LSTMCNNsucc: A Bidirectional LSTM and CNN-Based Deep Learning Method for Predicting Lysine Succinylation Sites.
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ABSTRACT:
SUBMITTER: Huang G
PROVIDER: S-EPMC8188601 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Succinylation is a type of protein post-translational modification (PTM), which can play important roles in a variety of cellular processes. Due to an increasing number of site-specific succinylated peptides obtained from high-throughput mass spectrometry (MS), various tools have been developed for computationally identifying succinylated sites on proteins. However, most of these tools predict succinylation sites based on traditional machine learning methods. Hence, this work aimed to carry out the succinylation site prediction based on a deep learning model. The abundance of MS-verified succinylated peptides enabled the investigation of substrate site specificity of succinylation sites through sequence-based attributes, such as position-specific amino acid composition, the composition of k-spaced amino acid pairs (CKSAAP), and position-specific scoring matrix (PSSM). Additionally, the maximal dependence decomposition (MDD) was adopted to detect the substrate signatures of lysine succinylation sites by dividing all succinylated sequences into several groups with conserved substrate motifs. According to the results of ten-fold cross-validation, the deep learning model trained using PSSM and informative CKSAAP attributes can reach the best predictive performance and also perform better than traditional machine-learning methods. Moreover, an independent testing dataset that truly did not exist in the training dataset was used to compare the proposed method with six existing prediction tools. The testing dataset comprised of 218 positive and 2621 negative instances, and the proposed model could yield a promising performance with 84.40% sensitivity, 86.99% specificity, 86.79% accuracy, and an MCC value of 0.489. Finally, the proposed method has been implemented as a web-based prediction tool (CNN-SuccSite), which is now freely accessible at http://csb.cse.yzu.edu.tw/CNN-SuccSite/ .
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Project description:Subjective well-being is a comprehensive psychological indicator for measuring quality of life. Studies have found that emotional measurement methods and measurement accuracy are important for well-being-related research. Academic emotion is an emotion description in the field of education. The subjective well-being of learners in an online learning environment can be studied by analyzing academic emotions. However, in a large-scale online learning environment, it is extremely challenging to classify learners' academic emotions quickly and accurately for specific comment aspects. This study used literature analysis and data pre-analysis to build a dimensional classification system of academic emotion aspects for students' comments in an online learning environment, as well as to develop an aspect-oriented academic emotion automatic recognition method, including an aspect-oriented convolutional neural network (A-CNN) and an academic emotion classification algorithm based on the long short-term memory with attention mechanism (LSTM-ATT) and the attention mechanism. The experiments showed that this model can provide quick and effective identification. The A-CNN model accuracy on the test set was 89%, and the LSTM-ATT model accuracy on the test set was 71%. This research provides a new method for the measurement of large-scale online academic emotions, as well as support for research related to students' well-being in online learning environments.
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Project description:COVID-19 has resulted in significant morbidity and mortality globally. We develop a model that uses data from thirty days before a fixed time point to forecast the daily number of new COVID-19 cases fourteen days later in the early stages of the pandemic. Various time-dependent factors including the number of daily confirmed cases, reproduction number, policy measures, mobility and flight numbers were collected. A deep-learning model using Bidirectional Long-Short Term Memory (Bi-LSTM) architecture was trained on data from 22nd Jan 2020 to 8 Jan 2021 to forecast the new daily number of COVID-19 cases 14 days in advance across 190 countries, from 9 to 31 Jan 2021. A second model with fewer variables but similar architecture was developed. Results were summarised by mean absolute error (MAE), root mean squared error (RMSE), mean absolute percentage error (MAPE), and total absolute percentage error and compared against results from a classical ARIMA model. Median MAE was 157 daily cases (IQR: 26-666) under the first model, and 150 (IQR: 26-716) under the second. Countries with more accurate forecasts had more daily cases and experienced more waves of COVID-19 infections. Among countries with over 10,000 cases over the prediction period, median total absolute percentage error was 33% (IQR: 18-59%) and 34% (IQR: 16-66%) for the first and second models respectively. Both models had comparable median total absolute percentage errors but lower maximum total absolute percentage errors as compared to the classical ARIMA model. A deep-learning approach using Bi-LSTM architecture and open-source data was validated on 190 countries to forecast the daily number of cases in the early stages of the COVID-19 outbreak. Fewer variables could potentially be used without impacting prediction accuracy.
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Project description:BackgroundLysine acetylation in protein is one of the most important post-translational modifications (PTMs). It plays an important role in essential biological processes and is related to various diseases. To obtain a comprehensive understanding of regulatory mechanism of lysine acetylation, the key is to identify lysine acetylation sites. Previously, several shallow machine learning algorithms had been applied to predict lysine modification sites in proteins. However, shallow machine learning has some disadvantages. For instance, it is not as effective as deep learning for processing big data.ResultsIn this work, a novel predictor named DeepAcet was developed to predict acetylation sites. Six encoding schemes were adopted, including a one-hot, BLOSUM62 matrix, a composition of K-space amino acid pairs, information gain, physicochemical properties, and a position specific scoring matrix to represent the modified residues. A multilayer perceptron (MLP) was utilized to construct a model to predict lysine acetylation sites in proteins with many different features. We also integrated all features and implemented the feature selection method to select a feature set that contained 2199 features. As a result, the best prediction achieved 84.95% accuracy, 83.45% specificity, 86.44% sensitivity, 0.8540 AUC, and 0.6993 MCC in a 10-fold cross-validation. For an independent test set, the prediction achieved 84.87% accuracy, 83.46% specificity, 86.28% sensitivity, 0.8407 AUC, and 0.6977 MCC.ConclusionThe predictive performance of our DeepAcet is better than that of other existing methods. DeepAcet can be freely downloaded from https://github.com/Sunmile/DeepAcet .
