Biased Predecessor Search

Predecessor search with distance-sensitive query time

A predecessor (successor) search finds the largest element x smaller than the input string x (the smallest element x larger than or equal to x, respectively) out of a given set S; in this paper, we consider the static case (i.e., S is fixed and does not change over time) and assume that the n elements of S are available for inspection. We present a number of algorithms that, with a small additi...

Biased Search Trees

Non-Adaptive Data Structure Bounds for Dynamic Predecessor Search

In this work, we continue the examination of the role non-adaptivity plays in maintaining dynamic data structures, initiated by Brody and Larsen. We consider non-adaptive data structures for predecessor search in the w-bit cell probe model. In this problem, the goal is to dynamically maintain a subset T of up to n elements from t1, . . . ,mu, while supporting insertions, deletions, and a predec...

Homology Search for Genes Using Biased HMMs

Motivation: Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs). These HSPs then need to be correlated with existing sequence annotations, or assembled manually into putative gene structures. This process is error-prone...

Predecessor problem on smooth distributions

We follow a research thread studying the predecessor problem on “smooth” distribution families. We propose a conceptually simpler solution utilizing wellknown results from much better studied variant of the problem that assumes nothing about the input. As a side effect, we are able to extend the range of handled input distributions for the most studied case needing expected O (log log n) time, ...