Adaptive simulated annealing: A near-optimal connection between sampling and counting

Simulated annealing for near-optimal dual-channel mi- croarray designs

Dual-channel microarray experiments can be regarded as designs with block-size two. Our aim is to find D-optimal, A-optimal and related L-optimal designs for such experiments. Previous work has focussed on exhaustive search algorithms, which in many practical, large-scale experiments is infeasible. We propose using simulated annealing to search for near-optimal designs. We also consider a sub-c...

Constrained Sampling Using Simulated Annealing

Scientific image processing involves a variety of problems including image modeling, reconstruction, and synthesis. In this paper we develop a constrained sampling approach for porous media synthesis and reconstruction in order to generate artificial samples of porous media. Our approach is different from current porous media reconstruction methods in which the Gibbs probability distribution is...

Annealing and Tempering for Sampling and Counting

iii ACKNOWLEDGEMENTS I would like to thank my advisors Dana Randall and Eric Vigoda for their guidance and support, which they gave generously. I was fortunate to have the opportunity to work with two of the leading researchers in my field. Dana never ceased to surprise me with her quick insights and ability to get to crux of a problem. I thoroughly enjoyed working with Eric and am always inspi...

Simulated Annealing and Optimal Codes

Simulated Annealing and Optimal Protocols

Many human tumors cannot easily be avoided. In most cases a prophylactic vaccination prevents the tumor growth. In particular the Triplex vaccine prevented mammary carcinoma formation using a Chronic schedule, but it is not known if this schedule is minimal. A computational model named SimTriplex was able to reproduce in silico the in vivo experiments. The combination of SimTriplex and Genetic ...