A Runtime Analysis of Parallel Evolutionary Algorithms in Dynamic Optimization

A simple island model with λλ islands and migration occurring after every ττ iterations is studied on the dynamic fitness function Maze. This model is equivalent to a (1+λ)(1+λ) EA if τ=1τ=1 , i. e., migration occurs during every iteration. It is proved that even for an increased offspring population size up to λ=O(n1−ϵ)λ=O(n1−ϵ) , the (1+λ)(1+λ) EA is still not able to track the optimum of Maze. If the migration interval is chosen carefully, the algorithm is able to track the optimum even for logarithmic λλ . The relationship of τ,λτ,λ , and the ability of the island model to track the optimum is then investigated more closely. Finally, experiments are performed to supplement the asymptotic results, and investigate the impact of the migration topology

Computational structure‐based drug design: Predicting target flexibility

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft

Probabilistic and artificial intelligence modelling of drought and agricultural crop yield in Pakistan

Pakistan is a drought-prone, agricultural nation with hydro-meteorological imbalances that increase the scarcity of water resources, thus, constraining water availability and leading major risks to the agricultural productivity sector and food security. Rainfall and drought are imperative matters of consideration, both for hydrological and agricultural applications. The aim of this doctoral thesis is to advance new knowledge in designing hybridized probabilistic and artificial intelligence forecasts models for rainfall, drought and crop yield within the agricultural hubs in Pakistan. The choice of these study regions is a strategic decision, to focus on precision agriculture given the importance of rainfall and drought events on agricultural crops in socioeconomic activities of Pakistan. The outcomes of this PhD contribute to efficient modelling of seasonal rainfall, drought and crop yield to assist farmers and other stakeholders to promote more strategic decisions for better management of climate risk for agriculturalreliant nations

When is it Beneficial to Reject Improvements?

We investigate two popular trajectory-based algorithms from biology and physics to answer a question of general significance: when is it beneficial to reject improvements? A distinguishing factor of SSWM (Strong Selection Weak Mutation), a popular model from population genetics, compared to the Metropolis algorithm (MA), is that the former can reject improvements, while the latter always accepts them. We investigate when one strategy outperforms the other. Since we prove that both algorithms converge to the same stationary distribution, we concentrate on identifying a class of functions inducing large mixing times, where the algorithms will outperform each other over a long period of time. The outcome of the analysis is the definition of a function where SSWM is efficient, while Metropolis requires at least exponential time

Multi-cycle Boiling Water Reactor Fuel Cycle Optimization

A multi-cycle nuclear fuel cycle optimization code, BWROPT (Boiling Water Reactor OPTimization), has been developed. BWROPT uses the Parallel Simulated Annealing (PSA) algorithm to solve the coupled out-of-core and in-core optimization problems. There are two depletion methods used for the in-core optimization: the Haling depletion and a Control Rod Pattern (CRP) search. The result of this optimization is the optimum new fuel inventory and the core loading pattern for the first cycle considered in the optimization. Several changes were made to the optimization algorithm with respect to other nuclear fuel cycle optimization codes that use PSA. Instead of using constant sampling probabilities for the solution perturbation types throughout the optimization, as is usually done, the sampling probabilities can be varied to get a better solution and/or decrease runtime. Also, the new fuel types available for use can be sorted into an array based on any parameter so that each parameter can be incremented or decremented. In addition several evaluations were performed to test the CRP search option. Using the variable sampling probabilities was found to produce slightly better results in less time than the standard method of having constant sampling probabilities. Performing ordered and random sampling of the new fuel types using the new fuel type array was found to yield slightly better solutions on average than random sampling alone, but with a somewhat higher runtime. Using variable length Markov chains for optimizations in which a CRP search is performed for the first cycle and the Haling depletion is used for the remaining cycles was found to increase CPU utilization by 33%. Starting the CRP search with the CRP determined for the previous solution was found to be better than starting the CRP search with all of the rods fully withdrawn. Using the CRP search in an optimization was slow and produced inferior results compared to using the Haling depletion, indicating the need for more work in this area

Bayesian Decision Trees Inspired from Evolutionary Algorithms

Bayesian Decision Trees (DTs) are generally considered a more advanced and accurate model than a regular Decision Tree (DT) because they can handle complex and uncertain data. Existing work on Bayesian DTs uses Markov Chain Monte Carlo (MCMC) with an accept-reject mechanism and sample using naive proposals to proceed to the next iteration, which can be slow because of the burn-in time needed. We can reduce the burn-in period by proposing a more sophisticated way of sampling or by designing a different numerical Bayesian approach. In this paper, we propose a replacement of the MCMC with an inherently parallel algorithm, the Sequential Monte Carlo (SMC), and a more effective sampling strategy inspired by the Evolutionary Algorithms (EA). Experiments show that SMC combined with the EA can produce more accurate results compared to MCMC in 100 times fewer iterations.Comment: arXiv admin note: text overlap with arXiv:2301.0909