Assefaw Gebremedhin, Software


Robust software tool for tracking, managing, analysing and cataloguing short-sequence repeats and genotypes using Anaplasma marginale as a model species. Code and further information available here.

Associated Paper: H.N. Catanese, K.A. Brayton and A.H. Gebremedhin, RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data , BMC Genomics 2016 17:422. DOI: 10.1186/s12864-016-2686-2


Software for Live-variables based Hessian computation via Automatic Differentiation (implelemted on top of ADOL-C). Code and further information available here.

Associated Paper: M. Wang, A.H. Gebremedhin and A. Pothen, Capitalizing on Live Variables: New Algorithms for Efficient Hessian Computation via Automatic Differentiation. Mathematical Programming Computation, pp 1--43, 2016. DOI = 10.1007/s12532-016-0100-3.

Parallel Maximum Clique Finder (PMC)

This is implementation of fast algorithms for maximum clique finding and related problem in large graphs that are designed to exploit features of social and information networks. See here for info on the code and its usage.

Associated Paper: R.A. Rossi, D.F. Gleich, A.H. Gebremedhin and M.M.A. Patwary, Parallel Maximum Clique Algorithms with Applications to Network Analysis, SIAM Journal on Scientific Computing, Vol 37, Issue 5, pages C589-C618, 2015.


ColPack is a software package consisting of implementations of fast and effective algorithms for a variety of graph coloring, vertex ordering, and related problems. Many of the coloring problems model partitioning needs arising in compression-based computation of Jacobian and Hessian matrices using Automatic Differentiation. Several of the coloring problems also find important applications in various areas outside derivative computation. ColPack is implemented in C++ in an object-oriented fashion heavily using STL.

ColPack, Other Tools, and Impact (selected stories)