Sparse matrix operations achieve only small fractions of peak CPU speeds because of the use of specialized, indexbased matrix representations, which degrade cache utilization by i...
In recent years, many networks have become available for analysis, including social networks, sensor networks, biological networks, etc. Graph clustering has shown its effectivenes...
Let G = (V, E, w) be a directed graph, where w : V → R is an arbitrary weight function defined on its vertices. The bottleneck weight, or the capacity, of a path is the smalles...
Background: The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest ap...
Background: Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from ...