Research of a Recurrent Neural Network for the Vector Representation of Nucleotide Sequences

2020 ◽  
Author(s):  
Daniil O. Komarovskikh ◽  
Vladislav L. Litvinov ◽  
Ilia A. Kiselev ◽  
Artur M. Paniukov ◽  
Nikita I. Trofimov
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Nucleotide Sequences ◽  
Vector Representation

scholarly journals Prediction of PCR amplification from primer and template sequences using recurrent neural network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kotetsu Kayama ◽  
Miyuki Kanno ◽  
Naoto Chisaki ◽  
Misaki Tanaka ◽  
Reika Yao ◽  
...  
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Pcr Amplification ◽  
Nucleotide Sequences ◽  
Specific Primer ◽  
First Report ◽  
Novel Method ◽  
Primer Sequence ◽  
Dna Template ◽  
The Relationship

AbstractWe have developed a novel method to predict the success of PCR amplification for a specific primer set and DNA template based on the relationship between the primer sequence and the template. To perform the prediction using a recurrent neural network, the usual double-stranded formation between the primer and template nucleotide sequences was herein expressed as a five-lettered word. The set of words (pseudo-sentences) was placed to indicate the success or failure of PCR targeted to learn recurrent neural network (RNN). After learning pseudo-sentences, RNN predicted PCR results from pseudo-sentences which were created by primer and template sequences with 70% accuracy. These results suggest that PCR results could be predicted using learned RNN and the trained RNN could be used as a replacement for preliminary PCR experimentation. This is the first report which utilized the application of neural network for primer design and prediction of PCR results.

scholarly journals Easy-First Dependency Parsing with Hierarchical Tree LSTMs

2016 ◽  
Vol 4 ◽  
pp. 445-461 ◽  
Author(s):  
Eliyahu Kiperwasser ◽  
Yoav Goldberg
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Word Embeddings ◽  
Dependency Parsing ◽  
Vector Representation ◽  
Bottom Up ◽  
Hierarchical Tree ◽  
Parse Trees ◽  
Dependency Parser

We suggest a compositional vector representation of parse trees that relies on a recursive combination of recurrent-neural network encoders. To demonstrate its effectiveness, we use the representation as the backbone of a greedy, bottom-up dependency parser, achieving very strong accuracies for English and Chinese, without relying on external word embeddings. The parser’s implementation is available for download at the first author’s webpage.

scholarly journals Tourism Review Sentiment Classification Using a Bidirectional Recurrent Neural Network with an Attention Mechanism and Topic-Enriched Word Vectors

2018 ◽  
Vol 10 (9) ◽  
pp. 3313 ◽  
Author(s):  
Qin Li ◽  
Shaobo Li ◽  
Jie Hu ◽  
Sen Zhang ◽  
Jianjun Hu
Keyword(s):  
Neural Network ◽  
Data Analysis ◽  
Sentiment Analysis ◽  
Recurrent Neural Network ◽  
Topic Model ◽  
Online Reviews ◽  
Attention Mechanism ◽  
Sentiment Classification ◽  
Vector Representation ◽  
Gated Recurrent Unit

Sentiment analysis of online tourist reviews is playing an increasingly important role in tourism. Accurately capturing the attitudes of tourists regarding different aspects of the scenic sites or the overall polarity of their online reviews is key to tourism analysis and application. However, the performances of current document sentiment analysis methods are not satisfactory as they either neglect the topics of the document or do not consider that not all words contribute equally to the meaning of the text. In this work, we propose a bidirectional gated recurrent unit neural network model (BiGRULA) for sentiment analysis by combining a topic model (lda2vec) and an attention mechanism. Lda2vec is used to discover all the main topics of review corpus, which are then used to enrich the word vector representation of words with context. The attention mechanism is used to learn to attribute different weights of the words to the overall meaning of the text. Experiments over 20 NewsGroup and IMDB datasets demonstrate the effectiveness of our model. Furthermore, we applied our model to hotel review data analysis, which allows us to get more coherent topics from these reviews and achieve good performance in sentiment classification.

Research on behavior recognition based on feature fusion of automatic coder and recurrent neural network

2020 ◽  
Vol 39 (6) ◽  
pp. 8927-8935
Author(s):  
Bing Zheng ◽  
Dawei Yun ◽  
Yan Liang
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Behavior Pattern ◽  
Rapid Development ◽  
Video Data ◽  
Support Vector ◽  
Behavior Recognition ◽  
Learning Methods ◽  
The Impact ◽  
Internet Of Things Technology

Under the impact of COVID-19, research on behavior recognition are highly needed. In this paper, we combine the algorithm of self-adaptive coder and recurrent neural network to realize the research of behavior pattern recognition. At present, most of the research of human behavior recognition is focused on the video data, which is based on the video number. At the same time, due to the complexity of video image data, it is easy to violate personal privacy. With the rapid development of Internet of things technology, it has attracted the attention of a large number of experts and scholars. Researchers have tried to use many machine learning methods, such as random forest, support vector machine and other shallow learning methods, which perform well in the laboratory environment, but there is still a long way to go from practical application. In this paper, a recursive neural network algorithm based on long and short term memory (LSTM) is proposed to realize the recognition of behavior patterns, so as to improve the accuracy of human activity behavior recognition.

