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Extraction of Pharmacokinetic Evidence of Drug–Drug Interactions from the Literature

Artemy Kolchinsky, Anália Lourenço, Heng-Yi Wu, Lang Li, Luis M. Rocha, Willy John Wilbur
2015 PLoS ONE  
Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases.  ...  Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which  ...  Acknowledgments The authors thank Shreyas Karnik for help with the preparation of the corpora. Author Contributions Conceived and designed the experiments: LL LMR. Performed the experiments: AK.  ... 
doi:10.1371/journal.pone.0122199 pmid:25961290 pmcid:PMC4427505 fatcat:abbceqoaovcsbaygbwpokosepa

Using computable knowledge mined from the literature to elucidate confounders for EHR-based pharmacovigilance [article]

Scott Alexander Malec, Elmer Victor Bernstam, Peng Wei, Trevor Cohen, Richard David Boyce
2020 medRxiv   pre-print
For our knowledge-base, we use SemMedDB, a database of computable knowledge mined from the biomedical literature.  ...  data to predict and estimate causal effects in light of the literature-derived confounders.  ...  Limitations and themes for future work Ideally, we would wish that our methods for studying observational data would possess sufficient rigor to approach the level of scientific confidence of an RCT.  ... 
doi:10.1101/2020.07.08.20113035 fatcat:symhqu3l25ayjdoxy457del6jq

An automated approach to identify scientific publications reporting pharmacokinetic parameters

Ferran Gonzalez Hernandez, Simon J Carter, Juha Iso-Sipilä, Paul Goldsmith, Ahmed A. Almousa, Silke Gastine, Watjana Lilaonitkul, Frank Kloprogge, Joseph F Standing
2021 Wellcome Open Research  
scientific literature.  ...  This automated, open-access repository can be used to accelerate the search and comparison of PK results, curate ADME datasets, and facilitate subsequent text mining tasks in the PK domain.  ...  The Alan Turing Institute for providing advice and engineering support. Nicolas Ford, Yalman Ahadi and Pongpol Lorthongpaisarn for contributing on the deployment of the final pipeline.  ... 
doi:10.12688/wellcomeopenres.16718.1 pmid:34381873 pmcid:PMC8343403 fatcat:qw6tsnzchzfjfcd2tcw7igu4qu

A deep learning relation extraction approach to support a biomedical semi-automatic curation task: the case of the gluten bibliome

Martín Pérez-Pérez, Tânia Ferreira, Gilberto Igrejas, Florentino Fdez-Riverola
2022 Expert systems with applications  
Discover relevant biomedical interactions in the literature is crucial for enhancing biology research.  ...  This curation process has an essential role in studying the different processes and interactions reported that affect the biological process (e.g., genome, metabolome, and transcriptome).  ...  This work was supported by: the Associate Laboratory for Green Chemistry -LAQV financed by the Portuguese Foundation for Science and Technology (FCT/MCTES) Ref.  ... 
doi:10.1016/j.eswa.2022.116616 fatcat:7mera4djvbd7rgqglpvmn4gdti

Potential and Pitfalls of Domain-Specific Information Extraction at Web Scale

Astrid Rheinländer, Mario Lehmann, Anja Kunkel, Jörg Meier, Ulf Leser
2016 Proceedings of the 2016 International Conference on Management of Data - SIGMOD '16  
The focus of this paper is to provide a large, real-life use case to inspire future research into robust, easy-to-use, and scalable methods for domainspecific IE at web scale.  ...  eventually named entity recognition for several types of entities.  ...  We thank Philippe Thomas and Tim Rocktäschel for providing models and software we used during entity recognition.  ... 
doi:10.1145/2882903.2903736 dblp:conf/sigmod/RheinlanderLKML16 fatcat:i745iiaicjan3lnfyybachvahy

Text analytics in industry: Challenges, desiderata and trends

Ashwin Ittoo, Le Minh Nguyen, Antal van den Bosch
2016 Computers in industry (Print)  
Each tweet was evaluated by the judges on a 3-level Likert scale for their interestingness and informativeness.  ...  Concerning the NER task pertaining to the detection of an effect, the F1-score of the proposed system is estimated at 0.6.  ...  Antal van den Bosch (Ph.D. 1997, Universiteit Maastricht) is professor of language and speech technology at the Centre for Language Studies at Radboud University, Nijmegen, the Netherlands.  ... 
doi:10.1016/j.compind.2015.12.001 fatcat:3cp4p55qn5bincjfr4jidqs6ie

Automatic Extraction of Rarely Explored Materials and Methods Sections from Research Journals using Machine Learning Techniques

Kavitha Jayaram, Prakash G, Jayaram V
2020 International Journal of Advanced Computer Science and Applications  
The scientific community is expanding by leaps and bounds every day owing to pioneering and path breaking scientific literature published in journals around the globe.  ...  The essence and importance of scientific research papers for the expert lies in their experimental and theoretical results along with the sanctioned research projects from the organizations.  ...  Since the data is in PDF format, it is a difficult task to use all the information available in the research documents. Therefore, data pre-processing becomes an important and time consuming task.  ... 
doi:10.14569/ijacsa.2020.0110857 fatcat:4rm7w6i2z5efnpbggx7foxdcuu

