Semblance: A Rank-Based Kernel on Probability Spaces for Niche Detection

Abstract: In data science, determining proximity between observations is critical to many downstream analyses such as clustering, information retrieval and classification. However, when the underlying structure of the data probability space is unclear, the function used to compute similarity between data points is often arbitrarily chosen. Here, we present a novel concept of proximity, Semblance, that uses the empirical distribution across all observations to inform the similarity between each pair. The advantage of Semblance lies in its distribution free formulation and its ability to detect niche features by placing greater emphasis on similarity between observation pairs that fall at the outskirts of the data distribution, as opposed to those that fall towards the center. We prove that Semblance is a valid Mercer kernel, thus allowing its principled use in kernel based learning machines. Semblance can be applied to any data modality, and we demonstrate its consistently improved performance against conventional methods through simulations and three real case studies from very different applications, viz. cell type classification using single cell RNA sequencing, selecting predictors of positive return on real estate investments, and image compression.