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A vast body of theoretical research has focused either on overly simplistic models of parallel computation, notably the PRAM, or overly specific models that have few representatives in the real world. Both kinds of models encourage exploitation of formal loopholes, rather than rewarding development of techniques that yield performance across a range of(More)
serve as a basis for the design and analysis of fast, portable parallel algorithms, such as algorithms that can be implemented effectively on a wide variety of current and future parallel machines. If we look at the body of parallel algorithms developed under current parallel models, many are impractical because they exploit artificial factors not present(More)
In many distributed-memory parallel computers the only built-in communication primitive is point-to-point message transmission, and more powerful operations such as broadcast and synchronization must be realized using this primitive. Within the LogP model of parallel computation we present algorithms that yield optimal communication schedules for several(More)
We present a new and simple algorithmic approach to help predict protein structures from amino acid sequences based on energy minimization. In the search for the minimal energy conformation, we analyze and exploit the protein structures found at the various local minima to direct the search the global minimum. As such, we explore the energy landscape(More)
We address the problem of information fusion in uncertain environments. Imagine there are multiple experts building probabilistic models of the same situation and we wish to aggregate the information they provide. There are several problems we may run into by naively merging the information from each. For example, the experts may disagree on the probability(More)
Predicting the native conformation using computational protein models requires a large number of energy evaluations even with simplified models such as hydrophobic-hydrophilic (HP) models. Clearly, energy evaluations constitute a significant portion of computational time. We hypothesize that given the structured nature of algorithms that search for(More)