scholarly journals Target Binding and Sequence Prediction With LSTMs

2018 ◽  
Author(s):  
Michael Teti ◽  
Rachel StClair ◽  
Mirjana Pavlovic ◽  
Elan Barenholtz ◽  
William Hahn
Keyword(s):  
Neural Networks ◽  
Language Processing ◽  
Protein Function ◽  
Short Term Memory ◽  
Sequence Data ◽  
Computational Time ◽  
Literature Mining ◽  
Binding Motif ◽  
Sequential Data ◽  
Conserved Sequence

Deep recurrent neural networks (DRNNs) have recently demonstrated strong performance in sequential data analysis, such as natural language processing. These capabilities make them a promising tool for inferential analysis of sequentially structured bioinformatics data as well. Here, we assessed the ability of Long Short-Term Memory (LSTM) networks, a class of DRNNs, to predict properties of proteins based on their primary structures. The proposed architecture is trained and tested on two different datasets to predict whether a given sequence falls into a certain class or not. The first dataset, directly imported from Uniprot, was used to train the network on whether a given protein contained or did not contain a conserved sequence (homeodomain), and the second dataset, derived by literature mining, was used to train a network on whether a given protein binds or doesn't bind to Artemisinin, a drug typically used to treat malaria. In each case, the model was able to differentiate between the two different classes of sequences it was given with high accuracy, illustrating successful learning and generalization. Upon completion of training, an ROC curve was created using the homeodomain and artemisinin validation datasets. The AUC of these datasets was 0.80 and 0.87 respectively, further indicating the models' effectiveness. Furthermore, using these trained models, it was possible to derive a protocol for sequence detection of homeodomain and binding motif, which are well-documented in literature, and a known Artemisinin binding site, respectively [1-3]. Along with these contributions, we developed a python API to directly connect to Uniprot data sourcing, train deep neural networks on this primary sequence data using TensorFlow, and uniquely visualize the results of this analysis. Such an approach has the potential to drastically increase accuracy and reduce computational time and, current major limitations in informatics, from inquiry to discovery in protein function research

scholarly journals Object Detection, Distributed Cloud Computing and Parallelization Techniques for Autonomous Driving Systems

2021 ◽  
Vol 11 (7) ◽  
pp. 2925
Author(s):  
Edgar Cortés Gallardo Medina ◽  
Victor Miguel Velazquez Espitia ◽  
Daniela Chípuli Silva ◽  
Sebastián Fernández Ruiz de las Cuevas ◽  
Marco Palacios Hirata ◽  
...  
Keyword(s):  
Neural Networks ◽  
Cloud Computing ◽  
Path Planning ◽  
Object Detection ◽  
Short Term Memory ◽  
Smart Cities ◽  
Autonomous Vehicle ◽  
Computational Time ◽  
End To End ◽  
On The Road

Autonomous vehicles are increasingly becoming a necessary trend towards building the smart cities of the future. Numerous proposals have been presented in recent years to tackle particular aspects of the working pipeline towards creating a functional end-to-end system, such as object detection, tracking, path planning, sentiment or intent detection, amongst others. Nevertheless, few efforts have been made to systematically compile all of these systems into a single proposal that also considers the real challenges these systems will have on the road, such as real-time computation, hardware capabilities, etc. This paper reviews the latest techniques towards creating our own end-to-end autonomous vehicle system, considering the state-of-the-art methods on object detection, and the possible incorporation of distributed systems and parallelization to deploy these methods. Our findings show that while techniques such as convolutional neural networks, recurrent neural networks, and long short-term memory can effectively handle the initial detection and path planning tasks, more efforts are required to implement cloud computing to reduce the computational time that these methods demand. Additionally, we have mapped different strategies to handle the parallelization task, both within and between the networks.

scholarly journals Part-of-Speech Tagging via Deep Neural Networks for Northern-Ethiopic Languages

2020 ◽  
Vol 49 (4) ◽  
pp. 482-494
Author(s):  
Jurgita Kapočiūtė-Dzikienė ◽  
Senait Gebremichael Tesfagergish
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Language Processing ◽  
Deep Neural Networks ◽  
Short Term Memory ◽  
Parameter Tuning ◽  
Feed Forward Neural Network ◽  
Pos Tagging ◽  
Part Of Speech ◽  
Pos Tagger

Deep Neural Networks (DNNs) have proven to be especially successful in the area of Natural Language Processing (NLP) and Part-Of-Speech (POS) tagging—which is the process of mapping words to their corresponding POS labels depending on the context. Despite recent development of language technologies, low-resourced languages (such as an East African Tigrinya language), have received too little attention. We investigate the effectiveness of Deep Learning (DL) solutions for the low-resourced Tigrinya language of the Northern-Ethiopic branch. We have selected Tigrinya as the testbed example and have tested state-of-the-art DL approaches seeking to build the most accurate POS tagger. We have evaluated DNN classifiers (Feed Forward Neural Network – FFNN, Long Short-Term Memory method – LSTM, Bidirectional LSTM, and Convolutional Neural Network – CNN) on a top of neural word2vec word embeddings with a small training corpus known as Nagaoka Tigrinya Corpus. To determine the best DNN classifier type, its architecture and hyper-parameter set both manual and automatic hyper-parameter tuning has been performed. BiLSTM method was proved to be the most suitable for our solving task: it achieved the highest accuracy equal to 92% that is 65% above the random baseline.

