Classification of Chromosomal DNA Sequence Using A Hybrid Deep Learning Architecture

2020 ◽  
Vol 15 ◽  
Author(s):  
Zhihua Du ◽  
Xiangdong Xiao ◽  
Vladimir N. Uversky
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Dna Sequence ◽  
Convolutional Neural Networks ◽  
Dna Sequences ◽  
Short Term Memory ◽  
Chromosomal Dna ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

: Chromosomal DNA contains most of the genetic information of eukaryotes and plays an important role in the growth, development and reproduction of living organisms. Most chromosomal DNA sequences are known to wrap around histones, and distinguishing these DNA sequences from ordinary DNA sequences is important for understanding the genetic code of life. The main difficulty behind this problem is the feature selection process. DNA sequences have no explicit features, and the common representation methods, such as one-hot coding, introduced the major drawback of high dimensionality. Recently, deep learning models have been proved to be able to automatically extract useful features from input patterns. In this paper, we present four different deep learning architectures using convolutional neural networks and long short-term memory networks for the purpose of chromosomal DNA sequence classification. Natural language model（Word2vec）was used to generate word embedding of sequence and learn features from it by deep learning. The comparison of these four architectures is carried out on 10 chromosomal DNA datasets. The results show that the architecture of convolutional neural networks combined with long short-term memory networks is superior to other methods in accuracy of chromosomal DNA prediction.

scholarly journals iEnhancer-EBLSTM: Identifying Enhancers and Strengths by Ensembles of Bidirectional Long Short-Term Memory

2021 ◽  
Vol 12 ◽  
Author(s):  
Kun Niu ◽  
Ximei Luo ◽  
Shumei Zhang ◽  
Zhixia Teng ◽  
Tianjiao Zhang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Time Series Data ◽  
Short Term Memory ◽  
Critical Issue ◽  
Series Data ◽  
Sequence Information ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

Enhancers are regulatory DNA sequences that could be bound by specific proteins named transcription factors (TFs). The interactions between enhancers and TFs regulate specific genes by increasing the target gene expression. Therefore, enhancer identification and classification have been a critical issue in the enhancer field. Unfortunately, so far there has been a lack of suitable methods to identify enhancers. Previous research has mainly focused on the features of the enhancer’s function and interactions, which ignores the sequence information. As we know, the recurrent neural network (RNN) and long short-term memory (LSTM) models are currently the most common methods for processing time series data. LSTM is more suitable than RNN to address the DNA sequence. In this paper, we take the advantages of LSTM to build a method named iEnhancer-EBLSTM to identify enhancers. iEnhancer-ensembles of bidirectional LSTM (EBLSTM) consists of two steps. In the first step, we extract subsequences by sliding a 3-mer window along the DNA sequence as features. Second, EBLSTM model is used to identify enhancers from the candidate input sequences. We use the dataset from the study of Quang H et al. as the benchmarks. The experimental results from the datasets demonstrate the efficiency of our proposed model.

scholarly journals Groundwater level forecasting with artificial neural networks: a comparison of long short-term memory (LSTM), convolutional neural networks (CNNs), and non-linear autoregressive networks with exogenous input (NARX)

2021 ◽  
Vol 25 (3) ◽  
pp. 1671-1687
Author(s):  
Andreas Wunsch ◽  
Tanja Liesch ◽  
Stefan Broda
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Convolutional Neural Networks ◽  
Groundwater Level ◽  
Short Term Memory ◽  
State Of The Art ◽  
Short Term ◽  
Term Memory ◽  
Non Linear ◽  
Long Short Term Memory

