristovski
2020 arXiv   pre-print
Literature-based discovery (LBD) aims to discover valuable latent relationships between disparate sets of literatures.  ...  We utilize a comprehensive scientometric approach incorporating CiteSpace to systematically analyze the literature on LBD from the last four decades (1986-2020).  ...  Acknowledgements The authors thank Petra Hrovat Hristovski for proof-reading the manuscript. The authors also thank Halil Kilicoglu for his helpful comments and suggestions.  ... 
arXiv:2006.08486v1 fatcat:fhtplszgcrft3j6prvvtdbuw6u

Bisociative Literature-Based Discovery: Lessons Learned and New Word Embedding Approach

Nada Lavrač, Matej Martinc, Senja Pollak, Maruša Pompe Novak, Bojan Cestnik
2020 New generation computing  
The paper addresses also new prospects in bisociative literature-based discovery, proposing an advanced embeddings-based technology for cross-domain literature mining.  ...  This paper outlines several outlier-based literature mining approaches to bridging term detection and the lessons learned from selected biomedical literature-based discovery applications.  ...  Background and Related Work This section presents the related work. "Literature-based discovery" introduces literature-based discovery (LBD), which is the main topic of this research.  ... 
doi:10.1007/s00354-020-00108-w fatcat:ypxsjir5tjamdn7fenzxd7oqky

Context-driven automatic subgraph creation for literature-based discovery

Delroy Cameron, Ramakanth Kavuluru, Thomas C. Rindflesch, Amit P. Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider
2015 Journal of Biomedical Informatics  
Literature-based discovery (LBD) is characterized by uncovering hidden associations in non-interacting scientific literature.  ...  Results: The subgraphs generated using this approach facilitated the rediscovery of 8 out of 9 existing scientific discoveries.  ...  Acknowledgement This research was supported in part by the Intramural Research Program of the US National Institutes of Health, National Library of Medicine.  ... 
doi:10.1016/j.jbi.2015.01.014 pmid:25661592 pmcid:PMC4888806 fatcat:hiladpi4jjhr7e72rtyrzyqtl4

Rediscovering Don Swanson:The Past, Present and Future of Literature-based Discovery

Neil R. Smalheiser
2017 Journal of Data and Information Science  
Research limitations This paper reflects the opinions of the author and is not a comprehensive nor technically based review of literature-based discovery.  ...  Practical implications The general scientific public is still not aware of the availability of tools for literature-based discovery.  ...  methods that are being applied to the field of literature-based discovery.  ... 
doi:10.1515/jdis-2017-0019 pmid:29355246 pmcid:PMC5771422 fatcat:hsjohjmc5rccznx6mg6eqqz2fq

Using Literature Based Discovery to Gain Insights Into the Metabolomic Processes of Cardiac Arrest

Sam Henry, D. Shanaka Wijesinghe, Aidan Myers, Bridget T. McInnes
2021 Frontiers in Research Metrics and Analytics  
Metabolites are the end product of many biochemical pathways within the human body.  ...  These insights lead to our proposal (for the first time) of LCAT as a druggable target; the effects of which are supported by in vivo studies which were brought forth by this work.  ...  Literature Based Discovery Literature based discovery (LBD) was first conceptualized by Dr Don Swanson, who formalized his approach of finding implicit links in the literature to discover new knowledge  ... 
doi:10.3389/frma.2021.644728 pmid:34250435 pmcid:PMC8267364 fatcat:5y6v6e7afrcxxmvrgnmt4wtzem

Exploration of Shared Themes Between Food Security and Internet of Things Research Through Literature-Based Discovery

Cristian Mejia, Yuya Kajikawa
2021 Frontiers in Research Metrics and Analytics  
This paper applied a literature-based discovery methodology utilizing citation networks and text mining in order to extract and represent shared terminologies found in disjoint academic literature on food  ...  security and the Internet of Things.  ...  INTRODUCTION Literature-based discovery (LBD) refers to text mining methodologies aimed at connecting disjoint literature by finding intermediary terms or concepts.  ... 
doi:10.3389/frma.2021.652285 pmid:34056514 pmcid:PMC8159171 fatcat:wrisbsg3ebbcfk6fstdhtmzf7a

Ontology-based identification and prioritization of candidate drugs for epilepsy from literature

Bernd Müller, Leyla Jael Castro, Dietrich Rebholz-Schuhmann
2022 Journal of Biomedical Semantics  
validate approaches in the drug discovery process.  ...  Literature-based analyses exploit factual knowledge on drugs and diseases, e.g. from databases, and combine it with information from scholarly publications.  ...  Acknowledgements The authors thank ZB MED for the ongoing support of their research.  ... 
doi:10.1186/s13326-021-00258-w pmid:35073996 pmcid:PMC8785029 fatcat:cz7d2pzt4fetxbchenc4y6corm

Efficient discovery of sequence outlier patterns

Lei Cao, Yizhou Yan, Samuel Madden, Elke A. Rundensteiner, Mathan Gopalsamy
2019 Proceedings of the VLDB Endowment  
To solve the fundamental limitation of existing pattern mining semantics that miss outlier patterns hidden inside of larger frequent patterns, TOP offers new pattern semantics based on contextual patterns  ...  Effective optimization techniques such as context-driven search space pruning and inverted index-based outlier pattern detection are also proposed to further speed up contextual pattern mining.  ...  Beyond the contextual constraint, other constraints in the literature continue to be applicable, such as the gap constraint [5] . DEFINITION 2.2. Gap Constraint. Given a pattern P = E1 E2 . . .  ... 
doi:10.14778/3324301.3324308 fatcat:64rs4dr4g5divhjpd3habnx5h4
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