10,608 research outputs found
Using Neural Networks for Relation Extraction from Biomedical Literature
Using different sources of information to support automated extracting of
relations between biomedical concepts contributes to the development of our
understanding of biological systems. The primary comprehensive source of these
relations is biomedical literature. Several relation extraction approaches have
been proposed to identify relations between concepts in biomedical literature,
namely, using neural networks algorithms. The use of multichannel architectures
composed of multiple data representations, as in deep neural networks, is
leading to state-of-the-art results. The right combination of data
representations can eventually lead us to even higher evaluation scores in
relation extraction tasks. Thus, biomedical ontologies play a fundamental role
by providing semantic and ancestry information about an entity. The
incorporation of biomedical ontologies has already been proved to enhance
previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1
Improving Term Extraction with Terminological Resources
Studies of different term extractors on a corpus of the biomedical domain
revealed decreasing performances when applied to highly technical texts. The
difficulty or impossibility of customising them to new domains is an additional
limitation. In this paper, we propose to use external terminologies to
influence generic linguistic data in order to augment the quality of the
extraction. The tool we implemented exploits testified terms at different steps
of the process: chunking, parsing and extraction of term candidates.
Experiments reported here show that, using this method, more term candidates
can be acquired with a higher level of reliability. We further describe the
extraction process involving endogenous disambiguation implemented in the term
extractor YaTeA
Annotating patient clinical records with syntactic chunks and named entities: the Harvey corpus
The free text notes typed by physicians during patient consultations contain valuable information for the study of disease and treatment. These notes are difficult to process by existing natural language analysis tools since they are highly telegraphic (omitting many words), and contain many spelling mistakes, inconsistencies in punctuation, and non-standard word order. To support information extraction and classification tasks over such text, we describe a de-identified corpus of free text notes, a shallow syntactic and named entity annotation scheme for this kind of text, and an approach to training domain specialists with no linguistic background to annotate the text. Finally, we present a statistical chunking system for such clinical text with a stable learning rate and good accuracy, indicating that the manual annotation is consistent and that the annotation scheme is tractable for machine learning
Deep learning for extracting protein-protein interactions from biomedical literature
State-of-the-art methods for protein-protein interaction (PPI) extraction are
primarily feature-based or kernel-based by leveraging lexical and syntactic
information. But how to incorporate such knowledge in the recent deep learning
methods remains an open question. In this paper, we propose a multichannel
dependency-based convolutional neural network model (McDepCNN). It applies one
channel to the embedding vector of each word in the sentence, and another
channel to the embedding vector of the head of the corresponding word.
Therefore, the model can use richer information obtained from different
channels. Experiments on two public benchmarking datasets, AIMed and BioInfer,
demonstrate that McDepCNN compares favorably to the state-of-the-art
rich-feature and single-kernel based methods. In addition, McDepCNN achieves
24.4% relative improvement in F1-score over the state-of-the-art methods on
cross-corpus evaluation and 12% improvement in F1-score over kernel-based
methods on "difficult" instances. These results suggest that McDepCNN
generalizes more easily over different corpora, and is capable of capturing
long distance features in the sentences.Comment: Accepted for publication in Proceedings of the 2017 Workshop on
Biomedical Natural Language Processing, 10 pages, 2 figures, 6 table
Boosting terminology extraction through crosslingual resources
Terminology Extraction is an important Natural Language Processing task with multiple applications in many areas. The task has been approached from different points of view using different techniques. Language and domain independent systems have been proposed as well. Our contribution in this paper focuses on the improvements on Terminology Extraction using crosslingual resources and specifically the Wikipedia and on the use of a variant of PageRank for scoring the candidate terms. // La extracción de terminología es una tarea de procesamiento de la lengua sumamente importante y aplicable en numerosas áreas. La tarea se ha abordado desde múltiples perspectivas y utilizando técnicas diversas. También se han propuesto sistemas independientes de la lengua y del dominio. La contribución de este artículo se centra en las mejoras que los sistemas de extracción de terminología pueden lograr utilizando recursos translingües, y concretamente la Wikipedia y en el uso de una variante de PageRank para valorar los candidatos a términoPeer ReviewedPostprint (published version
In no uncertain terms : a dataset for monolingual and multilingual automatic term extraction from comparable corpora
Automatic term extraction is a productive field of research within natural language processing, but it still faces significant obstacles regarding datasets and evaluation, which require manual term annotation. This is an arduous task, made even more difficult by the lack of a clear distinction between terms and general language, which results in low inter-annotator agreement. There is a large need for well-documented, manually validated datasets, especially in the rising field of multilingual term extraction from comparable corpora, which presents a unique new set of challenges. In this paper, a new approach is presented for both monolingual and multilingual term annotation in comparable corpora. The detailed guidelines with different term labels, the domain- and language-independent methodology and the large volumes annotated in three different languages and four different domains make this a rich resource. The resulting datasets are not just suited for evaluation purposes but can also serve as a general source of information about terms and even as training data for supervised methods. Moreover, the gold standard for multilingual term extraction from comparable corpora contains information about term variants and translation equivalents, which allows an in-depth, nuanced evaluation
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