Decoding algorithms using side-effect machines

Bioinformatics applies computers to problems in molecular biology. Previous research has not addressed edit metric decoders. Decoders for quaternary edit metric codes are finding use in bioinformatics problems with applications to DNA. By using side effect machines we hope to be able to provide efficient decoding algorithms for this open problem. Two ideas for decoding algorithms are presented and examined. Both decoders use Side Effect Machines(SEMs) which are generalizations of finite state automata. Single Classifier Machines(SCMs) use a single side effect machine to classify all words within a code. Locking Side Effect Machines(LSEMs) use multiple side effect machines to create a tree structure of subclassification. The goal is to examine these techniques and provide new decoders for existing codes. Presented are ideas for best practices for the creation of these two types of new edit metric decoders.

Application of Reptation Quantum Monte Carlo and Related Methods to LiH

This work investigates mathematical details and computational aspects of Metropolis-Hastings reptation quantum Monte Carlo and its variants, in addition to the Bounce method and its variants. The issues that concern us include the sensitivity of these algorithms' target densities to the position of the trial electron density along the reptile, time-reversal symmetry of the propagators, and the length of the reptile. We calculate the ground-state energy and one-electron properties of LiH at its equilibrium geometry for all these algorithms. The importance sampling is performed with a single-determinant large Slater-type orbitals (STO) basis set. The computer codes were written to exploit the efficiencies engineered into modern, high-performance computing software. Using the Bounce method in the calculation of non-energy-related properties, those represented by operators that do not commute with the Hamiltonian, is a novel work. We found that the unmodified Bounce gives good ground state energy and very good one-electron properties. We attribute this to its favourable time-reversal symmetry in its target density's Green's functions. Breaking this symmetry gives poorer results. Use of a short reptile in the Bounce method does not alter the quality of the results. This suggests that in future applications one can use a shorter reptile to cut down the computational time dramatically.