Abstract. It is now well established to use shallow artificial neural networks (ANNs) to obtain accurate and reliable groundwater level forecasts, which are an important tool for sustainable groundwater management. However, we observe an increasing shift from conventional shallow ANNs to state-of-the-art deep-learning (DL) techniques, but a direct comparison of the performance is often lacking. Although they have already clearly proven their suitability, shallow recurrent networks frequently seem to be excluded from the study design due to the euphoria about new DL techniques and its successes in various disciplines. Therefore, we aim to provide an overview on the predictive ability in terms of groundwater levels of shallow conventional recurrent ANNs, namely non-linear autoregressive networks with exogenous input (NARX) and popular state-of-the-art DL techniques such as long short-term memory (LSTM) and convolutional neural networks (CNNs). We compare the performance on both sequence-to-value (seq2val) and sequence-to-sequence (seq2seq) forecasting on a 4-year period while using only few, widely available and easy to measure meteorological input parameters, which makes our approach widely applicable. Further, we also investigate the data dependency in terms of time series length of the different ANN architectures. For seq2val forecasts, NARX models on average perform best; however, CNNs are much faster and only slightly worse in terms of accuracy. For seq2seq forecasts, mostly NARX outperform both DL models and even almost reach the speed of CNNs. However, NARX are the least robust against initialization effects, which nevertheless can be handled easily using ensemble forecasting. We showed that shallow neural networks, such as NARX, should not be neglected in comparison to DL techniques especially when only small amounts of training data are available, where they can clearly outperform LSTMs and CNNs; however, LSTMs and CNNs might perform substantially better with a larger dataset, where DL really can demonstrate its strengths, which is rarely available in the groundwater domain though.

scholarly journals A Comparison of Power Quality Disturbance Detection and Classification Methods Using CNN, LSTM and CNN-LSTM

2020 ◽  
Vol 10 (19) ◽  
pp. 6755
Author(s):  
Carlos Iturrino Garcia ◽  
Francesco Grasso ◽  
Antonio Luchetta ◽  
Maria Cristina Piccirilli ◽  
Libero Paolucci ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Data Augmentation ◽  
Short Term Memory ◽  
Machine Learning Algorithms ◽  
Validation Dataset ◽  
Short Term ◽  
Current Time ◽  
Term Memory ◽  
Long Short Term Memory

The use of electronic loads has improved many aspects of everyday life, permitting more efficient, precise and automated process. As a drawback, the nonlinear behavior of these systems entails the injection of electrical disturbances on the power grid that can cause distortion of voltage and current. In order to adopt countermeasures, it is important to detect and classify these disturbances. To do this, several Machine Learning Algorithms are currently exploited. Among them, for the present work, the Long Short Term Memory (LSTM), the Convolutional Neural Networks (CNN), the Convolutional Neural Networks Long Short Term Memory (CNN-LSTM) and the CNN-LSTM with adjusted hyperparameters are compared. As a preliminary stage of the research, the voltage and current time signals are simulated using MATLAB Simulink. Thanks to the simulation results, it is possible to acquire a current and voltage dataset with which the identification algorithms are trained, validated and tested. These datasets include simulations of several disturbances such as Sag, Swell, Harmonics, Transient, Notch and Interruption. Data Augmentation techniques are used in order to increase the variability of the training and validation dataset in order to obtain a generalized result. After that, the networks are fed with an experimental dataset of voltage and current field measurements containing the disturbances mentioned above. The networks have been compared, resulting in a 79.14% correct classification rate with the LSTM network versus a 84.58% for the CNN, 84.76% for the CNN-LSTM and a 83.66% for the CNN-LSTM with adjusted hyperparameters. All of these networks are tested using real measurements.

scholarly journals A Blind Spectrum Sensing Method Based on Deep Learning

Sensors ◽  
2019 ◽  
Vol 19 (10) ◽  
pp. 2270 ◽  
Author(s):  
Kai Yang ◽  
Zhitao Huang ◽  
Xiang Wang ◽  
Xueqiong Li
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Spectrum Sensing ◽  
Short Term Memory ◽  
Signal To Noise Ratio ◽  
Signal To Noise ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory ◽  
Noise Ratio

Spectrum sensing is one of the technologies that is used to solve the current problem of low utilization of spectrum resources. However, when the signal-to-noise ratio is low, current spectrum sensing methods cannot well-handle a situation in which the prior information of the licensed user signal is lacking. In this paper, a blind spectrum sensing method based on deep learning is proposed that uses three kinds of neural networks together, namely convolutional neural networks, long short-term memory, and fully connected neural networks. Experiments show that the proposed method has better performance than an energy detector, especially when the signal-to-noise ratio is low. At the same time, this paper also analyzes the effect of different long short-term memory layers on detection performance, and explores why the deep-learning-based detector can achieve better performance.

Sign in / Sign up

Export Citation Format

Share Document