18,358 research outputs found
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
A Robust Interpretable Deep Learning Classifier for Heart Anomaly Detection Without Segmentation
Traditionally, abnormal heart sound classification is framed as a three-stage
process. The first stage involves segmenting the phonocardiogram to detect
fundamental heart sounds; after which features are extracted and classification
is performed. Some researchers in the field argue the segmentation step is an
unwanted computational burden, whereas others embrace it as a prior step to
feature extraction. When comparing accuracies achieved by studies that have
segmented heart sounds before analysis with those who have overlooked that
step, the question of whether to segment heart sounds before feature extraction
is still open. In this study, we explicitly examine the importance of heart
sound segmentation as a prior step for heart sound classification, and then
seek to apply the obtained insights to propose a robust classifier for abnormal
heart sound detection. Furthermore, recognizing the pressing need for
explainable Artificial Intelligence (AI) models in the medical domain, we also
unveil hidden representations learned by the classifier using model
interpretation techniques. Experimental results demonstrate that the
segmentation plays an essential role in abnormal heart sound classification.
Our new classifier is also shown to be robust, stable and most importantly,
explainable, with an accuracy of almost 100% on the widely used PhysioNet
dataset
PaperRobot: Incremental Draft Generation of Scientific Ideas
We present a PaperRobot who performs as an automatic research assistant by
(1) conducting deep understanding of a large collection of human-written papers
in a target domain and constructing comprehensive background knowledge graphs
(KGs); (2) creating new ideas by predicting links from the background KGs, by
combining graph attention and contextual text attention; (3) incrementally
writing some key elements of a new paper based on memory-attention networks:
from the input title along with predicted related entities to generate a paper
abstract, from the abstract to generate conclusion and future work, and finally
from future work to generate a title for a follow-on paper. Turing Tests, where
a biomedical domain expert is asked to compare a system output and a
human-authored string, show PaperRobot generated abstracts, conclusion and
future work sections, and new titles are chosen over human-written ones up to
30%, 24% and 12% of the time, respectively.Comment: 12 pages. Accepted by ACL 2019 Code and resource is available at
https://github.com/EagleW/PaperRobo
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