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An approach for identifying cytokines based on a novel ensemble classifier.

ABSTRACT: Biology is meaningful and important to identify cytokines and investigate their various functions and biochemical mechanisms. However, several issues remain, including the large scale of benchmark datasets, serious imbalance of data, and discovery of new gene families. In this paper, we employ the machine learning approach based on a novel ensemble classifier to predict cytokines. We directly selected amino acids sequences as research objects. First, we pretreated the benchmark data accurately. Next, we analyzed the physicochemical properties and distribution of whole amino acids and then extracted a group of 120-dimensional (120D) valid features to represent sequences. Third, in the view of the serious imbalance in benchmark datasets, we utilized a sampling approach based on the synthetic minority oversampling technique algorithm and K-means clustering undersampling algorithm to rebuild the training set. Finally, we built a library for dynamic selection and circulating combination based on clustering (LibD3C) and employed the new training set to realize cytokine classification. Experiments showed that the geometric mean of sensitivity and specificity obtained through our approach is as high as 93.3%, which proves that our approach is effective for identifying cytokines.

SUBMITTER: Zou Q

PROVIDER: S-EPMC3763580 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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An approach for identifying cytokines based on a novel ensemble classifier.

Zou Quan Q Wang Zhen Z Guan Xinjun X Liu Bin B Wu Yunfeng Y Lin Ziyu Z

BioMed research international 20130821

Biology is meaningful and important to identify cytokines and investigate their various functions and biochemical mechanisms. However, several issues remain, including the large scale of benchmark datasets, serious imbalance of data, and discovery of new gene families. In this paper, we employ the machine learning approach based on a novel ensemble classifier to predict cytokines. We directly selected amino acids sequences as research objects. First, we pretreated the benchmark data accurately. ...[more]

PMID: 24027761

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Project description:The main cause of stroke is the unexpected blockage of blood flow to the brain. The brain cells die if blood is not supplied to them, resulting in body disability. The timely identification of medical conditions ensures patients receive the necessary treatments and assistance. This early diagnosis plays a crucial role in managing symptoms effectively and enhancing the overall quality of life for individuals affected by the stroke. The research proposed an ensemble machine learning (ML) model that predicts brain stroke while reducing parameters and computational complexity. The dataset was obtained from an open-source website Kaggle and the total number of participants is 3,254. However, this dataset needs a significant class imbalance problem. To address this issue, we utilized Synthetic Minority Over-sampling Technique (SMOTE) and Adaptive Synthetic Sampling (ADAYSN), a technique for oversampling issues. The primary focus of this study centers around developing a stacking and voting approach that exhibits exceptional performance. We propose a stacking ensemble classifier that is more accurate and effective in predicting stroke disease in order to improve the classifier's performance and minimize overfitting problems. To create a final stronger classifier, the study used three tree-based ML classifiers. Hyperparameters are used to train and fine-tune the random forest (RF), decision tree (DT), and extra tree classifier (ETC), after which they were combined using a stacking classifier and a k-fold cross-validation technique. The effectiveness of this method is verified through the utilization of metrics such as accuracy, precision, recall, and F1-score. In addition, we utilized nine ML classifiers with Hyper-parameter tuning to predict the stroke and compare the effectiveness of Proposed approach with these classifiers. The experimental outcomes demonstrated the superior performance of the stacking classification method compared to other approaches. The stacking method achieved a remarkable accuracy of 100% as well as exceptional F1-score, precision, and recall score. The proposed approach demonstrates a higher rate of accurate predictions compared to previous techniques.

Dataset Information

An approach for identifying cytokines based on a novel ensemble classifier.

Publications

An approach for identifying cytokines based on a novel ensemble classifier.

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