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Besides precision & recall: exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE
2006
AMIA Annual Symposium Proceedings
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This paper explores alternative approaches for the evaluation of an automatic indexing tool for MEDLINE, complementing the traditional precision and recall method. ...
The performance of MTI, the Medical Text Indexer used at NLM to produce MeSH recommendations for biomedical journal articles is evaluated on a random set of MEDLINE citations. ...
Tao for her groundwork on using MeSH semantic similarity for MTI evaluation. ...
pmid:17238409
pmcid:PMC1839480
fatcat:pm7ze4mdxvcq5h6tvt4p3yjnhy
Besides Precision & Recall: Exploring Alternative Approaches to Evaluating an Automatic Indexing Tool for MEDLINE
unpublished
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Objective: This paper explores alternative approaches for the evaluation of an automatic indexing tool for MEDLINE, complementing the traditional precision and recall method. ...
Materials and methods: The performance of MTI, the Medical Text Indexer used at NLM to produce MeSH recommendations for biomedical journal articles is evaluated on a random set of MEDLINE citations. ...
Tao for her groundwork on using MeSH semantic similarity for MTI evaluation. ...
fatcat:7s7tjnv5fzhpdbk4ql2hpyxc3a
An Integrated Approach to Biomedical Term Identification Systems
2020
Applied Sciences
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In order to evaluate our proposal on medical term identification, we present the results obtained by our system using the MANTRA corpus and compare its performance with the Freeling-Med tool. ...
By applying several Natural Language Processing (NLP) technologies, we have developed a prototype that offers an easy interface for helping to understand biomedical specialized terminology present in Spanish ...
Evaluation Metrics The primary evaluation metrics consisted of standard measures from the NLP community, namely micro-averaged precision, recall, and balanced F-score, the last one being the official evaluation ...
doi:10.3390/app10051726
fatcat:ct7kc3opinfvvaf2mka6wtugm4
Frontiers of biomedical text mining: current progress
2007
Briefings in Bioinformatics
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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. ...
Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. ...
We wish to thank the journal's anonymous reviewers, whose insightful comments helped significantly improve this article. ...
doi:10.1093/bib/bbm045
pmid:17977867
pmcid:PMC2516302
fatcat:4nfbokb7lfdjbnkijw2v6754qy
Identifying important concepts from medical documents
2006
Journal of Biomedical Informatics
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In this paper, we present a software tool called keyphrase identification program (KIP) for identifying topical concepts from medical documents. ...
The latter assigns weights to extracted noun phrases for a medical document based on how important they are to that document and how domain specific they are in the medical domain. ...
for Museum and Library Services under grant LG-02-04-0002-04. ...
doi:10.1016/j.jbi.2006.02.001
pmid:16545986
fatcat:mysdq64h55hylduaihta3lgcni
Using statistical and knowledge-based approaches for literature-based discovery
2006
Journal of Biomedical Informatics
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We also evaluate LitLinker's performance by using the information retrieval metrics of precision and recall. ...
However, the current volume of information has become a great barrier for this task and new automated tools are needed to help researchers identify new knowledge that bridges gaps across distinct sections ...
Gordon and Dumais also explored alternative techniques for identifying the linking literature [5] by using latent semantic indexing to extract close terms that occur in overlapping sets of documents. ...
doi:10.1016/j.jbi.2005.11.010
pmid:16442852
fatcat:n2g7uishbzbg7dognbjfydjvju
SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes
2018
BMC Bioinformatics
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The service, developed during the Semantic Indexing of French Biomedical Data Resources (2013-2019) project is included in the SIFR BioPortal, an open platform to host French biomedical ontologies and ...
However, semantic resources are required to design semantic indexes and transform biomedical (text)data into knowledge for better information mining and retrieval. ...
Data for CLEF eHealth evaluation: CépiDC data not publicly available due to privacy constraints (clinical text), access to data possible upon signature of a data use agreement as per the official instructions ...
doi:10.1186/s12859-018-2429-2
pmid:30400805
pmcid:PMC6218966
fatcat:dmwmnr4qs5fbfgcz2obqualfpq
Combining Thesauri-Based Methods for Biomedical Retrieval
2005
Text Retrieval Conference
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One method uses blind relevance feedback on MeSH terms, the second uses an index of the MeSH thesaurus for query expansion. ...
