Constrained Minkowski Sums: A Geometric Framework for Solving Interval Problems in Computational Biology Efficiently

In this paper, we introduce the notion of a constrained Minkowski sum: for two (finite) point-sets P, Q subset of R-2 and a set of k inequalities Ax >= b, it is defined as the point-set (P circle plus Q)(Ax >= b) = {x = p + q vertical bar p is an element of P, q is an element of Q, Ax >= b}. We show that typical interval problems from computational biology can be solved by computing a set containing the vertices of the convex hull of an appropriately constrained Minkowski sum. We provide an algorithm for computing such a set with running time O (N log N), where N = vertical bar P vertical bar + vertical bar Q vertical bar if k is fixed. For the special case (P circle plus Q)(x1 >=beta) where P and Q consist of points with integer x(1)-coordinates whose absolute values are bounded by O(N), we even achieve a linear running time O(N). We thereby obtain a linear running time for many interval problems from the literature and improve upon the best known running times for some of them. The main advantage of the presented approach is that it provides a general framework within which a broad variety of interval problems can be modeled and solved.