Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier

Predicting Protein–Protein Interactions Based on Ensemble Learning-Based Model from Protein Sequence

Simple Summary

Due to most traditional high-throughput experiments are tedious and laborious in identifying potential protein–protein interaction. To better improve accuracy prediction in protein–protein interactions. We proposed a novel computational method that can identify unknown protein–protein interaction efficiently and hope this method can provide a helpful idea and tool for proteomics research.

Abstract

Protein–protein interactions (PPIs) play an essential role in many biological cellular functions. However, it is still tedious and time-consuming to identify protein–protein interactions through traditional experimental methods. For this reason, it is imperative and necessary to develop a computational method for predicting PPIs efficiently. This paper explores a novel computational method for detecting PPIs from protein sequence, the approach which mainly adopts the feature extraction method: Locality Preserving Projections (LPP) and classifier: Rotation Forest (RF). Specifically, we first employ the Position Specific Scoring Matrix (PSSM), which can remain evolutionary information of biological for representing protein sequence efficiently. Then, the LPP descriptor is applied to extract feature vectors from PSSM. The feature vectors are fed into the RF to obtain the final results. The proposed method is applied to two datasets: Yeast and H. pylori, and obtained an average accuracy of 92.81% and 92.56%, respectively. We also compare it with K nearest neighbors (KNN) and support vector machine (SVM) to better evaluate the performance of the proposed method. In summary, all experimental results indicate that the proposed approach is stable and robust for predicting PPIs and promising to be a useful tool for proteomics research.

SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction

BACKGROUND

Protein-protein interactions (PPIs) dominate intracellular molecules to perform a series of tasks such as transcriptional regulation, information transduction, and drug signalling. The traditional wet experiment method to obtain PPIs information is costly and time-consuming.

RESULT

In this paper, SDNN-PPI, a PPI prediction method based on self-attention and deep learning is proposed. The method adopts amino acid composition (AAC), conjoint triad (CT), and auto covariance (AC) to extract global and local features of protein sequences, and leverages self-attention to enhance DNN feature extraction to more effectively accomplish the prediction of PPIs. In order to verify the generalization ability of SDNN-PPI, a 5-fold cross-validation on the intraspecific interactions dataset of Saccharomyces cerevisiae (core subset) and human is used to measure our model in which the accuracy reaches 95.48% and 98.94% respectively. The accuracy of 93.15% and 88.33% are obtained in the interspecific interactions dataset of human-Bacillus Anthracis and Human-Yersinia pestis, respectively. In the independent data set Caenorhabditis elegans, Escherichia coli, Homo sapiens, and Mus musculus, all prediction accuracy is 100%, which is higher than the previous PPIs prediction methods. To further evaluate the advantages and disadvantages of the model, the one-core and crossover network are conducted to predict PPIs, and the data show that the model correctly predicts the interaction pairs in the network.

CONCLUSION

In this paper, AAC, CT and AC methods are used to encode the sequence, and SDNN-PPI method is proposed to predict PPIs based on self-attention deep learning neural network. Satisfactory results are obtained on interspecific and intraspecific data sets, and good performance is also achieved in cross-species prediction. It can also correctly predict the protein interaction of cell and tumor information contained in one-core network and crossover network.The SDNN-PPI proposed in this paper not only explores the mechanism of protein-protein interaction, but also provides new ideas for drug design and disease prevention.

Machine learning: its challenges and opportunities in plant system biology

Sequencing technologies are evolving at a rapid pace, enabling the generation of massive amounts of data in multiple dimensions (e.g., genomics, epigenomics, transcriptomic, metabolomics, proteomics, and single-cell omics) in plants. To provide comprehensive insights into the complexity of plant biological systems, it is important to integrate different omics datasets. Although recent advances in computational analytical pipelines have enabled efficient and high-quality exploration and exploitation of single omics data, the integration of multidimensional, heterogenous, and large datasets (i.e., multi-omics) remains a challenge. In this regard, machine learning (ML) offers promising approaches to integrate large datasets and to recognize fine-grained patterns and relationships. Nevertheless, they require rigorous optimizations to process multi-omics-derived datasets. In this review, we discuss the main concepts of machine learning as well as the key challenges and solutions related to the big data derived from plant system biology. We also provide in-depth insight into the principles of data integration using ML, as well as challenges and opportunities in different contexts including multi-omics, single-cell omics, protein function, and protein-protein interaction. KEY POINTS: • The key challenges and solutions related to the big data derived from plant system biology have been highlighted. • Different methods of data integration have been discussed. • Challenges and opportunities of the application of machine learning in plant system biology have been highlighted and discussed.