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Project description:Yield prediction is of great significance for yield mapping, crop market planning, crop insurance, and harvest management. Remote sensing is becoming increasingly important in crop yield prediction. Based on remote sensing data, great progress has been made in this field by using machine learning, especially the Deep Learning (DL) method, including Convolutional Neural Network (CNN) or Long Short-Term Memory (LSTM). Recent experiments in this area suggested that CNN can explore more spatial features and LSTM has the ability to reveal phenological characteristics, which both play an important role in crop yield prediction. However, very few experiments combining these two models for crop yield prediction have been reported. In this paper, we propose a deep CNN-LSTM model for both end-of-season and in-season soybean yield prediction in CONUS at the county-level. The model was trained by crop growth variables and environment variables, which include weather data, MODIS Land Surface Temperature (LST) data, and MODIS Surface Reflectance (SR) data; historical soybean yield data were employed as labels. Based on the Google Earth Engine (GEE), all these training data were combined and transformed into histogram-based tensors for deep learning. The results of the experiment indicate that the prediction performance of the proposed CNN-LSTM model can outperform the pure CNN or LSTM model in both end-of-season and in-season. The proposed method shows great potential in improving the accuracy of yield prediction for other crops like corn, wheat, and potatoes at fine scales in the future.
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Project description:Knowledge about protein-protein interactions is beneficial in understanding cellular mechanisms. Protein-protein interactions are usually determined according to their protein-protein interaction sites. Due to the limitations of current techniques, it is still a challenging task to detect protein-protein interaction sites. In this article, we presented a method based on deep learning and XGBoost (called DeepPPISP-XGB) for predicting protein-protein interaction sites. The deep learning model served as a feature extractor to remove redundant information from protein sequences. The Extreme Gradient Boosting algorithm was used to construct a classifier for predicting protein-protein interaction sites. The DeepPPISP-XGB achieved the following results: area under the receiver operating characteristic curve of 0.681, a recall of 0.624, and area under the precision-recall curve of 0.339, being competitive with the state-of-the-art methods. We also validated the positive role of global features in predicting protein-protein interaction sites.
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Project description:Hajj (pilgrimage) is a unique social and religious event in which many Muslims worldwide come to perform Hajj. More than two million people travel to Makkah, Saudi Arabia annually to perform various Hajj rituals for four to five days. However, given the recent outbreak of the coronavirus (COVID-19) and its variants, Hajj in the last 2 years 2020-2021 has been different because pilgrims were limited down to a few thousand to control and prevent the spread of COVID-19. This study employs a deep learning approach to investigate the impressions of pilgrims and others from within and outside the Makkah community during the 1442 AH Hajj season. Approximately 4,300 Hajj-related posts and interactions were collected from social media channels, such as Twitter and YouTube, during the Hajj season Dhul-Hijjah 1-13, 1442 (July 11-23, 2021). Convolutional neural networks (CNNs) and long short-term memory (LSTM) deep learning methods were utilized to investigate people's impressions from the collected data. The CNN-LSTM approach showed superior performance results compared with other widely used classification models in terms of F-score and accuracy. Findings revealed significantly positive sentiment rates for tweets collected from Mina and Arafa holy sites, with ratios exceeding 4 out of 5. Furthermore, the sentiment analysis (SA) rates for tweets about Hajj and pilgrims varied during the days of Hajj. Some were classified as positive tweets, such as describing joy at receiving the days of Hajj, and some were negative tweets, such as expressing the impression about the hot weather and the level of satisfaction for some services. Moreover, the SA of comments on several YouTube videos revealed positive classified comments, including praise and supplications, and negative classified comments, such as expressing regret that the Hajj was limited to a small number of pilgrims.
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Project description:DNA N6-methyladenine (6mA) is an important epigenetic modification, which is involved in many biology regulation processes. An accurate and reliable method for 6mA identification can help us gain a better insight into the regulatory mechanism of the modification. Although many experimental techniques have been proposed to identify 6mA sites genome-wide, these techniques are time consuming and laborious. Recently, several machine learning methods have been developed to identify 6mA sites genome-wide. However, there is room for the improvement on their performance for predicting 6mA sites in rice genome. In this paper, we developed a simple and lightweight deep learning model to identify DNA 6mA sites in rice genome. Our model needs no prior knowledge of 6mA or manually crafted sequence feature. We built our model based on two rice 6mA benchmark datasets. Our method got an average prediction accuracy of ?93% and ?92% on the two datasets we used. We compared our method with existing 6mA prediction tools. The comparison results show that our model outperforms the state-of-the-art methods.
| S-EPMC6797597 | biostudies-literature
Project description:MotivationTranslation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g. GTI-seq and QTI-seq, provides abundant data for systematically studying the general principles of translation initiation and the development of computational method for TIS identification.MethodsWe have developed a deep learning-based framework, named TITER, for accurately predicting TISs on a genome-wide scale based on QTI-seq data. TITER extracts the sequence features of translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network and further integrates the prior preference of TIS codon composition into a unified prediction framework.ResultsExtensive tests demonstrated that TITER can greatly outperform the state-of-the-art prediction methods in identifying TISs. In addition, TITER was able to identify important sequence signatures for individual types of TIS codons, including a Kozak-sequence-like motif for AUG start codon. Furthermore, the TITER prediction score can be related to the strength of translation initiation in various biological scenarios, including the repressive effect of the upstream open reading frames on gene expression and the mutational effects influencing translation initiation efficiency.Availability and implementationTITER is available as an open-source software and can be downloaded from https://github.com/zhangsaithu/titer .Contactlzhang20@mail.tsinghua.edu.cn or zengjy321@tsinghua.edu.cn.Supplementary informationSupplementary data are available at Bioinformatics online.
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