Detecting hedge cues and their scope in biomedical text with conditional random fields.
Detecting hedge cues and their scope in biomedical text with conditional random fields.
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DOI：
10.1016/j.jbi.2010.08.003
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发表时间：
2010-12
影响因子：
4.5
通讯作者：
Yu H
中科院分区：
文献类型：
--
作者：
Agarwal S;Yu H
套期保值在生物学文献和临床记录中经常被用来表示不确定性或推测。重要的是文本挖掘应用程序，以检测对冲线索和他们的范围，否则，不确定的事件被错误地识别为事实事件。然而，由于语言的复杂性，识别模糊限制语线索及其在句子中的范围并不是一项简单的任务。我们的目标是开发一种算法，将自动检测对冲线索和它们的范围在生物医学文献。我们使用条件随机场（CRF），一种有监督的机器学习算法，来训练模型，以检测对冲提示短语及其在生物医学文献中的范围。这些模型是在公开可用的BioScope语料库上训练的。我们通过计算召回率、精确率和F1分数来评估CRF模型在识别模糊限制语提示短语及其范围方面的性能。我们将我们的模型与三种竞争性基线系统进行了比较。我们最好的基于CRF的模型在统计学上比基线系统表现得更好，在检测生物学文献中的对冲提示短语及其范围时，F1得分为88%和86%，在检测临床笔记中的对冲提示短语及其范围时，F1得分为93%和90%。我们的方法是稳健的，因为它可以识别对冲线索及其在生物和临床文本的范围。为了使文本挖掘应用程序受益，我们的系统作为Java API和在线应用程序在http://hedgescope.askhermes.org上公开提供。据我们所知，这是第一个公开提供的系统来检测对冲线索及其在生物医学文献中的范围。
Hedging is frequently used in both the biological literature and clinical notes to denote uncertainty or speculation. It is important for text-mining applications to detect hedge cues and their scope; otherwise, uncertain events are incorrectly identified as factual events. However, due to the complexity of language, identifying hedge cues and their scope in a sentence is not a trivial task. Our objective was to develop an algorithm that would automatically detect hedge cues and their scope in biomedical literature. We used conditional random fields (CRF), a supervised machine-learning algorithm, to train models to detect hedge cue phrases and their scope in biomedical literature. The models were trained on the publicly available BioScope corpus. We evaluated the performance of the CRF models in identifying hedge cue phrases and their scope by calculating recall, precision and F1-score. We compared our models with three competitive baseline systems. Our best CRF-based model performed statistically better than the baseline systems, achieving an F1-score of 88% and 86% in detecting hedge cue phrases and their scope in biological literature and an F1-score of 93% and 90% in detecting hedge cue phrases and their scope in clinical notes. Our approach is robust, as it can identify hedge cues and their scope in both biological and clinical text. To benefit text-mining applications, our system is publicly available as a Java API and as an online application at http://hedgescope.askhermes.org. To our knowledge, this is the first publicly available system to detect hedge cues and their scope in biomedical literature.
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DOI：
10.1136/jamia.1994.95236146
发表时间：
1994-03-01
影响因子：
6.4
作者：
FRIEDMAN, C;ALDERSON, PO;JOHNSON, SB
通讯作者：
JOHNSON, SB
影响因子：
3
作者：
Kilicoglu H;Bergler S
通讯作者：
Bergler S
影响因子：
5.8
作者：
Settles, B
通讯作者：
Settles, B
影响因子：
3
作者：
Donaldson, I;Martin, J;de Bruijn, B;Wolting, C;Lay, V;Tuekam, B;Zhang, SD;Baskin, B;Bader, GD;Michalickova, K;Pawson, T;Hogue, CWV
通讯作者：
Hogue, CWV
影响因子：
5.8
作者：
Shatkay, Hagit;Pan, Fengxia;Rzhetsky, Andrey;Wilbur, W. John
通讯作者：
Wilbur, W. John