scholarly journals Boosted Prediction of Antihypertensive Peptides Using Deep Learning

2021 ◽  
Vol 11 (5) ◽  
pp. 2316
Author(s):  
Anum Rauf ◽  
Aqsa Kiran ◽  
Malik Tahir Hassan ◽  
Sajid Mahmood ◽  
Ghulam Mustafa ◽  
...  

Heart attack and other heart-related diseases are among the main causes of fatalities in the world. These diseases and some other severe problems like kidney failure and paralysis are mainly caused by hypertension. Since bioactive peptides extracted from naturally existing food substances possess antihypertensive activity, these antihypertensive peptides (AHTP) can function as prospective replacements for existing pharmacological drugs with no or fewer side effects. Such naturally existing peptides can be identified using in-silico approaches. The in-silico methods have been proven to save huge amounts of time and money in the identification of effective peptides. The proposed methodology is a deep learning-based in-silico approach for the identification of antihypertensive peptides (AHTPs). An ensemble method is proposed that combines convolutional neural network (CNN) and support vector machine (SVM) classifiers. Amino acid composition (AAC) and g-gap dipeptide composition (DPC) techniques are used for feature extraction. The proposed methodology has been evaluated on two standard antihypertensive peptide sequence datasets. The model yields 95% accuracy on the benchmarking dataset and 88.9% accuracy on the independent dataset. Comparative analysis is provided to demonstrate that the proposed method outperforms existing state-of-the-art methods on both of the benchmarking and independent datasets.

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Ramin Keivani ◽  
Sina Faizollahzadeh Ardabili ◽  
Farshid Aram

Deep learning (DL) and machine learning (ML) methods have recently contributed to the advancement of models in the various aspects of prediction, planning, and uncertainty analysis of smart cities and urban development. This paper presents the state of the art of DL and ML methods used in this realm. Through a novel taxonomy, the advances in model development and new application domains in urban sustainability and smart cities are presented. Findings reveal that five DL and ML methods have been most applied to address the different aspects of smart cities. These are artificial neural networks; support vector machines; decision trees; ensembles, Bayesians, hybrids, and neuro-fuzzy; and deep learning. It is also disclosed that energy, health, and urban transport are the main domains of smart cities that DL and ML methods contributed in to address their problems.


2016 ◽  
Vol 21 (9) ◽  
pp. 998-1003 ◽  
Author(s):  
Oliver Dürr ◽  
Beate Sick

Deep learning methods are currently outperforming traditional state-of-the-art computer vision algorithms in diverse applications and recently even surpassed human performance in object recognition. Here we demonstrate the potential of deep learning methods to high-content screening–based phenotype classification. We trained a deep learning classifier in the form of convolutional neural networks with approximately 40,000 publicly available single-cell images from samples treated with compounds from four classes known to lead to different phenotypes. The input data consisted of multichannel images. The construction of appropriate feature definitions was part of the training and carried out by the convolutional network, without the need for expert knowledge or handcrafted features. We compare our results against the recent state-of-the-art pipeline in which predefined features are extracted from each cell using specialized software and then fed into various machine learning algorithms (support vector machine, Fisher linear discriminant, random forest) for classification. The performance of all classification approaches is evaluated on an untouched test image set with known phenotype classes. Compared to the best reference machine learning algorithm, the misclassification rate is reduced from 8.9% to 6.6%.


2020 ◽  
Author(s):  
Alisson Hayasi da Costa ◽  
Renato Augusto C. dos Santos ◽  
Ricardo Cerri

AbstractPIWI-Interacting RNAs (piRNAs) form an important class of non-coding RNAs that play a key role in the genome integrity through the silencing of transposable elements. However, despite their importance and the large application of deep learning in computational biology for classification tasks, there are few studies of deep learning and neural networks for piRNAs prediction. Therefore, this paper presents an investigation on deep feedforward networks models for classification of transposon-derived piRNAs. We analyze and compare the results of the neural networks in different hyperparameters choices, such as number of layers, activation functions and optimizers, clarifying the advantages and disadvantages of each configuration. From this analysis, we propose a model for human piRNAs classification and compare our method with the state-of-the-art deep neural network for piRNA prediction in the literature and also traditional machine learning algorithms, such as Support Vector Machines and Random Forests, showing that our model has achieved a great performance with an F-measure value of 0.872, outperforming the state-of-the-art method in the literature.


