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Extracting Adverse Drug Events from Text Using Human Advice [chapter]

Phillip Odom, Vishal Bangera, Tushar Khot, David Page, Sriraam Natarajan
2015 Lecture Notes in Computer Science  
We demonstrate on a standard adverse drug events data base that the proposed approach can successfully extract existing adverse drug events from limited amount of training data and compares favorably with  ...  Consequently, we employ a novel relation extraction technique based on a recently developed probabilistic logic learning algorithm that exploits human advice.  ...  Consider the adverse drug event prediction task using the dependency paths from sentences.  ... 
doi:10.1007/978-3-319-19551-3_26 pmid:29119145 pmcid:PMC5673136 fatcat:ytnytfahafhybmbx6g2igi5mja

The DDI corpus: An annotated corpus with pharmacological substances and drug–drug interactions

María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, Thierry Declerck
2013 Journal of Biomedical Informatics  
and the detection of DDIs from biomedical texts.  ...  The management of drug-drug interactions (DDIs) is a critical issue resulting from the overwhelming amount of information available on them.  ...  The use of a brand-name drug instead of its generic name may be related to a higher risk of adverse drug events [33, 34] .  ... 
doi:10.1016/j.jbi.2013.07.011 pmid:23906817 fatcat:r3mnnfyyfjga3jtlx46ek5yagy

#Science: The potential and the challenges of utilizing social media and other electronic communication platforms in health care

Violette Gijsen, Michele Maddux, Adam Lavertu, Graciela Gonzalez‐Hernandez, Nilam Ram, Byron Reeves, Thomas Robinson, Victoria Ziesenitz, Valentina Shakhnovich, Russ Altman
2019 Clinical and Translational Science  
Electronic communication is becoming increasingly popular worldwide, as evidenced by its widespread and rapidly growing use.  ...  All these techniques are a valuable component of modern health care and will help us into the future of increasingly digital health care.  ...  The initial analysis focuses on using the extracted text to identify sessions related to diseases and drugs. 30 Disease and drug word groups were defined using word vectors trained on a publicly available  ... 
doi:10.1111/cts.12687 pmid:31392837 pmcid:PMC6951453 fatcat:huh73h7j6reufmyl7foby6f2di

A research framework for pharmacovigilance in health social media: Identification and evaluation of patient adverse drug event reports

Xiao Liu, Hsinchun Chen
2015 Journal of Biomedical Informatics  
However, extracting patient adverse drug event reports from social media continues to be an important challenge for health informatics research.  ...  The framework consists of medical entity extraction for recognizing patient discussions of drug and events, adverse drug event extraction with shortest dependency path kernel based statistical learning  ...  Chanadda Chinthammit for their advices from clinical and pharmaceutical perspectives in this study. We thank Jing Liu for her analytical work on the MedHelp forum.  ... 
doi:10.1016/j.jbi.2015.10.011 pmid:26518315 fatcat:53nu3jrxfbdmxe2yqpaaqyrija

Systematic drug repositioning through mining adverse event data in ClinicalTrials.gov

Eric Wen Su, Todd M. Sanger
2017 PeerJ  
An I2E query extracts "Serious Adverse Events" (SAE) data from randomized trials in ClinicalTrials.gov.  ...  Drug repositioning (i.e., drug repurposing) is the process of discovering new uses for marketed drugs. Historically, such discoveries were serendipitous.  ...  Marjo Gazak and Jane Reed, and insightful advice and review by Dr. Stephen Ruberg.  ... 
doi:10.7717/peerj.3154 pmid:28348935 pmcid:PMC5366063 fatcat:3o66yaiyqjhvdjkexbaesmn62a

