A hierarchical multi-label classification algorithm for gene function prediction
Summary: Gene function prediction is a complicated and challenging hierarchical multi-label classification (HMC) task, in which genes may have many functions at the same time and these functions are organized in a hierarchy. This paper proposed a novel HMC algorithm for solving this problem based on the Gene Ontology (GO), the hierarchy of which is a directed acyclic graph (DAG) and is more difficult to tackle. In the proposed algorithm, the HMC task is firstly changed into a set of binary classification tasks. Then, two measures are implemented in the algorithm to enhance the HMC performance by considering the hierarchy structure during the learning procedures. Firstly, negative instances selecting policy associated with the SMOTE approach are proposed to alleviate the imbalanced data set problem. Secondly, a nodes interaction method is introduced to combine the results of binary classifiers. It can guarantee that the predictions are consistent with the hierarchy constraint. The experiments on eight benchmark yeast data sets annotated by the Gene Ontology show the promising performance of the proposed algorithm compared with other state-of-the-art algorithms.
- Synergy of multi-label hierarchical ensembles, data fusion, and cost-sensitive methods for gene functional inference
- Predicting Gene Function using Predictive Clustering Trees
- Decision trees for hierarchical multi-label classification
- An evaluation of global-model hierarchical classification algorithms for hierarchical classification problems with single path of labels
- Hierarchical multilabel classification based on path evaluation
- A note on Platt's probabilistic outputs for support vector machines
- A survey of hierarchical classification across different application domains
- Decision trees for hierarchical multi-label classification
- Hierarchical multilabel classification based on path evaluation
- scientific article; zbMATH DE number 1753143 (Why is no real title available?)
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