Dataset Information

Classification of Biodegradable Substances Using Balanced Random Trees and Boosted C5.0 Decision Trees.

ABSTRACT: Substances that do not degrade over time have proven to be harmful to the environment and are dangerous to living organisms. Being able to predict the biodegradability of substances without costly experiments is useful. Recently, the quantitative structure-activity relationship (QSAR) models have proposed effective solutions to this problem. However, the molecular descriptor datasets usually suffer from the problems of unbalanced class distribution, which adversely affects the efficiency and generalization of the derived models. Accordingly, this study aims at validating the performances of balanced random trees (RTs) and boosted C5.0 decision trees (DTs) to construct QSAR models to classify the ready biodegradation of substances and their abilities to deal with unbalanced data. The balanced RTs model algorithm builds individual trees using balanced bootstrap samples, while the boosted C5.0 DT is modeled using cost-sensitive learning. We employed the two-dimensional molecular descriptor dataset, which is publicly available through the University of California, Irvine (UCI) machine learning repository. The molecular descriptors were ranked according to their contributions to the balanced RTs classification process. The performance of the proposed models was compared with previously reported results. Based on the statistical measures, the experimental results showed that the proposed models outperform the classification results of the support vector machine (SVM), K-nearest neighbors (KNN), and discrimination analysis (DA). Classification measures were analyzed in terms of accuracy, sensitivity, specificity, precision, false positive rate, false negative rate, F1 score, receiver operating characteristic (ROC) curve, and area under the ROC curve (AUROC).

SUBMITTER: Elsayad AM

PROVIDER: S-EPMC7763457 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Classification of Biodegradable Substances Using Balanced Random Trees and Boosted C5.0 Decision Trees.

Elsayad Alaa M AM Nassef Ahmed M AM Al-Dhaifallah Mujahed M Elsayad Khaled A KA

International journal of environmental research and public health 20201213 24

Substances that do not degrade over time have proven to be harmful to the environment and are dangerous to living organisms. Being able to predict the biodegradability of substances without costly experiments is useful. Recently, the quantitative structure-activity relationship (QSAR) models have proposed effective solutions to this problem. However, the molecular descriptor datasets usually suffer from the problems of unbalanced class distribution, which adversely affects the efficiency and gen ...[more]

PMID: 33322123

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Project description:Objectives:Little research has been done in pharmacoepidemiology on the use of machine learning for exploring medicinal treatment effectiveness in oncology. Therefore, the aim of this study was to explore the added value of machine learning methods to investigate individual treatment responses for glioblastoma patients treated with temozolomide. Methods:Based on a retrospective observational registry covering 3090 patients with glioblastoma treated with temozolomide, we proposed the use of a two-step iterative exploratory learning process consisting of an initialization phase and a machine learning phase. For initialization, we defined a binary response variable as the target label using one-by-one nearest neighbor propensity score matching. Secondly, a classification tree algorithm was trained and validated for dividing individual patients into treatment response and non-response groups. Theorizing about treatment response was then done by evaluating the tree performance. Results:The classification tree model has an area under the curve (AUC) classification performance of 67% corresponding to a sensitivity of 0.69 and a specificity of 0.51. This result in predicting patient-level response was slightly better than the logistic regression model featuring an AUC of 64% (0.63 sensitivity and 0.54 specificity). The tree confirms confounding by age and discovers further age-related stratification with chemotherapy-treatment dependency, both not revealed in preceding clinical studies. The model lacked genetic information confounding treatment response. Conclusions:A classification tree was found to be suitable for understanding patient-level effectiveness for this glioblastoma-temozolomide case because of its high interpretability and capability to deal with covariate interdependencies, essential in a real-world environment. Possible improvements in the model's classification can be achieved by including genetic information and collecting primary data on treatment response. The model can be valuable in clinical practice for predicting personal treatment pathways.

Dataset Information

Classification of Biodegradable Substances Using Balanced Random Trees and Boosted C5.0 Decision Trees.

Publications

Classification of Biodegradable Substances Using Balanced Random Trees and Boosted C5.0 Decision Trees.

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