Harnessing scientific literature reports for pharmacovigilance

Anna Ripple, Joseph Tonning, Monica Munoz, Rashedul Hasan, Thomas Ly, Henry Francis, Olivier Bodenreider, Alfred Sorbello
2017 Applied Clinical Informatics  
drug event (ADE) safety signal detection.  ...  We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining.  ...  The published literature complements the safety information that can be extracted from the FDA Adverse Event Reporting System (FAERS) [2] .  ... 
doi:10.4338/aci-2016-11-ra-0188 pmid:28326432 pmcid:PMC5373771 fatcat:ml26yskqyfan5dh6lhhbd3ttii

Applications of Clinical Text Mining [chapter]

Hercules Dalianis
2018 Clinical Text Mining  
events (ADE), followed by resources for adverse drug event detection and continuing with an application of automatic assignment and validation of ICD-10 diagnosis codes.  ...  This chapter will present the state of the art for a number of applications of clinical text mining such as detection and prediction of healthcare associated infections (HAI), detection of adverse drug  ...  In the text mining terminology of adverse drug events the following concepts are used: an adverse drug event (ADE) may occur when a drug is taken to treat a disease.  ... 
doi:10.1007/978-3-319-78503-5_10 fatcat:qctgcc6uo5hefdwmq6scrwnwma

Identifying potential adverse effects using the web: A new approach to medical hypothesis generation

Adrian Benton, Lyle Ungar, Shawndra Hill, Sean Hennessy, Jun Mao, Annie Chung, Charles E. Leonard, John H. Holmes
2011 Journal of Biomedical Informatics  
Using a corpus of posts to breast cancer message boards, we identified drug event pairs using co-occurrence statistics.  ...  We then compared the identified drug event pairs with adverse effects listed on the package labels of tamoxifen, anastrozole, exemestane, and letrozole.  ...  adverse drug events.  ... 
doi:10.1016/j.jbi.2011.07.005 pmid:21820083 pmcid:PMC4404640 fatcat:2f6gmy7pbjerhhg4lznnhkorp4

Automated Detection of Adverse Drug Reactions in the Biomedical Literature Using Convolutional Neural Networks and Biomedical Word Embeddings [article]

Diego Saldana Miranda
2018 arXiv   pre-print
Monitoring the biomedical literature for cases of Adverse Drug Reactions (ADRs) is a critically important and time consuming task in pharmacovigilance.  ...  Finally, we evaluate the use of word embeddings specifically developed for biomedical text and show that they lead to a better performance in this task.  ...  Gupta et al. proposed a two step approach for extracting mentions of adverse events from social media: (1) predicting the drug based on the context, unsupervised; (2) predicting adverse event mentions  ... 
arXiv:1804.09148v1 fatcat:gd352ruekvcl7bcusw7hxhvvki

Research of ddi based on multi-label conditional random field

Yangzhi Yu, Hongtao Deng, Xun Zhu, J.Q. Cheng, H.L. Moffitt, I. Kim, Z.T. Chi, J. Zhang
2017 BIO Web of Conferences  
According to the characteristics of medical texts, this paper extracts the good features of the description of DDI. The proposed method has good performance in DDIExtraction 2013 evaluation corpus.  ...  Compared to the traditional method, our method can not only identify drug names, but also can identify drug-drug interaction.  ...  There is a large number of entity relationship extraction researches, such as protein extraction, RNA molecules relationship extraction, DDI extraction and the drug adverse effects event extraction and  ... 
doi:10.1051/bioconf/20170801039 fatcat:byor5qeto5fq3nqkh5fygamoza

Natural Language Processing for Smart Healthcare [article]

Binggui Zhou, Guanghua Yang, Zheng Shi, Shaodan Ma
2022 arXiv   pre-print
We focus on feature extraction and modelling for various NLP tasks encountered in smart healthcare from a technical point of view.  ...  As an essential technology powered by AI, natural language processing (NLP) plays a key role in smart healthcare due to its capability of analysing and understanding human language.  ...  extraction drug review and safety monitoring adverse drug events discovery and drug safety monitoring [205] - [207] information extraction engines, and even wrong decisions made by decision support  ... 
arXiv:2110.15803v2 fatcat:3o6tx5wqezdb5mgyfub2jtuiqu

