Evolutionary Computation and QSAR Research

[Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P

Multiobjective global surrogate modeling, dealing with the 5-percent problem

When dealing with computationally expensive simulation codes or process measurement data, surrogate modeling methods are firmly established as facilitators for design space exploration, sensitivity analysis, visualization, prototyping and optimization. Typically the model parameter (=hyperparameter) optimization problem as part of global surrogate modeling is formulated in a single objective way. Models are generated according to a single objective (accuracy). However, this requires an engineer to determine a single accuracy target and measure upfront, which is hard to do if the behavior of the response is unknown. Likewise, the different outputs of a multi-output system are typically modeled separately by independent models. Again, a multiobjective approach would benefit the domain expert by giving information about output correlation and enabling automatic model type selection for each output dynamically. With this paper the authors attempt to increase awareness of the subtleties involved and discuss a number of solutions and applications. In particular, we present a multiobjective framework for global surrogate model generation to help tackle both problems and that is applicable in both the static and sequential design (adaptive sampling) case

Application of computational intelligence to explore and analyze system architecture and design alternatives

Systems Engineering involves the development or improvement of a system or process from effective need to a final value-added solution. Rapid advances in technology have led to development of sophisticated and complex sensor-enabled, remote, and highly networked cyber-technical systems. These complex modern systems present several challenges for systems engineers including: increased complexity associated with integration and emergent behavior, multiple and competing design metrics, and an expansive design parameter solution space. This research extends the existing knowledge base on multi-objective system design through the creation of a framework to explore and analyze system design alternatives employing computational intelligence. The first research contribution is a hybrid fuzzy-EA model that facilitates the exploration and analysis of possible SoS configurations. The second contribution is a hybrid neural network-EA in which the EA explores, analyzes, and evolves the neural network architecture and weights. The third contribution is a multi-objective EA that examines potential installation (i.e. system) infrastructure repair strategies. The final contribution is the introduction of a hierarchical multi-objective evolutionary algorithm (MOEA) framework with a feedback mechanism to evolve and simultaneously evaluate competing subsystem and system level performance objectives. Systems architects and engineers can utilize the frameworks and approaches developed in this research to more efficiently explore and analyze complex system design alternatives --Abstract, page iv

Advances in Evolutionary Algorithms

With the recent trends towards massive data sets and significant computational power, combined with evolutionary algorithmic advances evolutionary computation is becoming much more relevant to practice. Aim of the book is to present recent improvements, innovative ideas and concepts in a part of a huge EA field

Social transfer policies and child poverty in European countries: Evaluating policy alternatives through a multiobjective programming model

Child poverty remains a significant concern across Europe and citizens regard policy interventions that effec- tively address this issue to be of utmost importance. In this work, we analyse the potential of social transfer policy alternatives to alleviate child and overall poverty simultaneously in European countries. Using a logistic regression to define the objective functions and constraints, we rely on multiobjective programming to assess key features of national social transfer systems that can minimize child and overall poverty and tend to equal both levels downwards. Taking into account the starting levels of each country, the results underline the importance of finding an adequate combination of pro-child and pro-poor targeting of social transfer policies. For most Eu- ropean countries, an increase in the level of cash benefits for children is advisable – particularly universal benefits – except in Croatia, the Netherlands, and Norway. Nonetheless, in France, Greece, Italy, Ireland, the Netherlands, and Spain, the recommended proportion of GDP allocated to universal cash benefits is lower than the proportion allocated to means-tested benefits. In this regard, our research provides an innovative approach for policymakers to optimize poverty reduction strategies by contributing valuable insights for the design and implementation of effective social transfer policies to combat child and overall poverty in European countries.Funding for open access charge: Universidad de Málaga/CBU

Transparent but Accurate Evolutionary Regression Combining New Linguistic Fuzzy Grammar and a Novel Interpretable Linear Extension

Scientists must understand what machines do (systems should not behave like a black box), because in many cases how they predict is more important than what they predict. In this work, we propose a new extension of the fuzzy linguistic grammar and a mainly novel interpretable linear extension for regression problems, together with an enhanced new linguistic tree-based evolutionary multiobjective learning approach. This allows the general behavior of the data covered, as well as their specific variability, to be expressed as a single rule. In order to ensure the highest transparency and accuracy values, this learning process maximizes two widely accepted semantic metrics and also minimizes both the number of rules and the model mean squared error. The results obtained in 23 regression datasets show the effectiveness of the proposed method by applying statistical tests to the said metrics, which cover the different aspects of the interpretability of linguistic fuzzy models. This learning process has obtained the preservation of high-level semantics and less than 5 rules on average, while it still clearly outperforms some of the previous state-of-the-art linguistic fuzzy regression methods for learning interpretable regression linguistic fuzzy systems, and even to a competitive, pure accuracyoriented linguistic learning approach. Finally, we analyze a case study in a real problem related to childhood obesity, and a real expert carries out the analysis shown.Andalusian Government P18-RT-2248Health Institute Carlos III/Spanish Ministry of Science, Innovation and Universities PI20/00711Spanish Government PID2019-107793GB-I00 PID2020-119478GB-I0

