Multi-label text classification is a popular machine learning task where each document is assigned with multiple relevant labels. This task is challenging due to high dimensional features and correlated labels. Multi-label text classifiers need to be carefully regularized to prevent the severe over-fitting in the high dimensional space, and also need to take into account label dependencies in order to make accurate predictions under uncertainty. We demonstrate significant and practical improvement by carefully regularizing the model complexity during training phase, and also regularizing the label search space during prediction phase. Specifically, we regularize the classifier training using Elastic-net (L1+L2) penalty for reducing model complexity/size, and employ early stopping to prevent overfitting. At prediction time, we apply support inference to restrict the search space to label sets encountered in the training set, and F-optimizer GFM to make optimal predictions for the F1 metric. We show that although support inference only provides density estimations on existing label combinations, when combined with GFM predictor, the algorithm can output unseen label combinations. Taken collectively, our experiments show state of the art results on many benchmark datasets. Beyond performance and practical contributions, we make some interesting observations. Contrary to the prior belief, which deems support inference as purely an approximate inference procedure, we show that support inference acts as a strong regularizer on the label prediction structure. It allows the classifier to take into account label dependencies during prediction even if the classifiers had not modeled any label dependencies during training.

We have built KaBOB (Knowledge Base of Biomedicine) by integrating information from over 20 existing biomedical data sources about humans and seven major model organisms. The knowledge base is modeled in OWL and grounded in 14 prominent OBOs (Open Biomedical Ontologies). It is comprised of over 419 million RDF triples. Queries can be posed to KaBOB in terms of biomedical concepts and abstractions, instead of requiring knowledge of source-specific encodings and terminology.