Adverse effects of non-steroidal anti-inflammatory drugs in patients with viral respiratory infections: rapid systematic review

Peter von Philipsborn, Renke Biallas, Jacob Burns, Simon Drees, Karin Geffert, Ani Movsisyan, Lisa Maria Pfadenhauer, Kerstin Sell, Brigitte Strahwald, Jan M Stratil, Eva Rehfuess
2020 BMJ Open  
Due to methodological limitations of adverse event counts, this evidence should be interpreted with caution.ConclusionsIt is unclear whether the use of NSAIDs increases the risk of severe adverse outcomes  ...  Twenty-eight studies in adults and 42 studies in children report adverse event counts. Most report that no severe adverse events occurred.  ...  for support in obtaining full texts of studies included in this review.  ... 
doi:10.1136/bmjopen-2020-040990 pmid:33444207 fatcat:i64tje3snbc2zp4gnsfphp2tiy

Effects of food on pharmacokinetics of immediate release oral formulations of aspirin, dipyrone, paracetamol and NSAIDs - a systematic review

Robert Andrew Moore, Sheena Derry, Philip J. Wiffen, Sebastian Straube
2015 British Journal of Clinical Pharmacology  
AIMS It is common to advise that analgesics, and especially non-steroidal anti-inflammatory drugs (NSAIDs), be taken with food to reduce unwanted gastrointestinal adverse effects.  ...  This review sought evidence from single dose pharmacokinetic studies on the extent and timing of peak plasma concentrations of analgesic drugs in the fed and fasting states.  ...  The advice to take aspirin and NSAIDs with food stems from a desire to protect people from gastrointestinal adverse events; common events like dyspepsia, and rare, serious events like gastrointestinal  ... 
doi:10.1111/bcp.12628 pmid:25784216 pmcid:PMC4574824 fatcat:yjlmycu4mrdm7p3zjb7hbotfjy

The Adverse Drug Reactions From Patient Reports in Social Media Project: Protocol for an Evaluation Against a Gold Standard

Armelle Arnoux-Guenegou, Yannick Girardeau, Xiaoyi Chen, Myrtille Deldossi, Rim Aboukhamis, Carole Faviez, Badisse Dahamna, Pierre Karapetiantz, Sylvie Guillemin-Lanne, Agnès Lillo-Le Louët, Nathalie Texier, Anita Burgun (+1 others)
2019 JMIR Research Protocols  
The study is conducted as part of the Adverse Drug Reactions from Patient Reports in Social Media project. Messages from French health forums were extracted.  ...  Information technology solutions aiming at extracting adverse reactions (ADRs) from posts on health forums require a rigorous evaluation methodology if their results are to be used to make decisions.  ...  ADR-PRISM Adverse Drug Reaction Extraction Resources We used three lexicons to represent drug information and adverse events.  ... 
doi:10.2196/11448 pmid:31066711 pmcid:PMC6528435 fatcat:5ezghlbmrjfm3l4s47wyrpdtky

Systematic reviews of adverse effects: framework for a structured approach

Yoon K Loke, Deirdre Price, Andrew Herxheimer
2007 BMC Medical Research Methodology  
Detailed advice is given on designing electronic searches for studies with adverse effects data.  ...  Much of the current guidance on systematic reviews is directed towards the evaluation of effectiveness; but this differs in important ways from the methods used in assessing the safety and tolerability  ...  Acknowledgements The following colleagues (listed alphabetically) have contributed their expertise to the Cochrane Adverse Effects Subgroup, and we are very grateful for their advice in developing this  ... 
doi:10.1186/1471-2288-7-32 pmid:17615054 pmcid:PMC1933432 fatcat:swbgyefeorhzlgq52j7vznrcfm
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