A Machine-Learning-Based IoT System for Optimizing Nutrient Supply in Commercial Aquaponic Operations

Nutrient regulation in aquaponic environments has been a topic of research for many years. Most studies have focused on appropriate control of nutrients in an aquaponic set-up, but very little research has been conducted on commercial-scale applications. In our model, the input data were sourced on a weekly basis from three commercial aquaponic farms in Southeast Texas over the course of a year. Due to the limited number of data points, dimensionality reduction techniques such as pairwise correlation matrix were used to remove the highly correlated predictors. Feature selection techniques such as the XGBoost classifier and Recursive Feature Elimination with ExtraTreesClassifier were used to rank the features in order of their relative importance. Ammonium and calcium were found to be the top two nutrient predictors, and based on the months in which lettuce was cultivated, the median of these nutrient values from the historical dataset served as the optimal concentration to be maintained in the aquaponic solution to sustain healthy growth of tilapia fish and lettuce plants in a coupled set-up. To accomplish this, Vernier sensors were used to measure the nutrient values and actuator systems were built to dispense the appropriate nutrient into the ecosystem via a closed loop.

Integrative artificial intelligence models for Australian coastal sediment lead prediction: An investigation of in-situ measurements and meteorological parameters effects

Heavy metals (HMs) such as Lead (Pb) have played a vital role in increasing the sediments of the Australian bay's ecosystem. Several meteorological parameters (i.e., minimum, maximum and average temperature (T_min, T_max and T_avg^oC), rainfall (R_n mm) and their interactions with the other batch HMs, are hypothesized to have high impact for the decision-making strategies to minimize the impacts of Pb. Three feature selection (FS) algorithms namely the Boruta method, genetic algorithm (GA) and extreme gradient boosting (XGBoost) were investigated to select the highly important predictors for Pb concentration in the coastal bay sediments of Australia. These FS algorithms were statistically evaluated using principal component analysis (PCA) Biplot along with the correlation metrics describing the statistical characteristics that exist in the input and output parameter space of the models. To ensure a high accuracy attained by the applied predictive artificial intelligence (AI) models i.e., XGBoost, support vector machine (SVM) and random forest (RF), an auto-hyper-parameter tuning process using a Grid-search approach was also implemented. Cu, Ni, Ce, and Fe were selected by all the three applied FS algorithms whereas the T_avg and R_n inputs remained the essential parameters identified by GA and Boruta. The order of the FS outcome was XGBoost > GA > Boruta based on the applied statistical examination and the PCA Biplot results and the order of applied AI predictive models was XGBoost-SVM > GA-SVM > Boruta-SVM, where the SVM model remained at the top performance among the other statistical metrics. Based on the Taylor diagram for model evaluation, the RF model was reflected only marginally different so overall, the proposed integrative AI model provided an evidence a robust and reliable predictive technique used for coastal sediment Pb prediction.

Objective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.)

Active breeding programs specifically for root system architecture (RSA) phenotypes remain rare; however, breeding for branch and taproot types in the perennial crop alfalfa is ongoing. Phenotyping in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root types. While image-based methods have been developed, translation to applied breeding is limited. This research is aimed at developing and comparing image-based RSA phenotyping methods using machine and deep learning algorithms for objective classification of 617 root images from mature alfalfa plants collected from the field to support the ongoing breeding efforts. Our results show that unsupervised machine learning tends to incorrectly classify roots into a normal distribution with most lines predicted as the intermediate root type. Encouragingly, random forest and TensorFlow-based neural networks can classify the root types into branch-type, taproot-type, and an intermediate taproot-branch type with 86% accuracy. With image augmentation, the prediction accuracy was improved to 97%. Coupling the predicted root type with its prediction probability will give breeders a confidence level for better decisions to advance the best and exclude the worst lines from their breeding program. This machine and deep learning approach enables accurate classification of the RSA phenotypes for genomic breeding of climate-resilient alfalfa.

DWPPI: A Deep Learning Approach for Predicting Protein–Protein Interactions in Plants Based on Multi-Source Information With a Large-Scale Biological Network

The prediction of protein–protein interactions (PPIs) in plants is vital for probing the cell function. Although multiple high-throughput approaches in the biological domain have been developed to identify PPIs, with the increasing complexity of PPI network, these methods fall into laborious and time-consuming situations. Thus, it is essential to develop an effective and feasible computational method for the prediction of PPIs in plants. In this study, we present a network embedding-based method, called DWPPI, for predicting the interactions between different plant proteins based on multi-source information and combined with deep neural networks (DNN). The DWPPI model fuses the protein natural language sequence information (attribute information) and protein behavior information to represent plant proteins as feature vectors and finally sends these features to a deep learning–based classifier for prediction. To validate the prediction performance of DWPPI, we performed it on three model plant datasets: Arabidopsis thaliana (A. thaliana), mazie (Zea mays), and rice (Oryza sativa). The experimental results with the fivefold cross-validation technique demonstrated that DWPPI obtains great performance with the AUC (area under ROC curves) values of 0.9548, 0.9867, and 0.9213, respectively. To further verify the predictive capacity of DWPPI, we compared it with some different state-of-the-art machine learning classifiers. Moreover, case studies were performed with the AC149810.2_FGP003 protein. As a result, 14 of the top 20 PPI pairs identified by DWPPI with the highest scores were confirmed by the literature. These excellent results suggest that the DWPPI model can act as a promising tool for related plant molecular biology.

