Original upload date: Fri, 17 Oct 2014 00:00:00 GMT
Archive date: Sun, 07 Nov 2021 19:57:19 GMT
Charles Brenner, DNA-View
Use a gun in a crime and, thanks to recent biochemical advances, you'll likely leave enough DNA to be detected. However, often the gun has also been handled by others and co
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nsequently the analysis of DNA mixtures has become increasingly important. The market for good DNA mixture software therefore has led me to recent and rapid progress in my long-delayed venture to convert my forensic DNA interpretation work into the modern world of Dyalog. Many people enjoy the scientific aspects of the story and I enjoy relating how, in my view, this project exemplifies the thesis that APL is a tool of thought. I credit APL with leading me to elegant and, therefore, very fast and flexible solutions to a problem for which the competing solutions are lumbered by complicated statistical and Monte Carlo methods.
Elegance and simplicity lead to several concrete benefits. The first is conceptual development. I made notes in APL as solutions to various aspects of the problem occurred to me last year. These brief APL notes ensured that the ideas really made sense, that they worked together and that I would not forget them. The brevity also revealed a simple but important point that others had overlooked: nesting the computation loops in the right order saves orders of magnitude in computation time. For another, execution speed makes it much easier to see the forest in many ways – testing, developing, designing. Competing programs take hours to find a partial answer, then having worked that hard succumb to a natural tendency to call it a day. The APL "DNA-VIEW Mixture Solution" program does the same in seconds which makes it much easier to think through to the fact that there's a lot more work to do before the result is logically defensible. At the end of 2013 I implemented the Mixture Solution and tested it on examples including a set of 5 proficiency exercises created at the National Institute of Standards and Technology. More than one hundred entrants, including the leading competition, had contributed analyses. One of the competitors (supported by years and millions of dollars of government grants) got four problems right and came close on the fifth, viewing it as a three person mixture although in fact it was four. Mixture Solution alone correctly analysed all five – as a bonus it correctly diagnosed one suspect as a mixed race person. We APLers try to be modest but it's not always easy. Sometimes there's just not much to be modest about!
