scholarly journals A Shortest Dependency Path Based Convolutional Neural Network for Protein-Protein Relation Extraction

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Lei Hua ◽  
Chanqin Quan
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Feature Selection ◽  
Protein Interaction ◽  
Kernel Methods ◽  
State Of The Art ◽  
Relation Extraction ◽  
Word Embedding ◽  
Protein Protein Interaction ◽  
Key Features

The state-of-the-art methods for protein-protein interaction (PPI) extraction are primarily based on kernel methods, and their performances strongly depend on the handcraft features. In this paper, we tackle PPI extraction by using convolutional neural networks (CNN) and propose a shortest dependency path based CNN (sdpCNN) model. The proposed method(1)only takes the sdp and word embedding as input and(2)could avoid bias from feature selection by using CNN. We performed experiments on standard Aimed and BioInfer datasets, and the experimental results demonstrated that our approach outperformed state-of-the-art kernel based methods. In particular, by tracking the sdpCNN model, we find that sdpCNN could extract key features automatically and it is verified that pretrained word embedding is crucial in PPI task.

scholarly journals Neural Relation Extraction within and across Sentence Boundaries

2019 ◽  
Vol 33 ◽  
pp. 6513-6520 ◽  
Author(s):  
Pankaj Gupta ◽  
Subburam Rajaram ◽  
Hinrich Schütze ◽  
Thomas Runkler
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Binary Relation ◽  
State Of The Art ◽  
Relation Extraction ◽  
Shared Task ◽  
Single Sentence ◽  
Winning Team ◽  
Recursive Neural Networks ◽  
Better Than

Past work in relation extraction mostly focuses on binary relation between entity pairs within single sentence. Recently, the NLP community has gained interest in relation extraction in entity pairs spanning multiple sentences. In this paper, we propose a novel architecture for this task: inter-sentential dependency-based neural networks (iDepNN). iDepNN models the shortest and augmented dependency paths via recurrent and recursive neural networks to extract relationships within (intra-) and across (inter-) sentence boundaries. Compared to SVM and neural network baselines, iDepNN is more robust to false positives in relationships spanning sentences. We evaluate our models on four datasets from newswire (MUC6) and medical (BioNLP shared task) domains that achieve state-of-the-art performance and show a better balance in precision and recall for inter-sentential relationships. We perform better than 11 teams participating in the BioNLP shared task 2016 and achieve a gain of 5.2% (0.587 vs 0.558) in F1 over the winning team. We also release the crosssentence annotations for MUC6.

scholarly journals SketchGNN: Semantic Sketch Segmentation with Graph Neural Networks

2021 ◽  
Vol 40 (3) ◽  
pp. 1-13
Author(s):  
Lumin Yang ◽  
Jiajie Zhuang ◽  
Hongbo Fu ◽  
Xiangzhi Wei ◽  
Kun Zhou ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Architecture ◽  
Large Scale ◽  
State Of The Art ◽  
Semantic Segmentation ◽  
Structure Information ◽  
Graph Neural Networks ◽  
Node Labels ◽  
Point Level

We introduce SketchGNN , a convolutional graph neural network for semantic segmentation and labeling of freehand vector sketches. We treat an input stroke-based sketch as a graph with nodes representing the sampled points along input strokes and edges encoding the stroke structure information. To predict the per-node labels, our SketchGNN uses graph convolution and a static-dynamic branching network architecture to extract the features at three levels, i.e., point-level, stroke-level, and sketch-level. SketchGNN significantly improves the accuracy of the state-of-the-art methods for semantic sketch segmentation (by 11.2% in the pixel-based metric and 18.2% in the component-based metric over a large-scale challenging SPG dataset) and has magnitudes fewer parameters than both image-based and sequence-based methods.

scholarly journals Communication Failure Resilient Distributed Neural Network for Edge Devices

Electronics ◽  
2021 ◽  
Vol 10 (14) ◽  
pp. 1614
Author(s):  
Jonghun Jeong ◽  
Jong Sung Park ◽  
Hoeseok Yang
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
High Performance ◽  
State Of The Art ◽  
Wearable Devices ◽  
Communication Failure ◽  
Canadian Institute ◽  
Multiple Devices ◽  
Knowledge Distillation ◽  
Partitioning Technique