A hybrid XGBoost-ISSA-LSTM model for accurate short-term and long-term dissolved oxygen prediction in ponds

Dissolved oxygen (DO) is one of the most critical factors to measure the water quality in ponds, which greatly impacts on healthy growth of aquatic organisms. To improve the prediction accuracy of DO and grasp its changing trends, a novel hybrid DO prediction model based on the long short-term memory network (LSTM) optimized by an improved sparrow search algorithm (ISSA) is proposed. Firstly, to discard redundant information and improve the calculation speed of the model, the key factors that have a greater correlation with DO are selected as the input parameters by extreme gradient boosting (XGBoost). Secondly, towards expanding the searching range of sparrows and balancing the global and local search, we introduce an adaptive factor exponential declining strategy for producers, and an arcsine decreasing strategy for scouters, which nonlinearly decreases with the increase of iterations. Besides, we also improve the position updating of scouters, making the sparrows gradually move to the best position. Finally, LSTM is optimized by ISSA to get the best initial weights and thresholds to construct an XGBoost-ISSA-LSTM DO prediction model. Specifically, we first analyze the method for water quality prediction, which can make short-term prediction (including about 1 h, 2 h) and long-term prediction (including about 12 h, 24 h) of DO. In 1-h prediction, the root mean square error (RMSE) of the model is 0.5571, the mean absolute error (MAE) is 0.2572, and the R² is 0.9276. In 24 h prediction, RMSE of the model is 0.6310, MAE is 0.4562, and R² is 0.9082. The experimental results show that the proposed model has better generalization performance and higher prediction accuracy compared with other common models. Therefore, the presented model based on XGBoost-ISSA-LSTM is more effective and could meet the actual demand of accurate prediction of DO.

Industrial Internet of Things for Condition Monitoring and Diagnosis of Dry Vacuum Pumps in Atomic Layer Deposition Equipment

In the modern semiconductor industry, defective products occur with unexpected small variables due to process miniaturization. Managing the condition of each part is an effective way of preventing unexpected errors. The industrial internet of things (IIoT) environment, which can monitor and analyze the performance degradation of parts that affect process results, enables advanced process yield management. This paper introduces the IIoT concept-based data monitoring and diagnostic system construction results. The process of pump vibration data acquisition is explained to evaluate the effectiveness of this system. The target process is deposition. The purpose of the system is to detect degradation of pumps due to by-products of the atomic layer deposition (ALD) process. The system consists of three areas: a data acquisition unit using six vibration sensors, a Web access-based monitoring unit that can monitor vibration data, and an Azure platform that searches for outliers in vibration data.

Research on the Computational Prediction of Essential Genes

Genes, the nucleotide sequences that encode a polypeptide chain or functional RNA, are the basic genetic unit controlling biological traits. They are the guarantee of the basic structures and functions in organisms, and they store information related to biological factors and processes such as blood type, gestation, growth, and apoptosis. The environment and genetics jointly affect important physiological processes such as reproduction, cell division, and protein synthesis. Genes are related to a wide range of phenomena including growth, decline, illness, aging, and death. During the evolution of organisms, there is a class of genes that exist in a conserved form in multiple species. These genes are often located on the dominant strand of DNA and tend to have higher expression levels. The protein encoded by it usually either performs very important functions or is responsible for maintaining and repairing these essential functions. Such genes are called persistent genes. Among them, the irreplaceable part of the body’s life activities is the essential gene. For example, when starch is the only source of energy, the genes related to starch digestion are essential genes. Without them, the organism will die because it cannot obtain enough energy to maintain basic functions. The function of the proteins encoded by these genes is thought to be fundamental to life. Nowadays, DNA can be extracted from blood, saliva, or tissue cells for genetic testing, and detailed genetic information can be obtained using the most advanced scientific instruments and technologies. The information gained from genetic testing is useful to assess the potential risks of disease, and to help determine the prognosis and development of diseases. Such information is also useful for developing personalized medication and providing targeted health guidance to improve the quality of life. Therefore, it is of great theoretical and practical significance to identify important and essential genes. In this paper, the research status of essential genes and the essential genome database of bacteria are reviewed, the computational prediction method of essential genes based on communication coding theory is expounded, and the significance and practical application value of essential genes are discussed.

DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost

Detection of somatic mutation in whole-exome sequencing data can help elucidate the mechanism of tumor progression. Most computational approaches require exome sequencing for both tumor and normal samples. However, it is more common to sequence exomes for tumor samples only without the paired normal samples. To include these types of data for extensive studies on the process of tumorigenesis, it is necessary to develop an approach for identifying somatic mutations using tumor exome sequencing data only. In this study, we designed a machine learning approach using Deep Neural Network (DNN) and XGBoost to identify somatic mutations in tumor-only exome sequencing data and we integrated this into a pipeline called DNN-Boost. The XGBoost algorithm is used to extract the features from the results of variant callers and these features are then fed into the DNN model as input. The XGBoost algorithm resolves issues of missing values and overfitting. We evaluated our proposed model and compared its performance with other existing benchmark methods. We noted that the DNN-Boost classification model outperformed the benchmark method in classifying somatic mutations from paired tumor-normal exome data and tumor-only exome data.