2021 ◽  
Author(s):  
William Dee

Antimicrobial peptides (AMPs) are increasingly being used in the development of new therapeutic drugs, in areas such as cancer therapy and hypertension. Additionally, they are seen as an alternative to antibiotics due to the increasing occurrence of bacterial resistance. Wet-laboratory experimental identification, however, is both time consuming and costly, so in-silico models are now commonly used in order to screen new AMP candidates. This paper proposes a novel approach of creating model inputs; using pre-trained language models to produce contextualized embeddings representing the amino acids within each peptide sequence, before a convolutional neural network is then trained as the classifier. The optimal model was validated on two datasets, being one previously used in AMP prediction research, and an independent dataset, created by this paper. Predictive accuracies of 93.33% and 88.26% were achieved respectively, outperforming all previous state-of-the-art classification models.


Biotecnia ◽  
2018 ◽  
Vol 20 (3) ◽  
pp. 165-169
Author(s):  
GI Ramírez-Torres ◽  
N Ontiveros ◽  
V López-Teros ◽  
GM Suarez-Jiménez ◽  
F Cabrera-Chávez

Many food-derived peptides with antihypertensive activity have been reported. However, a reduced number of studies have been conducted to prove in vivo the efficacy of most of the currently reported antihypertensive peptides. Thus, just a few of these bioactive peptides are utilized as supplements or ingredients for functional foods production. In addition to in vivo evaluations, another challenging task is the delivery of bioactive peptides in physiological conditions, but studies about this topic are scarce. Notably, some proteins are able to form gels that have different characteristics related to the pH of the environment. Bioactive peptides can be entrapped into such gels structure and be released in different physiological environments (e. g. low pH in the stomach and neutral in the intestine). Thus, the selection of macronutrients could play a critical role in the design of food matrices intended to be used as containers and releasers of antihypertensive peptides.


Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 353 ◽  
Author(s):  
Phasit Charoenkwan ◽  
Sakawrat Kanthawong ◽  
Nalini Schaduangrat ◽  
Janchai Yana ◽  
Watshara Shoombuatong

Although, existing methods have been successful in predicting phage (or bacteriophage) virion proteins (PVPs) using various types of protein features and complex classifiers, such as support vector machine and naïve Bayes, these two methods do not allow interpretability. However, the characterization and analysis of PVPs might be of great significance to understanding the molecular mechanisms of bacteriophage genetics and the development of antibacterial drugs. Hence, we herein proposed a novel method (PVPred-SCM) based on the scoring card method (SCM) in conjunction with dipeptide composition to identify and characterize PVPs. In PVPred-SCM, the propensity scores of 400 dipeptides were calculated using the statistical discrimination approach. Rigorous independent validation test showed that PVPred-SCM utilizing only dipeptide composition yielded an accuracy of 77.56%, indicating that PVPred-SCM performed well relative to the state-of-the-art method utilizing a number of protein features. Furthermore, the propensity scores of dipeptides were used to provide insights into the biochemical and biophysical properties of PVPs. Upon comparison, it was found that PVPred-SCM was superior to the existing methods considering its simplicity, interpretability, and implementation. Finally, in an effort to facilitate high-throughput prediction of PVPs, we provided a user-friendly web-server for identifying the likelihood of whether or not these sequences are PVPs. It is anticipated that PVPred-SCM will become a useful tool or at least a complementary existing method for predicting and analyzing PVPs.


Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Ramin Keivani ◽  
Sina Faizollahzadeh ardabili ◽  
Farshid Aram

Deep learning (DL) and machine learning (ML) methods have recently contributed to the advancement of models in the various aspects of prediction, planning, and uncertainty analysis of smart cities and urban development. This paper presents the state of the art of DL and ML methods used in this realm. Through a novel taxonomy, the advances in model development and new application domains in urban sustainability and smart cities are presented. Findings reveal that five DL and ML methods have been most applied to address the different aspects of smart cities. These are artificial neural networks; support vector machines; decision trees; ensembles, Bayesians, hybrids, and neuro-fuzzy; and deep learning. It is also disclosed that energy, health, and urban transport are the main domains of smart cities that DL and ML methods contributed in to address their problems.


