Modeling genome evolution with a DSEL for probabilistic programming

Authors:
Martin Erwig;Steve Kollmansberger
Affiliations:
School of EECS, Oregon State University;School of EECS, Oregon State University
Venue:
PADL'06 Proceedings of the 8th international conference on Practical Aspects of Declarative Languages
Year:
2006

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Abstract

Many scientific applications benefit from simulation. However, programming languages used in simulation, such as C++ or Matlab, approach problems from a deterministic procedural view, which seems to differ, in general, from many scientists’ mental representation. We apply a domain-specific language for probabilistic programming to the biological field of gene modeling, showing how the mental-model gap may be bridged. Our system assisted biologists in developing a model for genome evolution by separating the concerns of model and simulation and providing implicit probabilistic non-determinism.