Making the most of data:An information selection and assessment framework to improve water systems operations

Advances in Environmental monitoring systems are making a wide range of data available at increasingly higher temporal and spatial resolution. This creates an opportunity to enhance real-time understanding of water systems conditions and to improve prediction of their future evolution, ultimately increasing our ability to make better decisions. Yet, many water systems are still operated using very simple information systems, typically based on simple statistical analysis and the operator’s experience. In this work, we propose a framework to automatically select the most valuable information to inform water systems operations supported by quantitative metrics to operationally and economically assess the value of this information. The Hoa Binh reservoir in Vietnam is used to demonstrate the proposed framework in a multiobjective context, accounting for hydropower production and flood control. First, we quantify the expected value of perfect information, meaning the potential space for improvement under the assumption of exact knowledge of the future system conditions. Second, we automatically select the most valuable information that could be actually used to improve the Hoa Binh operations. Finally, we assess the economic value of sample information on the basis of the resulting policy performance. Results show that our framework successfully select information to enhance the performance of the operating policies with respect to both the competing objectives, attaining a 40% improvement close to the target trade-off selected as potentially good compromise between hydropower production and flood control

Adaptive algorithms for history matching and uncertainty quantification

Numerical reservoir simulation models are the basis for many decisions in regard to predicting, optimising, and improving production performance of oil and gas reservoirs. History matching is required to calibrate models to the dynamic behaviour of the reservoir, due to the existence of uncertainty in model parameters. Finally a set of history matched models are used for reservoir performance prediction and economic and risk assessment of different development scenarios. Various algorithms are employed to search and sample parameter space in history matching and uncertainty quantification problems. The algorithm choice and implementation, as done through a number of control parameters, have a significant impact on effectiveness and efficiency of the algorithm and thus, the quality of results and the speed of the process. This thesis is concerned with investigation, development, and implementation of improved and adaptive algorithms for reservoir history matching and uncertainty quantification problems. A set of evolutionary algorithms are considered and applied to history matching. The shared characteristic of applied algorithms is adaptation by balancing exploration and exploitation of the search space, which can lead to improved convergence and diversity. This includes the use of estimation of distribution algorithms, which implicitly adapt their search mechanism to the characteristics of the problem. Hybridising them with genetic algorithms, multiobjective sorting algorithms, and real-coded, multi-model and multivariate Gaussian-based models can help these algorithms to adapt even more and improve their performance. Finally diversity measures are used to develop an explicit, adaptive algorithm and control the algorithm’s performance, based on the structure of the problem. Uncertainty quantification in a Bayesian framework can be carried out by resampling of the search space using Markov chain Monte-Carlo sampling algorithms. Common critiques of these are low efficiency and their need for control parameter tuning. A Metropolis-Hastings sampling algorithm with an adaptive multivariate Gaussian proposal distribution and a K-nearest neighbour approximation has been developed and applied

Population-based algorithms for improved history matching and uncertainty quantification of Petroleum reservoirs

In modern field management practices, there are two important steps that shed light on a multimillion dollar investment. The first step is history matching where the simulation model is calibrated to reproduce the historical observations from the field. In this inverse problem, different geological and petrophysical properties may provide equally good history matches. Such diverse models are likely to show different production behaviors in future. This ties the history matching with the second step, uncertainty quantification of predictions. Multiple history matched models are essential for a realistic uncertainty estimate of the future field behavior. These two steps facilitate decision making and have a direct impact on technical and financial performance of oil and gas companies. Population-based optimization algorithms have been recently enjoyed growing popularity for solving engineering problems. Population-based systems work with a group of individuals that cooperate and communicate to accomplish a task that is normally beyond the capabilities of each individual. These individuals are deployed with the aim to solve the problem with maximum efficiency. This thesis introduces the application of two novel population-based algorithms for history matching and uncertainty quantification of petroleum reservoir models. Ant colony optimization and differential evolution algorithms are used to search the space of parameters to find multiple history matched models and, using a Bayesian framework, the posterior probability of the models are evaluated for prediction of reservoir performance. It is demonstrated that by bringing latest developments in computer science such as ant colony, differential evolution and multiobjective optimization, we can improve the history matching and uncertainty quantification frameworks. This thesis provides insights into performance of these algorithms in history matching and prediction and develops an understanding of their tuning parameters. The research also brings a comparative study of these methods with a benchmark technique called Neighbourhood Algorithms. This comparison reveals the superiority of the proposed methodologies in various areas such as computational efficiency and match quality