A challenging Pattern Recognition problem in Bioinformatics concerns the detection of a functional relation between two proteins even when they show very low sequence similarity – this is the so-called Protein Remote Homology Detection (PRHD) problem. In this paper we propose a novel approach to PRHD, which casts the problem into a Multiple Instance Learning (MIL) framework, which seems very suitable for this context. Experiments on a standard benchmark show very competitive performances, also in comparison with alternative discriminative methods.

In this paper we show that weighted K-Nearest Neighbor, a variation of the classic K-Nearest Neighbor, can be reinterpreted from a classifier combining perspective, specifically as a fixed combiner rule, the sum rule. Subsequently, we experimentally demonstrate that it can be rather beneficial to consider other combining schemes as well. In particular, we focus on trained combiners and illustrate the positive effect these can have on classification performance.