PETs: A Stable and Accurate Predictor of Protein-Protein Interacting Sites Based on Extremely-Randomized Trees

An improved deep forest model for prediction of e-commerce consumers' repurchase behavior

As the Internet retail industry continues to rise, more and more consumers choose to shop online, especially Chinese consumers. Using consumer behavior data left on the Internet to predict repurchase behavior is of great significance for companies to achieve precision marketing. This paper proposes an improved deep forest model, and the interactive behavior characteristics of users and goods are added into the original feature model to predict the repurchase behavior of e-commerce consumers. Based on the Alibaba mobile e-commerce platform data set, first construct a feature engineering that includes user characteristics, product characteristics, and interactive behavior characteristics. And then use our proposed model to make predictions. Experiments show that the model’s overall performance with increased interactive behavior features is better and has higher accuracy. Compared with the existing prediction models, the improved deep forest model has certain advantages, which not only improves the prediction accuracy but also reduces the cost of training time.

Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins

MOTIVATION

There are over 30 sequence-based predictors of the protein-binding residues (PBRs). They use either structure-annotated or disorder-annotated training datasets, potentially creating a dichotomy where the structure-/disorder-specific models may not be able to cross-over to accurately predict the other type. Moreover, the structure-trained predictors were shown to substantially cross-predict PBRs among residues that interact with non-protein partners (nucleic acids and small ligands). We address these issues by performing first-of-its-kind comparative study of a representative collection of disorder- and structure-trained predictors using a comprehensive benchmark set with the structure- and disorder-derived annotations of PBRs (to analyze the cross-over) and the protein-, nucleic acid- and small ligand-binding proteins (to study the cross-predictions).

RESULTS

Three predictors provide accurate results: SCRIBER, ANCHOR and disoRDPbind. Some of the structure-trained methods make accurate predictions on the structure-annotated proteins. Similarly, the disorder-trained predictors predict well on the disorder-annotated proteins. However, the considered predictors generally fail to cross-over, with the exception of SCRIBER. Our study also reveals that virtually all methods substantially cross-predict PBRs, except for SCRIBER for the structure-annotated proteins and disoRDPbind for the disorder-annotated proteins. We formulate a novel hybrid predictor, hybridPBRpred, that combines results produced by disoRDPbind and SCRIBER to accurately predict disorder- and structure-annotated PBRs. HybridPBRpred generates accurate results that cross-over structure- and disorder-annotated proteins and produces relatively low amount of cross-predictions, offering an accurate alternative to predict PBRs.

AVAILABILITY AND IMPLEMENTATION

HybridPBRpred webserver, benchmark dataset and supplementary information are available at http://biomine.cs.vcu.edu/servers/hybridPBRpred/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A Machine Learning Approach for Anomaly Detection in Industrial Control Systems Based on Measurement Data

Attack detection problems in industrial control systems (ICSs) are commonly known as a network traffic monitoring scheme for detecting abnormal activities. However, a network-based intrusion detection system can be deceived by attackers that imitate the system’s normal activity. In this work, we proposed a novel solution to this problem based on measurement data in the supervisory control and data acquisition (SCADA) system. The proposed approach is called measurement intrusion detection system (MIDS), which enables the system to detect any abnormal activity in the system even if the attacker tries to conceal it in the system’s control layer. A supervised machine learning model is generated to classify normal and abnormal activities in an ICS to evaluate the MIDS performance. A hardware-in-the-loop (HIL) testbed is developed to simulate the power generation units and exploit the attack dataset. In the proposed approach, we applied several machine learning models on the dataset, which show remarkable performances in detecting the dataset’s anomalies, especially stealthy attacks. The results show that the random forest is performing better than other classifier algorithms in detecting anomalies based on measured data in the testbed.

Extremely-randomized-tree-based Prediction of N6-Methyladenosine Sites in Saccharomyces cerevisiae

Introduction

N⁶-methyladenosine (m6A) is one of the most common post-transcriptional modifications in RNA, which has been related to several biological processes. The accurate prediction of m6A sites from RNA sequences is one of the challenging tasks in computational biology. Several computational methods utilizing machine-learning algorithms have been proposed that accelerate in silico screening of m6A sites, thereby drastically reducing the experimental time and labor costs involved.

Methodology

In this study, we proposed a novel computational predictor termed ERT-m6Apred, for the accurate prediction of m6A sites. To identify the feature encodings with more discriminative capability, we applied a two-step feature selection technique on seven different feature encodings and identified the corresponding optimal feature set.

Results

Subsequently, performance comparison of the corresponding optimal feature set-based extremely randomized tree model revealed that Pseudo k-tuple composition encoding, which includes 14 physicochemical properties significantly outperformed other encodings. Moreover, ERT-m6Apred achieved an accuracy of 78.84% during cross-validation analysis, which is comparatively better than recently reported predictors.

Conclusion

In summary, ERT-m6Apred predicts Saccharomyces cerevisiae m6A sites with higher accuracy, thus facilitating biological hypothesis generation and experimental validations.

Prediction of apoptosis protein subcellular location based on position-specific scoring matrix and isometric mapping algorithm

Apoptosis proteins are related to many diseases. Obtaining the subcellular localization information of apoptosis proteins is helpful to understand the mechanism of diseases and to develop new drugs. At present, the researchers mainly focus on the primary protein sequences, so there is still room for improvement in the prediction accuracy of the subcellular localization of apoptosis proteins. In this paper, a new method named ERT-ECT-PSSM-IS is proposed to predict apoptosis proteins based on the position-specific scoring matrix (PSSM). First, the local and global features of different directions are extracted by evolutionary row transformation (ERT) and cross-covariance of evolutionary column transformation (ECT) based on PSSM (ERT-ECT-PSSM). Second, an improved isometric mapping algorithm (I-SMA) is used to eliminate redundant features. Finally, we adopt a support vector machine (SVM) to classify our results, and the prediction accuracy is evaluated by jackknife cross-validation tests. The experimental results show that the proposed method not only extracts more abundant feature expression but also has better predictive performance and robustness for the subcellular localization of apoptosis proteins in ZD98, ZW225, and CL317 databases. Graphical abstract Framework of the proposed prediction model.

Research on a Mixed Gas Classification Algorithm Based on Extreme Random Tree

Because of the low accuracy of the current machine olfactory algorithms in detecting two mixed gases, this study proposes a hybrid gas detection algorithm based on an extreme random tree to greatly improve the classification accuracy and time efficiency. The method mainly uses the dynamic time warping algorithm (DTW) to perform data pre-processing and then extracts the gas characteristics from gas signals at different concentrations by applying a principal component analysis (PCA). Finally, the model is established by using a new extreme random tree algorithm to achieve the target gas classification. The sample data collected by the experiment was verified by comparison experiments with the proposed algorithm. The analysis results show that the proposed DTW algorithm improves the gas classification accuracy by 26.87%. Compared with the random forest algorithm, extreme gradient boosting (XGBoost) algorithm and gradient boosting decision tree (GBDT) algorithm, the accuracy rate increased by 4.53%, 5.11% and 8.10%, respectively, reaching 99.28%. In terms of the time efficiency of the algorithms, the actual runtime of the extreme random tree algorithm is 66.85%, 90.27%, and 81.61% lower than that of the random forest algorithm, XGBoost algorithm, and GBDT algorithm, respectively, reaching 103.2568 s.