Epistasis refers to fitness or functional effects of mutations that depend on the sequence background in which these mutations arise. Epistasis is prevalent in nature, including populations of viruses, bacteria, and cancers, and can contribute to the evolution of drug resistance and immune escape. However, it is difficult to directly estimate epistatic effects from sampled observations of a population. At present, there are very few methods that can disentangle the effects of selection (including epistasis), mutation, recombination, genetic drift, and genetic linkage in evolving populations. Here we develop a method to infer epistasis, along with the fitness effects of individual mutations, from observed evolutionary histories. Simulations show that we can accurately infer pairwise epistatic interactions provided that there is sufficient genetic diversity in the data. Our method also allows us to identify which fitness parameters can be reliably inferred from a particular data set and which ones are unidentifiable. Our approach therefore allows for the inference of more complex models of selection from time series genetic data, while also quantifying uncertainty in the inferred parameters.

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Particle swam optimization (PSO) is a popular stochastic optimization method that has found wide applications in diverse fields. However, PSO suffers from high computational complexity and slow convergence speed. High computational complexity hinders its use in applications that have limited power resources while slow convergence speed makes it unsuitable for time critical applications. In this paper, we propose two techniques to overcome these limitations. The first technique reduces the computational complexity of PSO while the second technique speeds up its convergence. These techniques can be applied, either separately or in conjunction, to any existing PSO variant.The proposed techniques are robust to the number of dimensions of the optimization problem. Simulation results are presented for the proposed techniques applied to the standard PSO as well as to several PSO variants. The results show that the use of both these techniques in conjunction results in a reduction in the number of computations required as well as faster convergence speed while maintaining an acceptable error performance for time-critical applications.