• Journal of the Korea Society of Computer and Information
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• v.27 no.8
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• pp.49-59
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• 2022

In this paper, we designed a new enzyme function prediction model PSCREM based on a study that compared and evaluated CNN and LSTM/GRU models, which are the most widely used deep learning models in the field of predicting functions and structures using protein sequences in 2020, under the same conditions. Sequence evolution information was used to preserve detailed patterns which would miss in CNN convolution, and the relationship information between amino acids with functional significance was extracted through overlapping RNNs. It was referenced to feature map production. The RNN family of algorithms used in small CNN-RNN models are LSTM algorithms and GRU algorithms, which are usually stacked two to three times over 100 units, but in this paper, small RNNs consisting of 10 and 20 units are overlapped. The model used the PSSM profile, which is transformed from protein sequence data. The experiment proved 86.4% the performance for the problem of predicting the main classes of enzyme number, and it was confirmed that the performance was 84.4% accurate up to the sub-sub classes of enzyme number. Thus, PSCREM better identifies unique patterns related to protein function through overlapped RNN, and Overlapped RNN is proposed as a novel methodology for protein function and structure prediction extraction.

• Journal of KIISE
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• v.44 no.8
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• pp.774-781
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• 2017

Mention detection systems use nouns or noun phrases as a head and construct a chunk of text that defines any meaning, including a modifier. The term "mention detection" relates to the extraction of mentions in a document. In the mentions, a coreference resolution pertains to finding out if various mentions have the same meaning to each other. A pointer network is a model based on a recurrent neural network (RNN) encoder-decoder, and outputs a list of elements that correspond to input sequence. In this paper, we propose the use of mention detection using pointer networks. Our proposed model can solve the problem of overlapped mention detection, an issue that could not be solved by sequence labeling when applying the pointer network to the mention detection. As a result of this experiment, performance of the proposed mention detection model showed an F1 of 80.07%, a 7.65%p higher than rule-based mention detection; a co-reference resolution performance using this mention detection model showed a CoNLL F1 of 52.67% (mention boundary), and a CoNLL F1 of 60.11% (head boundary) that is high, 7.68%p, or 1.5%p more than coreference resolution using rule-based mention detection.