Pairwise Computations on the Cell Processor with Applications in Computational Biology
All-pairs computations occur in numerous and diverse applications across many areas. In many-body simulations and molecular dynamics, computation of pairwise gravitational or electrostatic forces is needed to study system evolution . A similar scenario occurs in computational electromagnetics except that the field is sampled in multiple directions, turning this into a vector computation . In the radiosity method in computer graphics, a scene is divided into patches and the reflection and refraction of light between every pair of patches is of interest to compute the equilibrium light energy distribution . In computational systems biology, correlations between pairs of genes are sought based on their expression levels over a large set of observations . Clustering algorithms typically use a distance metric and use all-pairs distances to guide the clustering process . While the details vary, common to these applications is computation between all pairs of entities from a given set.