scholarly journals Extending NegEx with Kernel Methods for Negation Detection in Clinical Text

2015 ◽  
Author(s):  
Chaitanya Shivade ◽  
Marie-Catherine de Marneffe ◽  
Eric Fosler-Lussier ◽  
Albert M. Lai
Keyword(s):  
Kernel Methods ◽  
Clinical Text ◽  
Negation Detection

Evaluation of lexicon- and syntax-based negation detection algorithms using clinical text data

2017 ◽  
Vol 13 (4) ◽  
Author(s):  
J. Manimaran ◽  
T. Velmurugan
Keyword(s):  
Language Processing ◽  
Patient Discharge ◽  
Computational Time ◽  
Practical Implementation ◽  
Automatic Identification ◽  
Kappa Statistics ◽  
Research Approach ◽  
Clinical Text ◽  
Medical Reports ◽  
Negation Detection

AbstractBackground:Clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing (NLP) system. In recent development modules of cTAKES, a negation detection (ND) algorithm is used to improve annotation capabilities and simplify automatic identification of negative context in large clinical documents. In this research, the two types of ND algorithms used are lexicon and syntax, which are analyzed using a database made openly available by the National Center for Biomedical Computing. The aim of this analysis is to find the pros and cons of these algorithms.Methods:Patient medical reports were collected from three institutions included the 2010 i2b2/VA Clinical NLP Challenge, which is the input data for this analysis. This database includes patient discharge summaries and progress notes. The patient data is fed into five ND algorithms: NegEx, ConText, pyConTextNLP, DEEPEN and Negation Resolution (NR). NegEx, ConText and pyConTextNLP are lexicon-based, whereas DEEPEN and NR are syntax-based. The results from these five ND algorithms are post-processed and compared with the annotated data. Finally, the performance of these ND algorithms is evaluated by computing standard measures including F-measure, kappa statistics and ROC, among others, as well as the execution time of each algorithm.Results:This research is tested through practical implementation based on the accuracy of each algorithm’s results and computational time to evaluate its performance in order to find a robust and reliable ND algorithm.Conclusions:The performance of the chosen ND algorithms is analyzed based on the results produced by this research approach. The time and accuracy of each algorithm are calculated and compared to suggest the best method.

scholarly journals Does BERT need domain adaptation for clinical negation detection?

2020 ◽  
Vol 27 (4) ◽  
pp. 584-591 ◽  
Author(s):  
Chen Lin ◽  
Steven Bethard ◽  
Dmitriy Dligach ◽  
Farig Sadeque ◽  
Guergana Savova ◽  
...  
Keyword(s):  
Transfer Learning ◽  
Domain Adaptation ◽  
Fine Tuning ◽  
Adaptation Algorithm ◽  
Learning Methods ◽  
Clinical Text ◽  
Unsupervised Domain Adaptation ◽  
Adversarial Training ◽  
Negation Detection ◽  
Adaptation Method

Abstract Introduction Classifying whether concepts in an unstructured clinical text are negated is an important unsolved task. New domain adaptation and transfer learning methods can potentially address this issue. Objective We examine neural unsupervised domain adaptation methods, introducing a novel combination of domain adaptation with transformer-based transfer learning methods to improve negation detection. We also want to better understand the interaction between the widely used bidirectional encoder representations from transformers (BERT) system and domain adaptation methods. Materials and Methods We use 4 clinical text datasets that are annotated with negation status. We evaluate a neural unsupervised domain adaptation algorithm and BERT, a transformer-based model that is pretrained on massive general text datasets. We develop an extension to BERT that uses domain adversarial training, a neural domain adaptation method that adds an objective to the negation task, that the classifier should not be able to distinguish between instances from 2 different domains. Results The domain adaptation methods we describe show positive results, but, on average, the best performance is obtained by plain BERT (without the extension). We provide evidence that the gains from BERT are likely not additive with the gains from domain adaptation. Discussion Our results suggest that, at least for the task of clinical negation detection, BERT subsumes domain adaptation, implying that BERT is already learning very general representations of negation phenomena such that fine-tuning even on a specific corpus does not lead to much overfitting. Conclusion Despite being trained on nonclinical text, the large training sets of models like BERT lead to large gains in performance for the clinical negation detection task.

scholarly journals DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx

2015 ◽  
Vol 54 ◽  
pp. 213-219 ◽  
Author(s):  
Saeed Mehrabi ◽  
Anand Krishnan ◽  
Sunghwan Sohn ◽  
Alexandra M. Roch ◽  
Heidi Schmidt ◽  
...  
Keyword(s):  
Detection System ◽  
Clinical Text ◽  
Dependency Relation ◽  
Negation Detection

scholarly journals A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text

2021 ◽  
Vol 130 ◽  
pp. 104216
Author(s):  
Luke T. Slater ◽  
William Bradlow ◽  
Dino FA. Motti ◽  
Robert Hoehndorf ◽  
Simon Ball ◽  
...  
Keyword(s):  
Detection Algorithm ◽  
Clinical Text ◽  
Negation Detection

scholarly journals A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text

2020 ◽  
Author(s):  
Luke T Slater ◽  
William Bradlow ◽  
Dino FA Motti ◽  
Robert Hoehndorf ◽  
Simon Ball ◽  
...  
Keyword(s):  
Text Mining ◽  
Gold Standard ◽  
Detection Algorithm ◽  
Heuristic Approach ◽  
University Hospitals ◽  
Rule Based ◽  
Clinical Text ◽  
Dependency Graphs ◽  
Negation Detection ◽  
Mimic Iii