Deadlift Recognition and Application based on Multiple Modalities using Recurrent Neural Network

2020 ◽  
Vol 2020 (17) ◽  
pp. 2-1-2-6
Author(s):  
Shih-Wei Sun ◽  
Ting-Chen Mou ◽  
Pao-Chi Chang
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Network Structure ◽  
Inertial Sensors ◽  
Body Movement ◽  
The Body ◽  
Body Parts ◽  
Multimodal Sensing ◽  
Multiple Devices ◽  
Neural Network Structure

To improve the workout efficiency and to provide the body movement suggestions to users in a “smart gym” environment, we propose to use a depth camera for capturing a user’s body parts and mount multiple inertial sensors on the body parts of a user to generate deadlift behavior models generated by a recurrent neural network structure. The contribution of this paper is trifold: 1) The multimodal sensing signals obtained from multiple devices are fused for generating the deadlift behavior classifiers, 2) the recurrent neural network structure can analyze the information from the synchronized skeletal and inertial sensing data, and 3) a Vaplab dataset is generated for evaluating the deadlift behaviors recognizing capability in the proposed method.

Molecular Generation Targeting Desired Electronic Properties via Deep Generative Models

2019 ◽  
Author(s):  
Qi Yuan ◽  
Alejandro Santana-Bonilla ◽  
Martijn Zwijnenburg ◽  
Kim Jelfs
Keyword(s):  
Neural Network ◽  
Electronic Properties ◽  
Transfer Learning ◽  
Recurrent Neural Network ◽  
Chemical Space ◽  
Generative Models ◽  
Molecular Features ◽  
Donor Acceptor ◽  
Homo Lumo ◽  
Training Sets

<p>The chemical space for novel electronic donor-acceptor oligomers with targeted properties was explored using deep generative models and transfer learning. A General Recurrent Neural Network model was trained from the ChEMBL database to generate chemically valid SMILES strings. The parameters of the General Recurrent Neural Network were fine-tuned via transfer learning using the electronic donor-acceptor database from the Computational Material Repository to generate novel donor-acceptor oligomers. Six different transfer learning models were developed with different subsets of the donor-acceptor database as training sets. We concluded that electronic properties such as HOMO-LUMO gaps and dipole moments of the training sets can be learned using the SMILES representation with deep generative models, and that the chemical space of the training sets can be efficiently explored. This approach identified approximately 1700 new molecules that have promising electronic properties (HOMO-LUMO gap <2 eV and dipole moment <2 Debye), 6-times more than in the original database. Amongst the molecular transformations, the deep generative model has learned how to produce novel molecules by trading off between selected atomic substitutions (such as halogenation or methylation) and molecular features such as the spatial extension of the oligomer. The method can be extended as a plausible source of new chemical combinations to effectively explore the chemical space for targeted properties.</p>

IMPLEMENTASI CHATBOT PADA PENDAFTARAN MAHASISWA BARU MENGGUNAKAN RECURRENT NEURAL NETWORK

2019 ◽  
Vol 24 (2) ◽  
pp. 91-101
Author(s):  
Tjut Awaliyah Zuraiyah ◽  
Dian Kartika Utami ◽  
Degi Herlambang
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network

Chatbot adalah perangkat lunak yang dapat berkomunikasi dengan manusia menggunakan bahasa alami. Model percakapan menggunakan kecerdasan buatan agar mampu memahami ucapan pengguna dan memberi tanggapan yang relevan dengan masalah yang dibahas oleh pengguna. Pendaftaran mahasiswa baru memerlukan banyak informasi mengenai prosedur pendaftaran di perguruan tinggi. Website pendaftaran online di Universitas Pakuan masih sebatas berisi informasi umum. Penelitian ini bertujuan untuk membuat suatu aplikasi Chatbot otomatis yang dapat berkomunikasi dengan manusia mengenai informasi pendaftaran mahasiswa baru di Universitas Pakuan menggunakan Recurrent Neural Network (RNN) untuk klasifikasi teks. Aplikasi Chatbot diimplementasikan menggunakan bahasa pemrograman Python dan Telegram API. Tahapan pada implementasi Chatbot terdiri dari preprocessing, transformasi data ke format .JSON, pelatihan data, bag of word dan full connection. Pengujian aplikasi Chatbot menggunakan data sebanyak 251 kalimat pertanyaan tentang pendaftaran mahasiswa baru di Universitas Pakuan. Hasil pengujian menunjukkan bahwa Chatbot dapat menjawab pertanyaan mengenai pendaftaran mahasiswa baru dengan akurasi sebesar 88%, presisi sebesar 95% dan recall sebesar 92%.

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