Background: Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus).
Uncertainty is an important linguistic phenomenon that is relevant in various Natural Language Processing applications, in diverse genres from medical to community generated, newswire or scientific discourse, and domains from science to humanities. The semantic uncertainty of a proposition can be identified in most cases by using a finite dictionary (i.e., lexical cues) and the key steps of uncertainty detection in an application include the steps of locating the (genre- and domain-specific) lexical cues, disambiguating them, and linking them with the units of interest for the particular application (e.g., identified events in information extraction). In this study, we focus on the genre and domain differences of the context-dependent semantic uncertainty cue recognition task. We introduce a unified subcategorization of semantic uncertainty as different domain applications can apply different uncertainty categories. Based on this categorization, we normalized the annotation of three corpora and present results with a state-of-the-art uncertainty cue recognition model for four fine-grained categories of semantic uncertainty. Our results reveal the domain and genre dependence of the problem; nevertheless, we also show that even a distant source domain data set can contribute to the recognition and disambiguation of uncertainty cues, efficiently reducing the annotation costs needed to cover a new domain. Thus, the unified subcategorization and domain adaptation for training the models offer an efficient solution for cross-domain and cross-genre semantic uncertainty recognition.
Background: In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical records manually following clinical treatment. Since this labeling task requires expert knowledge in the field of medicine, the process itself is costly and is prone to errors as human annotators have to consider thousands of possible codes when assigning the right ICD-9-CM labels to a document. In this study we use the datasets made available for training and testing automated ICD-9-CM coding systems by the organisers of an International Challenge on Classifying Clinical Free Text Using Natural Language Processing in spring 2007. The challenge itself was dominated by entirely or partly rule-based systems that solve the coding task using a set of hand crafted expert rules. Since the feasibility of the construction of such systems for thousands of ICD codes is indeed questionable, we decided to examine the problem of automatically constructing similar rule sets that turned out to achieve a remarkable accuracy in the shared task challenge.
Joint morphological and syntactic analysis has been proposed as a way of improving parsing accuracy for richly inflected languages. Starting from a transition-based model for joint part-of-speech tagging and dependency parsing, we explore different ways of integrating morphological features into the model. We also investigate the use of rule-based morphological analyzers to provide hard or soft lexical constraints and the use of word clusters to tackle the sparsity of lexical features. Evaluation on five morphologically rich languages (Czech, Finnish, German, Hungarian, and Russian) shows consistent improvements in both morphological and syntactic accuracy for joint prediction over a pipeline model, with further improvements thanks to lexical constraints and word clusters. The final results improve the state of the art in dependency parsing for all languages.
We can say that our system is competitive with the current state-of-the-art solutions, while we describe here several techniques that can be beneficial in other tasks that need to handle structured documents such as clinical records.
Abstract. In this paper we introduce a multilingual Named Entity Recognition (NER) system that uses statistical modeling techniques. The system identifies and classifies NEs in the Hungarian and English languages by applying AdaBoostM1 and the C4.5 decision tree learning algorithm. We focused on building as large a feature set as possible, and used a split and recombine technique to fully exploit its potentials. This methodology provided an opportunity to train several independent decision tree classifiers based on different subsets of features and combine their decisions in a majority voting scheme. The corpus made for the CoNLL 2003 conference and a segment of Szeged Corpus was used for training and validation purposes. Both of them consist entirely of newswire articles. Our system remains portable across languages without requiring any major modification and slightly outperforms the best system of CoNLL 2003, and achieved a 94.77% F measure for Hungarian. The real value of our approach lies in its different basis compared to other top performing models for English, which makes our system extremely successful when used in combination with CoNLL modells.
BackgroundCompetitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions.ResultsAll four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best performance over all semantic groups were achieved from two annotation solutions that have been trained on the SSC-I.The data sets from participants were used to generate the harmonised Silver Standard Corpus II (SSC-II), if the participant did not make use of the annotated data set from the SSC-I for training purposes. The performances of the participants’ solutions were again measured against the SSC-II. The performances of the annotation solutions showed again better results for DISO and SPE in comparison to CHED and PRGE.ConclusionsThe SSC-I delivers a large set of annotations (1,121,705) for a large number of documents (100,000 Medline abstracts). The annotations cover four different semantic groups and are sufficiently homogeneous to be reproduced with a trained classifier leading to an average F-measure of 85%. Benchmarking the annotation solutions against the SSC-II leads to better performance for the CPs’ annotation solutions in comparison to the SSC-I.
BackgroundThe treatment of negation and hedging in natural language processing has received much interest recently, especially in the biomedical domain. However, open access corpora annotated for negation and/or speculation are hardly available for training and testing applications, and even if they are, they sometimes follow different design principles. In this paper, the annotation principles of the two largest corpora containing annotation for negation and speculation – BioScope and Genia Event – are compared. BioScope marks linguistic cues and their scopes for negation and hedging while in Genia biological events are marked for uncertainty and/or negation.ResultsDifferences among the annotations of the two corpora are thematically categorized and the frequency of each category is estimated. We found that the largest amount of differences is due to the issue that scopes – which cover text spans – deal with the key events and each argument (including events within events) of these events is under the scope as well. In contrast, Genia deals with the modality of events within events independently.ConclusionsThe analysis of multiple layers of annotation (linguistic scopes and biological events) showed that the detection of negation/hedge keywords and their scopes can contribute to determining the modality of key events (denoted by the main predicate). On the other hand, for the detection of the negation and speculation status of events within events, additional syntax-based rules investigating the dependency path between the modality cue and the event cue have to be employed.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.