Adaptive Memetic Particle Swarm Optimization with Variable Local Search Pool Size

We propose an adaptive Memetic Particle Swarm Optimization algorithm where local search is selected from a pool of different algorithms. The choice of local search is based on a probabilistic strategy that uses a simple metric to score the efficiency of local search. Our study investigates whether the pool size affects the memetic algorithm’s performance, as well as the possible benefit of using the adaptive strategy against a baseline static one. For this purpose, we employed the memetic algorithms framework provided in the recent MEMPSODE optimization software, and tested the proposed algorithms on the Benchmarking Black Box Optimization (BBOB 2012) test suite. The obtained results lead to a series of useful conclusions

More green and less blue water in the Alps during warmer summers

Climate change can reduce surface-water supply by enhancing evapotranspiration in forested mountains, especially during heatwaves. We investigate this ‘drought paradox’ for the European Alps using a 1,212-station database and hyper-resolution ecohydrological simulations to quantify blue (runoff) and green (evapotranspiration) water fluxes. During the 2003 heatwave, evapotranspiration in large areas over the Alps was above average despite low precipitation, amplifying the runoff deficit by 32% in the most runoff-productive areas (1,300–3,000 m above sea level). A 3 °C air temperature increase could enhance annual evapotranspiration by up to 100 mm (45 mm on average), which would reduce annual runoff at a rate similar to a 3% precipitation decrease. This suggests that green-water feedbacks—which are often poorly represented in large-scale model simulations—pose an additional threat to water resources, especially in dry summers. Despite uncertainty in the validation of the hyper-resolution ecohydrological modelling with observations, this approach permits more realistic predictions of mountain region water availability

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome’s role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics

Dynamically polarizable force fields for surface simulations via multi-output classification neural networks

Arxiv version submitted.We present a general procedure to introduce electronic polarization into classical Molecular Dynamics (MD) force fields using a Neural Network (NN) model. We apply this framework to the simulation of a solid-liquid interface where the polarization of the surface is essential to correctly capture the main features of the system. By introducing a multi-input, multi-output NN and treating the surface polarization as a discrete classification problem, we are able to obtain very good accuracy in terms of quality of predictions. Through the definition of a custom loss function we are able to impose a physically motivated constraint within the NN itself making this model extremely versatile, especially in the modeling of different surface charge states. The NN is validated considering the redistribution of electronic charge density within a graphene based electrode in contact with an aqueous electrolyte solution, a system highly relevant to the development of next generation low-cost supercapacitors. We compare the performances of our NN/MD model against Quantum Mechanics/Molecular Dynamics simulations where we obtain a most satisfactory agreement

Exploiting task-based parallelism in Bayesian Uncertainty Quantification

We introduce a task-parallel framework for non-intrusive Bayesian Uncertainty Quantification and Propagation of complex and computationally demanding physical models on massively parallel computing architectures. The framework incorporates Laplace asymptotic approximations and stochastic algorithms along with distributed numerical differentiation. Sampling is based on the Transitional Markov Chain Monte Carlo algorithm and its variants while the optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy. Exploitation of task-based parallelism is based on a platform-agnostic adaptive load balancing library that orchestrates scheduling of multiple physical model evaluations on computing platforms that range from multicore systems to hybrid GPU clusters. Experimental results using representative applications demonstrate the flexibility and excellent scalability of the proposed framework. © Springer-Verlag Berlin Heidelberg 2015

Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations

The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The LJ potential models atomistic attraction and repulsion with century old prescribed parameters (q = 6, p = 12, respectively), originally related by a factor of two for simplicity of calculations. We propose the inference of the repulsion exponent through Hierarchical Bayesian uncertainty quantification We use experimental data of the radial distribution function and dimer interaction energies from quantum mechanics simulations. We find that the repulsion exponent p ≈ 6.5 provides an excellent fit for the experimental data of liquid argon, for a range of thermodynamic conditions, as well as for saturated argon vapour. Calibration using the quantum simulation data did not provide a good fit in these cases. However, values p ≈ 12.7 obtained by dimer quantum simulations are preferred for the argon gas while lower values are promoted by experimental data. These results show that the proposed LJ 6-p potential applies to a wider range of thermodynamic conditions, than the classical LJ 6-12 potential. We suggest that calibration of the repulsive exponent in the LJ potential widens the range of applicability and accuracy of MD simulations. © 2017 The Author(s)

Approximate Bayesian computation for granular and molecular dynamics simulations

The effective integration of models with data through Bayesian uncertainty quantification hinges on the formulation of a suitable likelihood function. In many cases such a likelihood may not be readily available or it may be difficult to compute. The Approximate Bayesian Computation (ABC) proposes the formulation of a likelihood function through the comparison between low dimensional summary statistics of the model predictions and corresponding statistics on the data. In this work we report a computationally efficient approach to the Bayesian updating of Molecular Dynamics (MD) models through ABC using a variant of the Subset Simulation method. We demonstrate that ABC can also be used for Bayesian updating of models with an explicitly defined likelihood function, and compare ABCSubSim implementation and effciency with the transitional Markov chain Monte Carlo (TMCMC). ABC-SubSim is then used in force-field identification of MD simulations. Furthermore, we examine the concept of relative entropy minimization for the calibration of force fields and exploit it within ABC. Using different approximate posterior formulations, we showcase that assuming Gaussian ensemble uctuations of molecular systems quantities of interest can potentially lead to erroneous parameter identification. © 2016 ACM