A study of hierarchical and flat classification of proteins

Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area

A unifying view for performance measures in multi-class prediction

In the last few years, many different performance measures have been introduced to overcome the weakness of the most natural metric, the Accuracy. Among them, Matthews Correlation Coefficient has recently gained popularity among researchers not only in machine learning but also in several application fields such as bioinformatics. Nonetheless, further novel functions are being proposed in literature. We show that Confusion Entropy, a recently introduced classifier performance measure for multi-class problems, has a strong (monotone) relation with the multi-class generalization of a classical metric, the Matthews Correlation Coefficient. Computational evidence in support of the claim is provided, together with an outline of the theoretical explanation

Open-Category Classification by Adversarial Sample Generation

In real-world classification tasks, it is difficult to collect training samples from all possible categories of the environment. Therefore, when an instance of an unseen class appears in the prediction stage, a robust classifier should be able to tell that it is from an unseen class, instead of classifying it to be any known category. In this paper, adopting the idea of adversarial learning, we propose the ASG framework for open-category classification. ASG generates positive and negative samples of seen categories in the unsupervised manner via an adversarial learning strategy. With the generated samples, ASG then learns to tell seen from unseen in the supervised manner. Experiments performed on several datasets show the effectiveness of ASG.Comment: Published in IJCAI 201