Recently, the necessity to run high-performance neural networks (NN) is increasing even in resource-constrained embedded systems such as wearable devices. However, due to the high computational and memory requirements of the NN applications, it is typically infeasible to execute them on a single device. Instead, it has been proposed to run a single NN application cooperatively on top of multiple devices, a so-called distributed neural network. In the distributed neural network, workloads of a single big NN application are distributed over multiple tiny devices. While the computation overhead could effectively be alleviated by this approach, the existing distributed NN techniques, such as MoDNN, still suffer from large traffics between the devices and vulnerability to communication failures. In order to get rid of such big communication overheads, a knowledge distillation based distributed NN, called Network of Neural Networks (NoNN), was proposed, which partitions the filters in the final convolutional layer of the original NN into multiple independent subsets and derives smaller NNs out of each subset. However, NoNN also has limitations in that the partitioning result may be unbalanced and it considerably compromises the correlation between filters in the original NN, which may result in an unacceptable accuracy degradation in case of communication failure. In this paper, in order to overcome these issues, we propose to enhance the partitioning strategy of NoNN in two aspects. First, we enhance the redundancy of the filters that are used to derive multiple smaller NNs by means of averaging to increase the immunity of the distributed NN to communication failure. Second, we propose a novel partitioning technique, modified from Eigenvector-based partitioning, to preserve the correlation between filters as much as possible while keeping the consistent number of filters distributed to each device. Throughout extensive experiments with the CIFAR-100 (Canadian Institute For Advanced Research-100) dataset, it has been observed that the proposed approach maintains high inference accuracy (over 70%, 1.53× improvement over the state-of-the-art approach), on average, even when a half of eight devices in a distributed NN fail to deliver their partial inference results.

scholarly journals Fast and Deep Graph Neural Networks

2020 ◽  
Vol 34 (04) ◽  
pp. 3898-3905 ◽  
Author(s):  
Claudio Gallicchio ◽  
Alessio Micheli
Keyword(s):  
Neural Network ◽  
Dynamical System ◽  
Neural Networks ◽  
State Of The Art ◽  
Input Graph ◽  
Sparse Networks ◽  
Set Up ◽  
The Stability ◽  
Graph Neural Networks ◽  
Architectural Organization

We address the efficiency issue for the construction of a deep graph neural network (GNN). The approach exploits the idea of representing each input graph as a fixed point of a dynamical system (implemented through a recurrent neural network), and leverages a deep architectural organization of the recurrent units. Efficiency is gained by many aspects, including the use of small and very sparse networks, where the weights of the recurrent units are left untrained under the stability condition introduced in this work. This can be viewed as a way to study the intrinsic power of the architecture of a deep GNN, and also to provide insights for the set-up of more complex fully-trained models. Through experimental results, we show that even without training of the recurrent connections, the architecture of small deep GNN is surprisingly able to achieve or improve the state-of-the-art performance on a significant set of tasks in the field of graphs classification.

scholarly journals Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

2019 ◽  
Vol 35 (14) ◽  
pp. i305-i314 ◽  
Author(s):  
Muhao Chen ◽  
Chelsea J -T Ju ◽  
Guangyu Zhou ◽  
Xuelu Chen ◽  
Tianran Zhang ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Mutual Influence ◽  
State Of The Art ◽  
Supplementary Information ◽  
Interaction Type ◽  
Interaction Prediction ◽  
Protein Protein Interaction ◽  
Protein Interaction Prediction ◽  
Ppi Prediction ◽  
Limited Coverage

AbstractMotivationSequence-based protein–protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information.ResultsWe present an end-to-end framework, PIPR (Protein–Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short.Availability and implementationThe implementation is available at https://github.com/muhaochen/seq_ppi.git.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Sentiment Classification Using Convolutional Neural Networks

2019 ◽  
Vol 9 (11) ◽  
pp. 2347 ◽  
Author(s):  
Hannah Kim ◽  
Young-Seob Jeong
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Text Classification ◽  
State Of The Art ◽  
Sentiment Classification ◽  
Learning Models ◽  
Text Data ◽  
Textual Data ◽  
Better Than

As the number of textual data is exponentially increasing, it becomes more important to develop models to analyze the text data automatically. The texts may contain various labels such as gender, age, country, sentiment, and so forth. Using such labels may bring benefits to some industrial fields, so many studies of text classification have appeared. Recently, the Convolutional Neural Network (CNN) has been adopted for the task of text classification and has shown quite successful results. In this paper, we propose convolutional neural networks for the task of sentiment classification. Through experiments with three well-known datasets, we show that employing consecutive convolutional layers is effective for relatively longer texts, and our networks are better than other state-of-the-art deep learning models.

scholarly journals Uncertainty-Based Human-in-the-Loop Deep Learning for Land Cover Segmentation

2020 ◽  
Vol 12 (22) ◽  
pp. 3836
Author(s):  
Carlos García Rodríguez ◽  
Jordi Vitrià ◽  
Oscar Mora
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Land Cover ◽  
Satellite Images ◽  
State Of The Art ◽  
Low Cost ◽  
Human Intervention ◽  
Human In The Loop ◽  
Learning Techniques

In recent years, different deep learning techniques were applied to segment aerial and satellite images. Nevertheless, state of the art techniques for land cover segmentation does not provide accurate results to be used in real applications. This is a problem faced by institutions and companies that want to replace time-consuming and exhausting human work with AI technology. In this work, we propose a method that combines deep learning with a human-in-the-loop strategy to achieve expert-level results at a low cost. We use a neural network to segment the images. In parallel, another network is used to measure uncertainty for predicted pixels. Finally, we combine these neural networks with a human-in-the-loop approach to produce correct predictions as if developed by human photointerpreters. Applying this methodology shows that we can increase the accuracy of land cover segmentation tasks while decreasing human intervention.

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