Proteomic Approaches to Defining Remission and the Risk of Relapse in Rheumatoid Arthritis

Objectives

Patients with Rheumatoid Arthritis (RA) are increasingly achieving stable disease remission, yet the mechanisms that govern ongoing clinical disease and subsequent risk of future flare are not well understood. We sought to identify serum proteomic alterations that dictate clinically important features of stable RA, and couple broad-based proteomics with machine learning to predict future flare.

Methods

We studied baseline serum samples from a cohort of stable RA patients (RETRO, n = 130) in clinical remission (DAS28<2.6) and quantified 1307 serum proteins using the SOMAscan platform. Unsupervised hierarchical clustering and supervised classification were applied to identify proteomic-driven clusters and model biomarkers that were associated with future disease flare after 12 months of follow-up and RA medication withdrawal. Network analysis was used to define pathways that were enriched in proteomic datasets.

Results

We defined 4 proteomic clusters, with one cluster (Cluster 4) displaying a lower mean DAS28 score (p = 0.03), with DAS28 associating with humoral immune responses and complement activation. Clustering did not clearly predict future risk of flare, however an XGboost machine learning algorithm classified patients who relapsed with an AUC (area under the receiver operating characteristic curve) of 0.80 using only baseline serum proteomics.

Conclusions

The serum proteome provides a rich dataset to understand stable RA and its clinical heterogeneity. Combining proteomics and machine learning may enable prediction of future RA disease flare in patients with RA who aim to withdrawal therapy.

A comprehensive study of macro factors related to traffic fatality rates by XGBoost-based model and GIS techniques

With the fast development of economics, road safety is becoming a serious problem. Exploring macro factors is effective to improve road safety. However, the existing studies have some limitations: (1) The existing studies only considered one aspect of macro factors and constructed models based on a few data samples. (2) The methods commonly used cannot address the non-linear relationship or calculate the feature importance. The findings obtained from such models may be limited and biased. To address the limitations, this study proposes a BO-CV-XGBoost framework to explore the macro factors related to traffic fatality rate classes based on a high-dimensional dataset that fully considers the impact of multi-factor interaction with adequate data samples. The proposed framework is applied to a dataset in the US. 453 county-level macro factors are collected from various data sources, covering ten macro aspects, including topography, transportation, etc. The optimized BO-CV-XGBoost model obtains the best classification performance with an AUC of 0.8977 and an accuracy of 85.02%. Compared with other methods, the proposed model has superiority on fatality rate classification. Ten macro factors are identified, including 'Current-dollar GDP', 'highway miles per person', etc. The ten factors contain four aspects of information, including economics, transportation, education, and medical condition. Geographic information system (GIS) techniques are further used for spatial analysis of the identified macro factors. Therefore, targeted and effective measures are accordingly proposed to prevent traffic fatalities and improve road safety.

DeepStack-DTIs: Predicting Drug-Target Interactions Using LightGBM Feature Selection and Deep-Stacked Ensemble Classifier

Accurate prediction of drug-target interactions (DTIs), which is often used in the fields of drug discovery and drug repositioning, is regarded a key challenge in the study of drug science. In this paper, a new method called DeepStack-DTIs is proposed to predict DTIs. First, for the target protein, pseudo-position specific score matrix, pseudo amino acid composition and SPIDER3 are used to extract the different feature information of the target protein. Meanwhile, the path-based fingerprint features of each drug are extracted. Then, the synthetic minority oversampling technique (SMOTE) and light gradient boosting machine (LightGBM) are used for data balancing and feature selection, respectively. Finally, the processed features are input to the deep-stacked ensemble classifier composed of gated recurrent unit (GRU), deep neural network (DNN), support vector machine (SVM), eXtreme gradient boosting (XGBoost) and logistic regression (LR) to predict DTIs. Under the five-fold cross-validation and compared with existing methods, the proposed method achieves higher prediction accuracy on the gold standard dataset. To evaluate the predictive power of DeepStack-DTIs, we validate the method on another dataset and predict the drug-target interaction network. The results indicate that DeepStack-DTIs has excellent predictive ability than the other methods, and provides novel insights for the prediction of DTIs. A novel method DeepStack-DTIs for drug-target interactions prediction. PsePSSM, PseAAC, SPIDER3 and FP2 are fused to convert protein sequence and drug molecule information into digital information, respectively. The SMOTE algorithm is used to balance the dataset and LightGBM feature selection algorithm is employed to remove redundant and irrelevant features to select the optimal feature subset. This optimal feature subset is inputted into the deep-stacked ensemble classifier to predict drug-target interactions. The experimental results show DeepStack-DTIs method can significantly improve the prediction accuracy of drug-target interactions.

