Evolving cellular automata schemes for protein folding modeling using the Rosetta atomic representation

Protein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.

Genetic programming for iterative numerical methods

We introduce GPLS (Genetic Programming for Linear Systems) as a GP system that finds mathematical expressions defining an iteration matrix. Stationary iterative methods use this iteration matrix to solve a system of linear equations numerically. GPLS aims at finding iteration matrices with a low spectral radius and a high sparsity, since these properties ensure a fast error reduction of the numerical solution method and enable the efficient implementation of the methods on parallel computer architectures. We study GPLS for various types of system matrices and find that it easily outperforms classical approaches like the Gauss–Seidel and Jacobi methods. GPLS not only finds iteration matrices for linear systems with a much lower spectral radius, but also iteration matrices for problems where classical approaches fail. Additionally, solutions found by GPLS for small problem instances show also good performance for larger instances of the same problem.

Blood glucose prediction using multi-objective grammatical evolution: analysis of the “agnostic” and “what-if” scenarios

In this paper we investigate the benefits of applying a multi-objective approach for solving a symbolic regression problem by means of Grammatical Evolution. In particular, we extend previous work, obtaining mathematical expressions to model glucose levels in the blood of diabetic patients. Here we use a multi-objective Grammatical Evolution approach based on the NSGA-II algorithm, considering the root-mean-square error and an ad-hoc fitness function as objectives. This ad-hoc function is based on the Clarke Error Grid analysis, which is useful for showing the potential danger of mispredictions in diabetic patients. In this work, we use two datasets to analyse two different scenarios: What-if and Agnostic, the most common in daily clinical practice. In the What-if scenario, where future events are evaluated, results show that the multi-objective approach improves previous results in terms of Clarke Error Grid analysis by reducing the number of dangerous mispredictions. In the Agnostic situation, with no available information about future events, results suggest that we can obtain good predictions with only information from the previous hour for both Grammatical Evolution and Multi-Objective Grammatical Evolution.

Generating networks of genetic processors

The Networks of Genetic Processors (NGPs) are non-conventional models of computation based on genetic operations over strings, namely mutation and crossover operations as it was established in genetic algorithms. Initially, they have been proposed as acceptor machines which are decision problem solvers. In that case, it has been shown that they are universal computing models equivalent to Turing machines. In this work, we propose NGPs as enumeration devices and we analyze their computational power. First, we define the model and we propose its definition as parallel genetic algorithms. Once the correspondence between the two formalisms has been established, we carry out a study of the generation capacity of the NGPs under the research framework of the theory of formal languages. We investigate the relationships between the number of processors of the model and its generative power. Our results show that the number of processors is important to increase the generative capability of the model up to an upper bound, and that NGPs are universal models of computation if they are formulated as generation devices. This allows us to affirm that parallel genetic algorithms working under certain restrictions can be considered equivalent to Turing machines and, therefore, they are universal models of computation.

Evolving continuous optimisers from scratch

This work uses genetic programming to explore the space of continuous optimisers, with the goal of discovering novel ways of doing optimisation. In order to keep the search space broad, the optimisers are evolved from scratch using Push, a Turing-complete, general-purpose, language. The resulting optimisers are found to be diverse, and explore their optimisation landscapes using a variety of interesting, and sometimes unusual, strategies. Significantly, when applied to problems that were not seen during training, many of the evolved optimisers generalise well, and often outperform existing optimisers. This supports the idea that novel and effective forms of optimisation can be discovered in an automated manner. This paper also shows that pools of evolved optimisers can be hybridised to further increase their generality, leading to optimisers that perform robustly over a broad variety of problem types and sizes.