When controllers (brains) and morphologies (bodies) of robots simultaneously evolve, this can lead to a problem, namely the brain & body mismatch problem. In this research, we propose a solution of lifetime learning. We set up a system where modular
robots can create offspring that inherit the bodies of parents by recombination and mutation. With regards to the brains of the offspring, we use two methods to create them. The first one entails solely evolution which means the brain of a robot child is inherited from its parents. The second approach is evolution plus learning which means the brain of a child is inherited as well, but additionally is developed by a learning algorithm - RevDEknn. We compare these two methods by running experiments in a simulator called Revolve and use efficiency, efficacy, and the morphology intelligence of the robots for the comparison. The experiments show that the evolution plus learning method does not only lead to a higher fitness level, but also to more morphologically evolving robots. This constitutes a quantitative demonstration that changes in the brain can induce changes in the body, leading to the concept of morphological intelligence, which is quantified by the learning delta, meaning the ability of a morphology to facilitate learning.
Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production and consum
ption for the individual species. The ordinary differential equations that describe rates of the reactions in the model include a set of parameters. The parameters are important quantities to understand and analyze biological systems. Moreover, the perturbation of the kinetic parameters are correlated with upregulation of the system by cell-intrinsic and cell-extrinsic factors, including mutations and the environment changes. Here, we aim at using well-established models of biological pathways to identify parameter values and point their potential perturbation/deviation. We present our population-based optimization framework that is able to identify kinetic parameters in the dynamic model based on only input and output data (i.e., timecourses of selected metabolites). Our approach can deal with the identification of the non-measurable parameters as well as with discovering deviation of the parameters. We present our proposed optimization framework on the example of the well-studied glycolytic pathway in Saccharomyces cerevisiae.
Not all generate-and-test search algorithms are created equal. Bayesian Optimization (BO) invests a lot of computation time to generate the candidate solution that best balances the predicted value and the uncertainty given all previous data, taking
increasingly more time as the number of evaluations performed grows. Evolutionary Algorithms (EA) on the other hand rely on search heuristics that typically do not depend on all previous data and can be done in constant time. Both the BO and EA community typically assess their performance as a function of the number of evaluations. However, this is unfair once we start to compare the efficiency of these classes of algorithms, as the overhead times to generate candidate solutions are significantly different. We suggest to measure the efficiency of generate-and-test search algorithms as the expected gain in the objective value per unit of computation time spent. We observe that the preference of an algorithm to be used can change after a number of function evaluations. We therefore propose a new algorithm, a combination of Bayesian optimization and an Evolutionary Algorithm, BEA for short, that starts with BO, then transfers knowledge to an EA, and subsequently runs the EA. We compare the BEA with BO and the EA. The results show that BEA outperforms both BO and the EA in terms of time efficiency, and ultimately leads to better performance on well-known benchmark objective functions with many local optima. Moreover, we test the three algorithms on nine test cases of robot learning problems and here again we find that BEA outperforms the other algorithms.
Differential evolution (DE) is a well-known type of evolutionary algorithms (EA). Similarly to other EA variants it can suffer from small populations and loose diversity too quickly. This paper presents a new approach to mitigate this issue: We propo
se to generate new candidate solutions by utilizing reversible linear transformation applied to a triplet of solutions from the population. In other words, the population is enlarged by using newly generated individuals without evaluating their fitness. We assess our methods on three problems: (i) benchmark function optimization, (ii) discovering parameter values of the gene repressilator system, (iii) learning neural networks. The empirical results indicate that the proposed approach outperforms vanilla DE and a version of DE with applying differential mutation three times on all testbeds.
