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Gene function prediction is a complex multilabel classification problem with several distinctive features: the hierarchical relationships between functional classes, the presence of multiple sources of biomolecular data, the unbalance between positive and negative examples for each class, the complexity of the whole-ontology and genome-wide dimensions. Unlike previous works, which mostly looked at each one of these issues in isolation, we explore the interaction and potential synergy ofdoi:10.1007/s10994-011-5271-6 fatcat:5uvavmu6zjft3g7xvtc6sghsya