We show that, despite the relatively minor improvements in retrieval performance of individually applied methods, a combination works best and is able to deliver significant improvements over the baseline ...
In Section 2 we describe our data processing, indexing, tools and models employed for this year's edition of TREC Genomics. ...
dblp:conf/trec/MeijIAKR05
fatcat:ltzgkiuq35fijddwaloo73aniy
An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition
2015
BMC Bioinformatics
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Acknowledgements The research leading to these results has received funding from the European ...
The official scores were based on the manual evaluation; the automatic evaluation was performed mostly to explore how well automatic evaluation measures (e.g., from multi-document text summarization) correlate ...
The official scores were based on the manual evaluation; the automatic evaluation was performed mostly to explore how well automatic evaluation measures (e.g., from multi-document text summarization) correlate ...
doi:10.1186/s12859-015-0564-6
pmid:25925131
pmcid:PMC4450488
fatcat:u5enfjjos5gv5k3wkjxxa5ebry
Towards the automation of address identification
2012
Scientometrics
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Some tests are done to analyze possible association between both systems (automatic and hand-coding), calculating measures of recall and precision, and some statistical directional and symmetric measures ...
Although these results are quite general, this first overview of the address at the institutional sector level is a good way to develop a second approach for the selection of particular centers. ...
Measures of recall for INSPEC are 99% (1,192 possible address patterns), for CAB 98% (1,307) and for MEDLINE 94% (1,416) with an under-standardization, in this last database, of 4.2%. ...
doi:10.1007/s11192-012-0733-6
fatcat:kiyzags7k5hkvihqaqie45fvk4
Mining the pharmacogenomics literature--a survey of the state of the art
2012
Briefings in Bioinformatics
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extracted by text mining tools. ...
building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensiveways to disseminate andinteractwith the typicallyhuge amounts of semiformalknowledge structures ...
Evaluation results for all five categories range from 88.0 recall with 75.0 precision for predictions of pharmacokinetics, to 9.0 recall with 27.0 precision for the ClinicalOutcome category. ...
doi:10.1093/bib/bbs018
pmid:22833496
pmcid:PMC3404399
fatcat:por4dnthkrcxjdsir6uc64kdaq
Biomedical Informatics
[chapter]
2017
Encyclopedia of Machine Learning and Data Mining
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An alternative to improving the speed of our application would be to implement a local version of MEDLINE. ...
Dashed lines correspond to the precision levels of 0.8 and
0.5.
Figure 5 depicts the precision-recall curves from this comparative evaluation. ...
doi:10.1007/978-1-4899-7687-1_30
fatcat:45z6hsbczvaj3ajx3c3xf3bfpm
GLAD4U: deriving and prioritizing gene lists from PubMed literature
2012
BMC Genomics
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For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. ...
This process is not only time-consuming, but also prone to errors. Results: We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. ...
Hua Xu for useful comments on the analysis and Ms. Brandy Weidow for proofreading the manuscript. We appreciate the users who provided useful information through our interviews and online survey. ...
doi:10.1186/1471-2164-13-s8-s20
pmid:23282288
pmcid:PMC3535723
fatcat:mxi3lpcl3fdwtbpg7si6bvmrlm
BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature
2016
PLoS ONE
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To complement standard search engines such as PubMed, it is desirable to have an advanced search tool that directly returns relevant biomedical entities such as targets, drugs, and mutations rather than ...
Further, most existing tools cannot process sophisticated queries such as searches for mutations that co-occur with query terms in the literature. ...
Precision, Recall, and F1-score. To evaluate the biomedical entity extraction accuracy of BEST and PubTator, we used precision, recall, and F1-score as the evaluation metrics. ...
doi:10.1371/journal.pone.0164680
pmid:27760149
pmcid:PMC5070740
fatcat:atsxxpmwlzepbgrzkcussimnaa
Accomplishments and challenges in literature data mining for biology
2002
Bioinformatics
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We review recent results in literature data mining for biology and discuss the need and the steps for a challenge evaluation for this field. ...
To encourage participation and accelerate progress in this expanding field, we propose creating challenge evaluations, and we describe two specific applications in this context. ...
Applying the definitions for recall and precision, this reduces to F(E) = (2 × T P(E))/(2 × T P(E) + F N(E) + F P(E)). ...
doi:10.1093/bioinformatics/18.12.1553
pmid:12490438
fatcat:vaa7rx5ezzherntc5w4ct5ujle
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