Prediction of Decline in Global Cognitive Function Using Machine Learning with Feature Ranking of Gait and Physical Fitness Outcomes in Older Adults

Gait and physical fitness are related to cognitive function. A decrease in motor function and physical fitness can serve as an indicator of declining global cognitive function in older adults. This study aims to use machine learning (ML) to identify important features of gait and physical fitness to predict a decline in global cognitive function in older adults. A total of three hundred and six participants aged seventy-five years or older were included in the study, and their gait performance at various speeds and physical fitness were evaluated. Eight ML models were applied to data ranked by the p-value (LP) of linear regression and the importance gain (XI) of XGboost. Five optimal features were selected using elastic net on the LP data for men, and twenty optimal features were selected using support vector machine on the XI data for women. Thus, the important features for predicting a potential decline in global cognitive function in older adults were successfully identified herein. The proposed ML approach could inspire future studies on the early detection and prevention of cognitive function decline in older adults.

Sequence-Based Prediction of Plant Protein-Protein Interactions by Combining Discrete Sine Transformation With Rotation Forest

Protein-protein interactions (PPIs) in plants are essential for understanding the regulation of biological processes. Although high-throughput technologies have been widely used to identify PPIs, they are usually laborious, expensive, and suffer from high false-positive rates. Therefore, it is imperative to develop novel computational approaches as a supplement tool to detect PPIs in plants. In this work, we presented a method, namely DST-RoF, to identify PPIs in plants by combining an ensemble learning classifier-Rotation Forest (RoF) with discrete sine transformation (DST). Specifically, plant protein sequence is firstly converted into Position-Specific Scoring Matrix (PSSM). Then, the discrete sine transformation was employed to extract effective features for obtaining the evolutionary information of proteins. Finally, these optimal features were fed into the RoF classifier for training and prediction. When performed on the plant datasets Arabidopsis, Rice, and Maize, DST-RoF yielded high prediction accuracy of 82.95%, 88.82%, and 93.70%, respectively. To further evaluate the prediction ability of our approach, we compared it with 4 state-of-the-art classifiers and 3 different feature extraction methods. Comprehensive experimental results anticipated that our method is feasible and robust for predicting potential plant-protein interacted pairs.

Prediction for understanding the effectiveness of antiviral peptides

The low efficacy of current antivirals in conjunction with the resistance of viruses against existing antiviral drugs has resulted in the demand for the development of novel antiviral agents. Antiviral peptides (AVPs) are those bioactive peptides having virucidal activity and they can be developed into promising antiviral drugs. They are shorter length peptides having the ability to cease the progression of viral infections. The use of antiviral peptides in therapeutics has recently attracted the attention of the research community. The development and identification of AVPs is imperative for the discovery of novel therapeutics for viral infections. In the present work, a meta classifier (stacking) based approach is implemented for the prediction of IC₅₀ (half maximal inhibitory concentration) and pIC₅₀ (negative log of half maximal inhibitory concentration) values. The best prediction model with evolutionary information and local alignment scores as features achieved a correlation coefficient values of 0.670 and 0.753 on the training and testing sets respectively for IC₅₀. Further, the prediction of pIC₅₀ reached a correlation coefficient value of 0.797 and 0.789 for training and testing sets respectively. For the development of machine learning models involved in the prediction of IC₅₀, the use of pIC₅₀ over IC₅₀ is recommended as the target variable. Further on a systematic comparison of AVPs with high IC₅₀ values and Low IC₅₀ values, it is revealed that higher mean charge and tiny amino acids are preferred and higher length and consecutive hydrophilic amino acids are avoided in the former.

ANOVA-particle swarm optimization-based feature selection and gradient boosting machine classifier for improved protein-protein interaction prediction

Feature fusion and selection strategies have been applied to improve accuracy in the prediction of protein-protein interaction (PPI). In this paper, an embedded feature selection framework is developed by integrating a cost function based on analysis of variance (ANOVA) with the particle swarm optimization (PSO), termed AVPSO. Initially, the features of the protein sequences extracted using pseudo-amino acid composition (PseAAC), conjoint triad composition, and local descriptor are fused. Then, AVPSO is employed to select the optimal set of features. The light gradient boosting machine (LGBM) classifier is used to predict the PPIs using the optimal feature subset. On the five-fold cross-validation analysis, the proposed model (AVPSO-LGBM) achieved an average accuracy of 97.12% and 95.09%, respectively, on the intraspecies PPI datasets Saccharomyces cerevisiae and Helicobacter pylori. On the interspecies, PPI datasets of the Human-Bacillus and Human-Yersinia, an average accuracy of 95.20% and 93.44%, are achieved. Results obtained on independent test datasets, and network datasets show that the prediction accuracy of the AVPSO-LGBM is better than the existing methods, demonstrating its generalization ability. The improved prediction performance obtained by the proposed model makes it a reliable and effective PPI prediction model.

