Inheritance-Based Diversity Measures for Explicit Convergence Control in Evolutionary Algorithms

Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze approaches to diversity that (a) have an explicit and quantifiable influence on fitness at the individual level and (b) require no (or very little) additional domain knowledge such as domain-specific distance functions. We also introduce the concept of genealogical diversity in a broader study. We show that employing these approaches can help evolutionary algorithms for global optimization in many cases.Comment: GECCO '18: Genetic and Evolutionary Computation Conference, 2018, Kyoto, Japa

Highly efficient Bayesian joint inversion for receiver-based data and its application to lithospheric structure beneath the southern Korean Peninsula

With the deployment of extensive seismic arrays, systematic and efficient parameter and uncertainty estimation is of increasing importance and can provide reliable, regional models for crustal and upper-mantle structure.We present an efficient Bayesian method for the joint inversion of surface-wave dispersion and receiver-function data that combines trans-dimensional (trans-D) model selection in an optimization phase with subsequent rigorous parameter uncertainty estimation. Parameter and uncertainty estimation depend strongly on the chosen parametrization such that meaningful regional comparison requires quantitative model selection that can be carried out efficiently at several sites. While significant progress has been made for model selection (e.g. trans-D inference) at individual sites, the lack of efficiency can prohibit application to large data volumes or cause questionable results due to lack of convergence. Studies that address large numbers of data sets have mostly ignored model selection in favour of more efficient/simple estimation techniques (i.e. focusing on uncertainty estimation but employing ad-hoc model choices). Our approach consists of a two-phase inversion that combines trans-D optimization to select the most probable parametrization with subsequent Bayesian sampling for uncertainty estimation given that parametrization. The trans-D optimization is implemented here by replacing the likelihood function with the Bayesian information criterion (BIC). The BIC provides constraints on model complexity that facilitate the search for an optimal parametrization. Parallel tempering (PT) is applied as an optimization algorithm. After optimization, the optimal model choice is identified by the minimum BIC value from all PT chains. Uncertainty estimation is then carried out in fixed dimension. Data errors are estimated as part of the inference problem by a combination of empirical and hierarchical estimation. Data covariance matrices are estimated from data residuals (the difference between prediction and observation) and periodically updated. In addition, a scaling factor for the covariance matrix magnitude is estimated as part of the inversion. The inversion is applied to both simulated and observed data that consist of phase- and group-velocity dispersion curves (Rayleigh wave), and receiver functions. The simulation results show that model complexity and important features are well estimated by the fixed dimensional posterior probability density. Observed data for stations in different tectonic regions of the southern Korean Peninsula are considered. The results are consistent with published results, but important features are better constrained than in previous regularized inversions and are more consistent across the stations. For example, resolution of crustal and Moho interfaces, and absolute values and gradients of velocities in lower crust and upper mantle are better constrained

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Is One Hyperparameter Optimizer Enough?

Hyperparameter tuning is the black art of automatically finding a good combination of control parameters for a data miner. While widely applied in empirical Software Engineering, there has not been much discussion on which hyperparameter tuner is best for software analytics. To address this gap in the literature, this paper applied a range of hyperparameter optimizers (grid search, random search, differential evolution, and Bayesian optimization) to defect prediction problem. Surprisingly, no hyperparameter optimizer was observed to be `best' and, for one of the two evaluation measures studied here (F-measure), hyperparameter optimization, in 50\% cases, was no better than using default configurations. We conclude that hyperparameter optimization is more nuanced than previously believed. While such optimization can certainly lead to large improvements in the performance of classifiers used in software analytics, it remains to be seen which specific optimizers should be applied to a new dataset.Comment: 7 pages, 2 columns, accepted for SWAN1