Dataset Information

Developing Sustainable Classification of Diseases via Deep Learning and Semi-Supervised Learning.

ABSTRACT: Disease classification based on machine learning has become a crucial research topic in the fields of genetics and molecular biology. Generally, disease classification involves a supervised learning style; i.e., it requires a large number of labelled samples to achieve good classification performance. However, in the majority of the cases, labelled samples are hard to obtain, so the amount of training data are limited. However, many unclassified (unlabelled) sequences have been deposited in public databases, which may help the training procedure. This method is called semi-supervised learning and is very useful in many applications. Self-training can be implemented using high- to low-confidence samples to prevent noisy samples from affecting the robustness of semi-supervised learning in the training process. The deep forest method with the hyperparameter settings used in this paper can achieve excellent performance. Therefore, in this work, we propose a novel combined deep learning model and semi-supervised learning with self-training approach to improve the performance in disease classification, which utilizes unlabelled samples to update a mechanism designed to increase the number of high-confidence pseudo-labelled samples. The experimental results show that our proposed model can achieve good performance in disease classification and disease-causing gene identification.

SUBMITTER: Yin C

PROVIDER: S-EPMC7551840 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Developing Sustainable Classification of Diseases via Deep Learning and Semi-Supervised Learning.

Yin Chunwu C Chen Zhanbo Z

Healthcare (Basel, Switzerland) 20200824 3

Disease classification based on machine learning has become a crucial research topic in the fields of genetics and molecular biology. Generally, disease classification involves a supervised learning style; i.e., it requires a large number of labelled samples to achieve good classification performance. However, in the majority of the cases, labelled samples are hard to obtain, so the amount of training data are limited. However, many unclassified (unlabelled) sequences have been deposited in publ ...[more]

PMID: 32846941

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Project description:BackgroundPrecision medicine for cancer treatment relies on an accurate pathological diagnosis. The number of known tumor classes has increased rapidly, and reliance on traditional methods of histopathologic classification alone has become unfeasible. To help reduce variability, validation costs, and standardize the histopathological diagnostic process, supervised machine learning models using DNA-methylation data have been developed for tumor classification. These methods require large labeled training data sets to obtain clinically acceptable classification accuracy. While there is abundant unlabeled epigenetic data across multiple databases, labeling pathology data for machine learning models is time-consuming and resource-intensive, especially for rare tumor types. Semi-supervised learning (SSL) approaches have been used to maximize the utility of labeled and unlabeled data for classification tasks and are effectively applied in genomics. SSL methods have not yet been explored with epigenetic data nor demonstrated beneficial to central nervous system (CNS) tumor classification.ResultsThis paper explores the application of semi-supervised machine learning on methylation data to improve the accuracy of supervised learning models in classifying CNS tumors. We comprehensively evaluated 11 SSL methods and developed a novel combination approach that included a self-training with editing using support vector machine (SETRED-SVM) model and an L2-penalized, multinomial logistic regression model to obtain high confidence labels from a few labeled instances. Results across eight random forest and neural net models show that the pseudo-labels derived from our SSL method can significantly increase prediction accuracy for 82 CNS tumors and 9 normal controls.ConclusionsThe proposed combination of semi-supervised technique and multinomial logistic regression holds the potential to leverage the abundant publicly available unlabeled methylation data effectively. Such an approach is highly beneficial in providing additional training examples, especially for scarce tumor types, to boost the prediction accuracy of supervised models.

Dataset Information

Developing Sustainable Classification of Diseases via Deep Learning and Semi-Supervised Learning.

Publications

Developing Sustainable Classification of Diseases via Deep Learning and Semi-Supervised Learning.

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