Author(s):  
Shikhar Saxena ◽  
Sambhavi Animesh ◽  
Melissa J. Fullwood ◽  
Yuguang Mu

Abstract The peptide binding to Major Histocompatibility Complex (MHC) proteins is an important step in the antigen-presentation pathway. Thus, predicting the binding potential of peptides with MHC is essential for the design of peptide-based therapeutics. Most of the available machine learning-based models predict the peptide-MHC binding based on the sequence of amino acids alone. Given the importance of structural information in determining the stability of the complex, here we have utilized both the complex structure and the peptide sequence features to predict the binding affinity of peptides to human receptor HLA-A*02:01. To our knowledge, no such model has been developed for the human HLA receptor before that incorporates both structure and sequence-based features. Results: We have applied machine learning techniques through the natural language processing (NLP) and convolutional neural network to design a model that performs comparably with the existing state-of-the-art models. Our model shows that the information from both sequence and structure domains results in enhanced performance in the binding prediction compared to the information from one domain alone. The testing results in 18 weekly benchmark datasets provided by the Immune Epitope Database (IEDB) as well as experimentally validated peptides from the whole-exome sequencing analysis of the breast cancer patients indicate that our model has achieved state-of-the-art performance. Conclusion: We have developed a deep-learning model (OnionMHC) that incorporates both structure as well as sequence-based features to predict the binding affinity of peptides with human receptor HLA-A*02:01. The model demonstrates state-of-the-art performance on the IEDB benchmark dataset as well as the experimentally validated peptides. The model can be used in the screening of potential neo-epitopes for the development of cancer vaccines or designing peptides for peptide-based therapeutics. OnionMHC is freely available at https://github.com/shikhar249/OnionMHC .


Energies ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 147 ◽  
Author(s):  
Muhammad Aslam ◽  
Jae-Myeong Lee ◽  
Hyung-Seung Kim ◽  
Seung-Jae Lee ◽  
Sugwon Hong

Microgrid is becoming an essential part of the power grid regarding reliability, economy, and environment. Renewable energies are main sources of energy in microgrids. Long-term solar generation forecasting is an important issue in microgrid planning and design from an engineering point of view. Solar generation forecasting mainly depends on solar radiation forecasting. Long-term solar radiation forecasting can also be used for estimating the degradation-rate-influenced energy potentials of photovoltaic (PV) panel. In this paper, a comparative study of different deep learning approaches is carried out for forecasting one year ahead hourly and daily solar radiation. In the proposed method, state of the art deep learning and machine learning architectures like gated recurrent units (GRUs), long short term memory (LSTM), recurrent neural network (RNN), feed forward neural network (FFNN), and support vector regression (SVR) models are compared. The proposed method uses historical solar radiation data and clear sky global horizontal irradiance (GHI). Even though all the models performed well, GRU performed relatively better compared to the other models. The proposed models are also compared with traditional state of the art methods for long-term solar radiation forecasting, i.e., random forest regression (RFR). The proposed models outperformed the traditional method, hence proving their efficiency.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Yang ◽  
Xiaohui Liu ◽  
Chengpin Shen ◽  
Yu Lin ◽  
Pengyuan Yang ◽  
...  

AbstractData-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of samples. However, sample-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA analysis, which is time-consuming and limits the identification/quantification by DIA to the peptides identified by DDA. Herein, we propose DeepDIA, a deep learning-based approach to generate in silico spectral libraries for DIA analysis. We demonstrate that the quality of in silico libraries predicted by instrument-specific models using DeepDIA is comparable to that of experimental libraries, and outperforms libraries generated by global models. With peptide detectability prediction, in silico libraries can be built directly from protein sequence databases. We further illustrate that DeepDIA can break through the limitation of DDA on peptide/protein detection, and enhance DIA analysis on human serum samples compared to the state-of-the-art protocol using a DDA library. We expect this work expanding the toolbox for DIA proteomics.


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