BERT-m7G: A Transformer Architecture Based on BERT and Stacking Ensemble to Identify RNA N7-Methylguanosine Sites from Sequence Information

As one of the most prevalent posttranscriptional modifications of RNA, N7-methylguanosine (m7G) plays an essential role in the regulation of gene expression. Accurate identification of m7G sites in the transcriptome is invaluable for better revealing their potential functional mechanisms. Although high-throughput experimental methods can locate m7G sites precisely, they are overpriced and time-consuming. Hence, it is imperative to design an efficient computational method that can accurately identify the m7G sites. In this study, we propose a novel method via incorporating BERT-based multilingual model in bioinformatics to represent the information of RNA sequences. Firstly, we treat RNA sequences as natural sentences and then employ bidirectional encoder representations from transformers (BERT) model to transform them into fixed-length numerical matrices. Secondly, a feature selection scheme based on the elastic net method is constructed to eliminate redundant features and retain important features. Finally, the selected feature subset is input into a stacking ensemble classifier to predict m7G sites, and the hyperparameters of the classifier are tuned with tree-structured Parzen estimator (TPE) approach. By 10-fold cross-validation, the performance of BERT-m7G is measured with an ACC of 95.48% and an MCC of 0.9100. The experimental results indicate that the proposed method significantly outperforms state-of-the-art prediction methods in the identification of m7G modifications.

Development of a Web-Based Ensemble Machine Learning Application to Select the Optimal Size of Posterior Chamber Phakic Intraocular Lens

Purpose

Selecting the optimal lens size by predicting the postoperative vault can reduce complications after implantation of an implantable collamer lens with a central-hole (ICL with KS-aquaport). We built a web-based machine learning application that incorporated clinical measurements to predict the postoperative ICL vault and select the optimal ICL size.

Methods

We applied the stacking ensemble technique based on eXtreme Gradient Boosting (XGBoost) and a light gradient boosting machine to pre-operative ocular data from two eye centers to predict the postoperative vault. We assigned the Korean patient data to a training (N = 2756 eyes) and internal validation (N = 693 eyes) datasets (prospective validation). Japanese patient data (N = 290 eyes) were used as an independent external dataset from different centers to validate the model.

Results

We developed an ensemble model that showed statistically better performance with a lower mean absolute error for ICL vault prediction (106.88 µm and 143.69 µm in the internal and external validation, respectively) than the other machine learning techniques and the classic ICL sizing methods did when applied to both validation datasets. Considering the lens size selection accuracy, our proposed method showed the best performance for both reference datasets (75.9% and 67.4% in the internal and external validation, respectively).

Conclusions

Applying the ensemble approach to a large dataset of patients who underwent ICL implantation resulted in a more accurate prediction of vault size and selection of the optimal ICL size.

Translational Relevance

We developed a web-based application for ICL sizing to facilitate the use of machine learning calculators for clinicians.

Prediction of protein ubiquitination sites via multi-view features based on eXtreme gradient boosting classifier

Ubiquitination is a common and reversible post-translational protein modification that regulates apoptosis and plays an important role in protein degradation and cell diseases. However, experimental identification of protein ubiquitination sites is usually time-consuming and labor-intensive, so it is necessary to establish effective predictors. In this study, we propose a ubiquitination sites prediction method based on multi-view features, namely UbiSite-XGBoost. Firstly, we use seven single-view features encoding methods to convert protein sequence fragments into digital information. Secondly, the least absolute shrinkage and selection operator (LASSO) is applied to remove the redundant information and get the optimal feature subsets. Finally, these features are inputted into the eXtreme gradient boosting (XGBoost) classifier to predict ubiquitination sites. Five-fold cross-validation shows that the AUC values of Set1-Set6 datasets are 0.8258, 0.7592, 0.7853, 0.8345, 0.8979 and 0.8901, respectively. The synthetic minority oversampling technique (SMOTE) is employed in Set4-Set6 unbalanced datasets, and the AUC values are 0.9777, 0.9782 and 0.9860, respectively. In addition, we have constructed three independent test datasets which the AUC values are 0.8007, 0.6897 and 0.7280, respectively. The results show that the proposed method UbiSite-XGBoost is superior to other ubiquitination prediction methods and it provides new guidance for the identification of ubiquitination sites. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/UbiSite-XGBoost/.

Cytokine gene variants and socio-demographic characteristics as predictors of cervical cancer: A machine learning approach

Cervical cancer is still one of the most prevalent cancers in women and a significant cause of mortality. Cytokine gene variants and socio-demographic characteristics have been reported as biomarkers for determining the cervical cancer risk in the Indian population. This study was designed to apply a machine learning-based model using these risk factors for better prognosis and prediction of cervical cancer. This study includes the dataset of cytokine gene variants, clinical and socio-demographic characteristics of normal healthy control subjects, and cervical cancer cases. Different risk factors, including demographic details and cytokine gene variants, were analysed using different machine learning approaches. Various statistical parameters were used for evaluating the proposed method. After multi-step data processing and random splitting of the dataset, machine learning methods were applied and evaluated with 5-fold cross-validation and also tested on the unseen data records of a collected dataset for proper evaluation and analysis. The proposed approaches were verified after analysing various performance metrics. The logistic regression technique achieved the highest average accuracy of 82.25% and the highest average F1-score of 82.58% among all the methods. Ridge classifiers and the Gaussian Naïve Bayes classifier achieved the highest sensitivity-85%. The ridge classifier surpasses most of the machine learning classifiers with 84.78% accuracy and 97.83% sensitivity. The risk factors analysed in this study can be taken as biomarkers in developing a cervical cancer diagnosis system. The outcomes demonstrate that the machine learning assisted analysis of cytokine gene variants and socio-demographic characteristics can be utilised effectively for predicting the risk of developing cervical cancer.