AbstractBackgroundNegation detection is an important task in biomedical text mining. Particularly in clinical settings, it is of critical importance to determine whether findings mentioned in text are present or absent. Rule-based negation detection algorithms are a common approach to the task, and more recent investigations have resulted in the development of rule-based systems utilising the rich grammatical information afforded by typed dependency graphs. However, interacting with these complex representations inevitably necessitates complex rules, which are time-consuming to develop and do not generalise well. We hypothesise that a heuristic approach to determining negation via dependency graphs could offer a powerful alternative.ResultsWe describe and implement an algorithm for negation detection based on grammatical distance from a negatory construct in a typed dependency graph. To evaluate the algorithm, we develop two testing corpora comprised of sentences of clinical text extracted from the MIMIC-III database and documents related to hypertrophic cardiomyopathy patients routinely collected at University Hospitals Birmingham NHS trust. Gold-standard validation datasets were built by a combination of human annotation and examination of algorithm error. Finally, we compare the performance of our approach with four other rule-based algorithms on both gold-standard corpora.ConclusionsThe presented algorithm exhibits the best performance by f-measure over the MIMIC-III dataset, and a similar performance to the syntactic negation detection systems over the HCM dataset. It is also the fastest of the dependency-based negation systems explored in this study. Our results show that while a single heuristic approach to dependency-based negation detection is ignorant to certain advanced cases, it nevertheless forms a powerful and stable method, requiring minimal training and adaptation between datasets. As such, it could present a drop-in replacement or augmentation for many-rule negation approaches in clinical text-mining pipelines, particularly for cases where adaptation and rule development is not required or possible.

Spa-neg: An Approach for Negation Detection in Clinical Text Written in Spanish

2020 ◽  
pp. 323-337 ◽  
Author(s):  
Oswaldo Solarte-Pabón ◽  
Ernestina Menasalvas ◽  
Alejandro Rodriguez-González
Keyword(s):  
Clinical Text ◽  
Negation Detection

SemEval-2014 Task 7: Analysis of Clinical Text

2014 ◽  
Author(s):  
Sameer Pradhan ◽  
Noémie Elhadad ◽  
Wendy Chapman ◽  
Suresh Manandhar ◽  
Guergana Savova
Keyword(s):  
Clinical Text

Developing a RadLex-based Named Entity Recognition Tool for Mining Textual Radiology Reports (Preprint)

2020 ◽  
Author(s):  
Shintaro Tsuji ◽  
Andrew Wen ◽  
Naoki Takahashi ◽  
Hongjian Zhang ◽  
Katsuhiko Ogasawara ◽  
...  
Keyword(s):  
Named Entity Recognition ◽  
Noun Phrases ◽  
General Purpose ◽  
Entity Recognition ◽  
Free Text ◽  
Clinical Text ◽  
Named Entity ◽  
Radiology Reports ◽  
Two Measures ◽  
F Measure

BACKGROUND Named entity recognition (NER) plays an important role in extracting the features of descriptions for mining free-text radiology reports. However, the performance of existing NER tools is limited because the number of entities depends on its dictionary lookup. Especially, the recognition of compound terms is very complicated because there are a variety of patterns. OBJECTIVE The objective of the study is to develop and evaluate a NER tool concerned with compound terms using the RadLex for mining free-text radiology reports. METHODS We leveraged the clinical Text Analysis and Knowledge Extraction System (cTAKES) to develop customized pipelines using both RadLex and SentiWordNet (a general-purpose dictionary, GPD). We manually annotated 400 of radiology reports for compound terms (Cts) in noun phrases and used them as the gold standard for the performance evaluation (precision, recall, and F-measure). Additionally, we also created a compound-term-enhanced dictionary (CtED) by analyzing false negatives (FNs) and false positives (FPs), and applied it for another 100 radiology reports for validation. We also evaluated the stem terms of compound terms, through defining two measures: an occurrence ratio (OR) and a matching ratio (MR). RESULTS The F-measure of the cTAKES+RadLex+GPD was 32.2% (Precision 92.1%, Recall 19.6%) and that of combined the CtED was 67.1% (Precision 98.1%, Recall 51.0%). The OR indicated that stem terms of “effusion”, "node", "tube", and "disease" were used frequently, but it still lacks capturing Cts. The MR showed that 71.9% of stem terms matched with that of ontologies and RadLex improved about 22% of the MR from the cTAKES default dictionary. The OR and MR revealed that the characteristics of stem terms would have the potential to help generate synonymous phrases using ontologies. CONCLUSIONS We developed a RadLex-based customized pipeline for parsing radiology reports and demonstrated that CtED and stem term analysis has the potential to improve dictionary-based NER performance toward expanding vocabularies.

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