2,341 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
GumDrop at the DISRPT2019 Shared Task: A Model Stacking Approach to Discourse Unit Segmentation and Connective Detection
In this paper we present GumDrop, Georgetown University's entry at the DISRPT
2019 Shared Task on automatic discourse unit segmentation and connective
detection. Our approach relies on model stacking, creating a heterogeneous
ensemble of classifiers, which feed into a metalearner for each final task. The
system encompasses three trainable component stacks: one for sentence
splitting, one for discourse unit segmentation and one for connective
detection. The flexibility of each ensemble allows the system to generalize
well to datasets of different sizes and with varying levels of homogeneity.Comment: Proceedings of Discourse Relation Parsing and Treebanking
(DISRPT2019
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
Extracting protein-protein interactions from text using rich feature vectors and feature selection
Because of the intrinsic complexity of natural language, automatically extracting accurate information from text remains a challenge. We have applied rich featurevectors derived from dependency graphs to predict protein-protein interactions using machine learning techniques. We present the first extensive analysis of applyingfeature selection in this domain, and show that it can produce more cost-effective models. For the first time, our technique was also evaluated on several large-scalecross-dataset experiments, which offers a more realistic view on model performance.
During benchmarking, we encountered several fundamental problems hindering comparability with other methods. We present a set of practical guidelines to set up ameaningful evaluation.
Finally, we have analysed the feature sets from our experiments before and after feature selection, and evaluated the contribution of both lexical and syntacticinformation to our method. The gained insight will be useful to develop better performing methods in this domain
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