Experiment F: Total Run Time

Purpose

Comparing the run time of likelihood computations with the new optimization algorithm for determining an elimination order (v1.4) to the run time with the previous optimization algorithm (v1.3).

Description of the problem

We compared between the new optimization algorithm for determining an elimination order (v1.4) to the previous optimization algorithm (v1.3).  The run time includes both optimization time and inference time.  We tested 50 datasets, chosen so that the run times on the new version are above 10 seconds and below 10 hours.  Some of these datasets were randomly simulated, and some are based on real pedigree data.  On each dataset, v1.3 was run for up to a couple of hours, and the total run time was estimated according to the percentage of the computation that was completed at that time.

Experimental Results

The timing was improved in 48 out of the 51 datasets, often by an order of magnitude.

Detailed Results

The best time results are in bold. There are links to all files of simulated datasets.  The datasets that are based on real pedigree data are confidential and are therefore not posted.