scholarly journals Long Short-Term Memory with Dynamic Skip Connections

2019 ◽  
Vol 33 ◽  
pp. 6481-6488 ◽  
Author(s):  
Tao Gui ◽  
Qi Zhang ◽  
Lujun Zhao ◽  
Yaosong Lin ◽  
Minlong Peng ◽  
...  
Keyword(s):  
Language Processing ◽  
Short Term Memory ◽  
Training Data ◽  
Sequential Data ◽  
Short Term ◽  
Term Memory ◽  
Transition Functions ◽  
Proposed Model ◽  
Long Short Term Memory

In recent years, long short-term memory (LSTM) has been successfully used to model sequential data of variable length. However, LSTM can still experience difficulty in capturing long-term dependencies. In this work, we tried to alleviate this problem by introducing a dynamic skip connection, which can learn to directly connect two dependent words. Since there is no dependency information in the training data, we propose a novel reinforcement learning-based method to model the dependency relationship and connect dependent words. The proposed model computes the recurrent transition functions based on the skip connections, which provides a dynamic skipping advantage over RNNs that always tackle entire sentences sequentially. Our experimental results on three natural language processing tasks demonstrate that the proposed method can achieve better performance than existing methods. In the number prediction experiment, the proposed model outperformed LSTM with respect to accuracy by nearly 20%.

scholarly journals Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

2021 ◽  
Vol 17 (9) ◽  
pp. e1009345
Author(s):  
Zhengqiao Zhao ◽  
Stephen Woloszynek ◽  
Felix Agbavor ◽  
Joshua Chang Mell ◽  
Bahrad A. Sokhansanj ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Microbial Community ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Network Architecture ◽  
Sequence Data ◽  
Community Sample ◽  
Marker Genes ◽  
Link Type

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention-based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://github.com/EESI/sequence_attention (a python package) and https://github.com/EESI/seq2att (a command line tool).

scholarly journals Learning molecular dynamics with simple language model built upon long short-term memory neural network

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sun-Ting Tsai ◽  
En-Jui Kuo ◽  
Pratyush Tiwary
Keyword(s):  
Neural Networks ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Short Term Memory ◽  
Language Model ◽  
Short Term ◽  
Term Memory ◽  
Molecular Systems ◽  
Simple Language ◽  
Long Short Term Memory

Abstract Recurrent neural networks have led to breakthroughs in natural language processing and speech recognition. Here we show that recurrent networks, specifically long short-term memory networks can also capture the temporal evolution of chemical/biophysical trajectories. Our character-level language model learns a probabilistic model of 1-dimensional stochastic trajectories generated from higher-dimensional dynamics. The model captures Boltzmann statistics and also reproduces kinetics across a spectrum of timescales. We demonstrate how training the long short-term memory network is equivalent to learning a path entropy, and that its embedding layer, instead of representing contextual meaning of characters, here exhibits a nontrivial connectivity between different metastable states in the underlying physical system. We demonstrate our model’s reliability through different benchmark systems and a force spectroscopy trajectory for multi-state riboswitch. We anticipate that our work represents a stepping stone in the understanding and use of recurrent neural networks for understanding the dynamics of complex stochastic molecular systems.

A Review of Recurrent Neural Networks: LSTM Cells and Network Architectures

2019 ◽  
Vol 31 (7) ◽  
pp. 1235-1270 ◽  
Author(s):  
Yong Yu ◽  
Xiaosheng Si ◽  
Changhua Hu ◽  
Jianxun Zhang
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Short Term Memory ◽  
Cell Structure ◽  
Relevant Information ◽  
Future Research ◽  
Sequential Data ◽  
Learning Capacity ◽  
Research Areas ◽  
Almost All

Recurrent neural networks (RNNs) have been widely adopted in research areas concerned with sequential data, such as text, audio, and video. However, RNNs consisting of sigma cells or tanh cells are unable to learn the relevant information of input data when the input gap is large. By introducing gate functions into the cell structure, the long short-term memory (LSTM) could handle the problem of long-term dependencies well. Since its introduction, almost all the exciting results based on RNNs have been achieved by the LSTM. The LSTM has become the focus of deep learning. We review the LSTM cell and its variants to explore the learning capacity of the LSTM cell. Furthermore, the LSTM networks are divided into two broad categories: LSTM-dominated networks and integrated LSTM networks. In addition, their various applications are discussed. Finally, future research directions are presented for LSTM networks.