Proceedings of the second biocreative challenge evaluation workshop

Lynette Hirschman, Martin Krallinger, Alfonso Valencia
2007 Zenodo  
Matos is funded by FCT under the Ciência2007 programme. -5 - Acknowledgments This work was partially supported by Grants-in-Aid for Scientific Research on Priority Areas (MEXT, Japan) and for Solution-Oriented  ...  Acknowledgements We especially want to thank the BioGRID (Andrew Chatr-aryamontri) and MINT (Gianni Cesareni) databases and their curators for generating the data collections for this task; without their  ...  The ever increasing scientific literature now available electronically and the exponential growth of large-scale molecular data have prompted active research in biological text mining and information extraction  ... 
doi:10.5281/zenodo.6519852 fatcat:k6q4vrkd65hbthlvwnhy2ufiey

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni (+22 others)
2011 BMC Bioinformatics  
CONCLUSIONS: The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging.  ...  The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been  ...  We would like to thank Reverse Informatics and in particular Parthiban Srinivasan for their collaboration on the ACT.  ... 
doi:10.1186/1471-2105-12-s8-s3 pmid:22151929 pmcid:PMC3269938 fatcat:vireubnikbhgjg2y2fskgqvgse

Deep Learning applications for COVID-19

Connor Shorten, Taghi M. Khoshgoftaar, Borko Furht
2021 Journal of Big Data  
Deep Learning has additionally been utilized in Spread Forecasting for Epidemiology. Our literature review has found many examples of Deep Learning systems to fight COVID-19.  ...  Natural Language Processing applications include mining COVID-19 research for Information Retrieval and Question Answering, as well as Misinformation Detection, and Public Sentiment Analysis.  ...  Acknowledgements We would like to thank the reviewers in the Data Mining and Machine Learning Laboratory at Florida Atlantic University.  ... 
doi:10.1186/s40537-020-00392-9 pmid:33457181 pmcid:PMC7797891 fatcat:aokxo63z2rhdpfxo3egyf3xpcm

Classification and analysis of a large collection of in vivo bioassay descriptions

Magdalena Zwierzyna, John P. Overington, Nir London
2017 PLoS Computational Biology  
We retrieve our dataset from ChEMBL-an open-source literature-based database focused on preclinical drug discovery.  ...  We show that in vivo assay descriptions can be effectively mined for relevant information, including experimental factors that might influence the outcome and reproducibility of animal research: genetic  ...  Acknowledgments We thank our previous colleagues at EMBL-EBI, and current colleagues at BenevolentAI for much useful discussion and advice, in particular Anneli Karlsson, Anne Phelan (Mission Therapeutics  ... 
doi:10.1371/journal.pcbi.1005641 pmid:28678787 pmcid:PMC5517062 fatcat:oqirndgpv5cw3k77y2cbesyx7i

Automatic Classification of Purpose of software usages in scholarly articles

Bekalue Tadesse
2022 Zenodo  
Automatic extraction of the purpose of software usage creates an opportunity to identify a set of software tools used for the same purpose in a given context of scientific work.  ...  In addition, the use of software for scientific research entailed difficulty in reproducing research results mainly because of poor software citation practices.  ...  In terms of task, a software can be used for execution of rudimentary tasks to computation of extremely complex ones.  ... 
doi:10.5281/zenodo.6509907 fatcat:cqinviaovnf2vkjcmev2zapqla

Open challenges for data stream mining research

Georg Krempl, Myra Spiliopoulou, Jerzy Stefanowski, Indre Žliobaite, Dariusz Brzeziński, Eyke Hüllermeier, Mark Last, Vincent Lemaire, Tino Noack, Ammar Shaker, Sonja Sievi
2014 SIGKDD Explorations  
Another body of literature focuses on developing languages for querying Tweets.  ...  Another body of literature focuses on developing languages for querying Tweets.  ...  on the challenges in stream mining.  ... 
doi:10.1145/2674026.2674028 fatcat:y3bozzeohveibgxb5wmiwfcogm

Deep learning and explainable artificial intelligence techniques applied for detecting money laundering – a critical review

Dattatray V. Kute, Biswajeet Pradhan, Nagesh Shukla, Abdullah Alamri
2021 IEEE Access  
Literature shows the usage of statistical methods, data mining and Machine Learning (ML) techniques for money laundering detection, but limited research on Deep Learning (DL) techniques, primarily due  ...  This paper aims to review the current state-of-the-art literature on DL together with XAI for identifying suspicious money laundering transactions and identify future research areas.  ...  Document level SA classifier, trained on auto labelled 12,467 financial news articles, achieved 76.96 % accuracy. Author used a pipeline based method for relationship extraction tasks.  ... 
doi:10.1109/access.2021.3086230 fatcat:n4wwkfoiaff5rjpelnddtcruwu

Low-Resource Adaptation of Neural NLP Models [article]

Farhad Nooralahzadeh
2020 arXiv   pre-print
The objective of this thesis is to investigate methods for dealing with such low-resource scenarios in information extraction and natural language understanding.  ...  These resources are often based on language data available in large quantities, such as English newswire.  ...  ., and Dyer, C. (2016) . "Neural Architectures for Named Entity Recognition".  ... 
arXiv:2011.04372v1 fatcat:626mbe5ba5bkdflv755o35u5pq
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