The application of one-class machine learning is gaining attention in the computational biology community. Different studies have described the use of two-class machine learning to predict microRNAs (miRNAs) gene targ...The application of one-class machine learning is gaining attention in the computational biology community. Different studies have described the use of two-class machine learning to predict microRNAs (miRNAs) gene target. Most of these methods require the generation of an artificial negative class. However, designation of the negative class can be problematic and if it is not properly done can affect the performance of the classifier dramatically and/or yield a biased estimate of performance. We present a study using one-class machine learning for miRNA target discovery and compare one-class to two-class approaches. Of all the one-class methods tested, we found that most of them gave similar accuracy that range from 0.81 to 0.89 while the two-class naive Bayes gave 0.99 accuracy. One and two class methods can both give useful classification accuracies. The advantage of one class methods is that they don’t require any additional effort for choosing the best way of generating the negative class. In these cases one- class methods can be superior to two-class methods when the features which are chosen as representative of that positive class are well defined.展开更多
Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Biomarkers are used to measure the progress of disease or t...Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Biomarkers are used to measure the progress of disease or the physiological effects of therapeutic intervention in the treatment of disease. They are also used as early warning signs for various diseases such as cancer and inflammatory diseases. In this review, we outline recent progresses of computational biology application in research on biomarkers discovery. A brief discussion of some necessary preliminaries on machine learning techniques (e.g., clustering and support vector machines—SVM) which are commonly used in many applications to biomarkers discovery is given and followed by a description of biological background on biomarkers. We further examine the integration of computational biology approaches and biomarkers. Finally, we conclude with a discussion of key challenges for computational biology to biomarkers discovery.展开更多
文摘The application of one-class machine learning is gaining attention in the computational biology community. Different studies have described the use of two-class machine learning to predict microRNAs (miRNAs) gene target. Most of these methods require the generation of an artificial negative class. However, designation of the negative class can be problematic and if it is not properly done can affect the performance of the classifier dramatically and/or yield a biased estimate of performance. We present a study using one-class machine learning for miRNA target discovery and compare one-class to two-class approaches. Of all the one-class methods tested, we found that most of them gave similar accuracy that range from 0.81 to 0.89 while the two-class naive Bayes gave 0.99 accuracy. One and two class methods can both give useful classification accuracies. The advantage of one class methods is that they don’t require any additional effort for choosing the best way of generating the negative class. In these cases one- class methods can be superior to two-class methods when the features which are chosen as representative of that positive class are well defined.
文摘Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Biomarkers are used to measure the progress of disease or the physiological effects of therapeutic intervention in the treatment of disease. They are also used as early warning signs for various diseases such as cancer and inflammatory diseases. In this review, we outline recent progresses of computational biology application in research on biomarkers discovery. A brief discussion of some necessary preliminaries on machine learning techniques (e.g., clustering and support vector machines—SVM) which are commonly used in many applications to biomarkers discovery is given and followed by a description of biological background on biomarkers. We further examine the integration of computational biology approaches and biomarkers. Finally, we conclude with a discussion of key challenges for computational biology to biomarkers discovery.