scholarly journals Noisy Multipath Parallel Hybrid Model for Remaining Useful Life Estimation (NMPM)

2020 ◽  
Vol 12 (1) ◽  
pp. 10
Author(s):  
Ali AlDulaimi ◽  
Arash Mohammadi ◽  
Amir Asif
Keyword(s):  
Neural Networks ◽  
Hybrid Model ◽  
Short Term Memory ◽  
Sequence Data ◽  
Remaining Useful Life ◽  
Life Estimation ◽  
Parallel Path ◽  
Temporal Features ◽  
Parallel Hybrid ◽  
Useful Life

The parallel hybrid models of different deep neural networks architectures are the most promising approaches for remaining useful life (RUL) estimation. In light of that, this paper introduces for the first time in the literature a new parallel hybrid deep neural network (DNN) solution for RUL estimation, named as the Noisy Multipath Parallel Hybrid Model for Remaining Useful Life Estimation (NMPM). The proposed framework comprises of three parallel paths, the first one utilizes a noisy Bidirectional Long-short term memory (BLSTM) that used for extracting temporal features and learning the dependencies of sequence data in two directions, forward and backward, which can benefit completely from the input data. While the second parallel path employs noisy multilayer perceptron (MLP) that consists of three layers to extract different class of features. The third parallel path utilizes noisy convolutional neural networks (CNN) to extract another class of features. The concatenated output of the previous parallel paths is then fed into a noisy fusion center (NFC) to predict the RLU. The NMPM has been trained based on a noisy training to enhance the generalization behavior, as well as strengthen the model accuracy and robustness. The NMPM framework is tested and evaluated by using CMAPSS dataset provided by NASA.

scholarly journals Spam text classification using LSTM Recurrent Neural Network

2021 ◽  
Vol 9 (9) ◽  
pp. 1271-1275
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Language Processing ◽  
Text Classification ◽  
Short Term Memory ◽  
Experimental Studies ◽  
The Other ◽  
Support Vector ◽  
Data Points ◽  
Class Labels

Sequence Classification is one of the on-demand research projects in the field of Natural Language Processing (NLP). Classifying a set of images or text into an appropriate category or class is a complex task that a lot of Machine Learning (ML) models fail to accomplish accurately and end up under-fitting the given dataset. Some of the ML algorithms used in text classification are KNN, Naïve Bayes, Support Vector Machines, Convolutional Neural Networks (CNNs), Recursive CNNs, Recurrent Neural Networks (RNNs), Long Short Term Memory (LSTM), etc. For this experimental study, LSTM and a few other algorithms were chosen for a more comparative study. The dataset used is the SMS Spam Collection Dataset from Kaggle and 150 more entries were additionally added from different sources. Two possible class labels for the data points are spam and ham. Each entry consists of the class label, a few sentences of text followed by a few useless features that are eliminated. After converting the text to the required format, the models are run and then evaluated using various metrics. In experimental studies, the LSTM gives much better classification accuracy than the other machine learning models. F1-Scores in the high nineties were achieved using LSTM for classifying the text. The other models showed very low F1-Scores and Cosine Similarities indicating that they had underperformed on the dataset. Another interesting observation is that the LSTM had reduced the number of false positives and false negatives than any other model.

scholarly journals Persian sentences to phoneme sequences conversion based on recurrent neural networks

2016 ◽  
Vol 6 (1) ◽  
pp. 219-225 ◽  
Author(s):  
Yasser Mohseni Behbahani ◽  
Bagher Babaali ◽  
Mussa Turdalyuly
Keyword(s):  
Neural Networks ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Short Term Memory ◽  
Contextual Information ◽  
Short Term ◽  
Persian Language ◽  
Short Vowels ◽  
Sequential Labeling ◽  
Long Short Term Memory

AbstractGrapheme to phoneme conversion is one of the main subsystems of Text-to-Speech (TTS) systems. Converting sequence of written words to their corresponding phoneme sequences for the Persian language is more challenging than other languages; because in the standard orthography of this language the short vowels are omitted and the pronunciation ofwords depends on their positions in a sentence. Common approaches used in the Persian commercial TTS systems have several modules and complicated models for natural language processing and homograph disambiguation that make the implementation harder as well as reducing the overall precision of system. In this paper we define the grapheme-to-phoneme conversion as a sequential labeling problem; and use the modified Recurrent Neural Networks (RNN) to create a smart and integrated model for this purpose. The recurrent networks are modified to be bidirectional and equipped with Long-Short Term Memory (LSTM) blocks to acquire most of the past and future contextual information for decision making. The experiments conducted in this paper show that in addition to having a unified structure the bidirectional RNN-LSTM has a good performance in recognizing the pronunciation of the Persian sentences with the precision more than 98 percent.

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