Prediction of protein-protein interaction sites through eXtreme gradient boosting with kernel principal component analysis

Predicting protein-protein interaction sites (PPI sites) can provide important clues for understanding biological activity. Using machine learning to predict PPI sites can mitigate the cost of running expensive and time-consuming biological experiments. Here we propose PPISP-XGBoost, a novel PPI sites prediction method based on eXtreme gradient boosting (XGBoost). First, the characteristic information of protein is extracted through the pseudo-position specific scoring matrix (PsePSSM), pseudo-amino acid composition (PseAAC), hydropathy index and solvent accessible surface area (ASA) under the sliding window. Next, these raw features are preprocessed to obtain more optimal representations in order to achieve better prediction. In particular, the synthetic minority oversampling technique (SMOTE) is used to circumvent class imbalance, and the kernel principal component analysis (KPCA) is applied to remove redundant characteristics. Finally, these optimal features are fed to the XGBoost classifier to identify PPI sites. Using PPISP-XGBoost, the prediction accuracy on the training dataset Dset186 reaches 85.4%, and the accuracy on the independent validation datasets Dtestset72, PDBtestset164, Dset_448 and Dset_355 reaches 85.3%, 83.9%, 85.8% and 85.4%, respectively, which all show an increase in accuracy against existing PPI sites prediction methods. These results demonstrate that the PPISP-XGBoost method can further enhance the prediction of PPI sites.

Diabetic Retinopathy Prediction by Ensemble Learning Based on Biochemical and Physical Data

(1) Background: Diabetic retinopathy, one of the most serious complications of diabetes, is the primary cause of blindness in developed countries. Therefore, the prediction of diabetic retinopathy has a positive impact on its early detection and treatment. The prediction of diabetic retinopathy based on high-dimensional and small-sample-structured datasets (such as biochemical data and physical data) was the problem to be solved in this study. (2) Methods: This study proposed the XGB-Stacking model with the foundation of XGBoost and stacking. First, a wrapped feature selection algorithm, XGBIBS (Improved Backward Search Based on XGBoost), was used to reduce data feature redundancy and improve the effect of a single ensemble learning classifier. Second, in view of the slight limitation of a single classifier, a stacking model fusion method, Sel-Stacking (Select-Stacking), which keeps Label-Proba as the input matrix of meta-classifier and determines the optimal combination of learners by a global search, was used in the XGB-Stacking model. (3) Results: XGBIBS greatly improved the prediction accuracy and the feature reduction rate of a single classifier. Compared to a single classifier, the accuracy of the Sel-Stacking model was improved to varying degrees. Experiments proved that the prediction model of XGB-Stacking based on the XGBIBS algorithm and the Sel-Stacking method made effective predictions on diabetes retinopathy. (4) Conclusion: The XGB-Stacking prediction model of diabetic retinopathy based on biochemical and physical data had outstanding performance. This is highly significant to improve the screening efficiency of diabetes retinopathy and reduce the cost of diagnosis.

Regional Population Forecast and Analysis Based on Machine Learning Strategy

Regional population forecast and analysis is of essence to urban and regional planning, and a well-designed plan can effectively construct a sound national infrastructure and stabilize positive population growth. Traditionally, either urban or regional planning relies on the opinions of demographers in terms of how the population of a city or a region will grow. Multi-regional population forecast is currently possible, carried out mainly on the basis of the Interregional Cohort-Component model. While this model has its unique advantages, several demographic rates are determined based on the decisions made by primary planners. Hence, the only drawback for cohort-component type population forecasting is allowing the analyst to specify the demographic rates of the future, and it goes without saying that this tends to introduce a biased result in forecasting accuracy. To effectively avoid this problem, this work proposes a machine learning-based method to forecast multi-regional population growth objectively. Thus, this work, drawing upon the newly developed machine learning technology, attempts to analyze and forecast the population growth of major cities in Taiwan. By effectively using the advantage of the XGBoost algorithm, the evaluation of feature importance and the forecast of multi-regional population growth between the present and the near future can be observed objectively, and it can further provide an objective reference to the urban planning of regional population.

nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning

Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identification of Kcr sites. However, experimental approaches for identifying Kcr sites are often time-consuming and expensive when compared with computational approaches. To date, several predictors for Kcr site prediction have been developed, most of which are capable of predicting crotonylation sites on either histones alone or mixed histone and nonhistone proteins together. These methods exhibit high diversity in their algorithms, encoding schemes, feature selection techniques and performance assessment strategies. However, none of them were designed for predicting Kcr sites on nonhistone proteins. Therefore, it is desirable to develop an effective predictor for identifying Kcr sites from the large amount of nonhistone sequence data. For this purpose, we first provide a comprehensive review on six methods for predicting crotonylation sites. Second, we develop a novel deep learning-based computational framework termed as CNNrgb for Kcr site prediction on nonhistone proteins by integrating different types of features. We benchmark its performance against multiple commonly used machine learning classifiers (including random forest, logitboost, naïve Bayes and logistic regression) by performing both 10-fold cross-validation and independent test. The results show that the proposed CNNrgb framework achieves the best performance with high computational efficiency on large datasets. Moreover, to facilitate users' efforts to investigate Kcr sites on human nonhistone proteins, we implement an online server called nhKcr and compare it with other existing tools to illustrate the utility and robustness of our method. The nhKcr web server and all the datasets utilized in this study are freely accessible at http://nhKcr.erc.monash.edu/.

ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor

Adenoviruses (AdVs) constitute a diverse family with many pathogenic types that infect a broad range of hosts. Understanding the pathogenesis of adenoviral infections is not only clinically relevant but also important to elucidate the potential use of AdVs as vectors in therapeutic applications. For an adenoviral infection to occur, attachment of the viral ligand to a cellular receptor on the host organism is a prerequisite and, in this sense, it is a criterion to decide whether an adenoviral infection can potentially happen. The interaction between any virus and its corresponding host organism is a specific kind of protein-protein interaction (PPI) and several experimental techniques, including high-throughput methods are being used in exploring such interactions. As a result, there has been accumulating data on virus-host interactions including a significant portion reported at publicly available bioinformatics resources. There is not, however, a computational model to integrate and interpret the existing data to draw out concise decisions, such as whether an infection happens or not. In this study, accepting the cellular entry of AdV as a decisive parameter for infectivity, we have developed a machine learning, more precisely support vector machine (SVM), based methodology to predict whether adenoviral infection can take place in a given host. For this purpose, we used the sequence data of the known receptors of AdVs, we identified sets of adenoviral ligands and their respective host species, and eventually, we have constructed a comprehensive adenovirus–host interaction dataset. Then, we committed interaction predictions through publicly available virus-host PPI tools and constructed an AdV infection predictor model using SVM with RBF kernel, with the overall sensitivity, specificity, and AUC of 0.88 ± 0.011, 0.83 ± 0.064, and 0.86 ± 0.030, respectively. ML-AdVInfect is the first of its kind as an effective predictor to screen the infection capacity along with anticipating any cross-species shifts. We anticipate our approach led to ML-AdVInfect can be adapted in making predictions for other viral infections.

Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression

Streptococcus pneumoniae is a major cause of mortality in children under five years old. In recent years, the emergence of antibiotic-resistant strains of S. pneumoniae increases the threat level of this pathogen. For that reason, the exploration of S. pneumoniae protein virulence factors should be considered in developing new drugs or vaccines, for instance by the analysis of host-pathogen protein-protein interactions (HP-PPIs). In this research, prediction of protein-protein interactions was performed with a logistic regression model with the number of protein domain occurrences as features. By utilizing HP-PPIs of three different pathogens as training data, the model achieved 57-77 % precision, 64-75 % recall, and 96-98 % specificity. Prediction of human-S. pneumoniae protein-protein interactions using the model yielded 5823 interactions involving thirty S. pneumoniae proteins and 324 human proteins. Pathway enrichment analysis showed that most of the pathways involved in the predicted interactions are immune system pathways. Network topology analysis revealed β-galactosidase (BgaA) as the most central among the S. pneumoniae proteins in the predicted HP-PPI networks, with a degree centrality of 1.0 and a betweenness centrality of 0.451853. Further experimental studies are required to validate the predicted interactions and examine their roles in S. pneumoniae infection.

Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework

Origins of replication sites (ORIs), which refers to the initiative locations of genomic DNA replication, play essential roles in DNA replication process. Detection of ORIs' distribution in genome scale is one of key steps to in-depth understanding their regulation mechanisms. In this study, we presented a novel machine learning-based approach called Stack-ORI encompassing 10 cell-specific prediction models for identifying ORIs from four different eukaryotic species (Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana). For each cell-specific model, we employed 12 feature encoding schemes that cover nucleic acid composition, position-specific and physicochemical properties information. The optimal feature set was identified from each encoding individually and developed their respective baseline models using the eXtreme Gradient Boosting (XGBoost) classifier. Subsequently, the predicted scores of 12 baseline models are integrated as a novel feature vector to train XGBoost and develop the final model. Extensive experimental results show that Stack-ORI achieves significantly better performance as compared with their baseline models on both training and independent datasets. Interestingly, Stack-ORI consistently outperforms existing predictor in all cell-specific models, not only on training but also on independent test. Moreover, our novel approach provides necessary interpretations that help understanding model success by leveraging the powerful SHapley Additive exPlanation algorithm, thus underlining the most important feature encoding schemes significant for predicting cell-specific ORIs.