We propose a new method based on discrete Fourier analysis to analyze the time evolutionary algorithms spend on plateaus. This immediately gives a concise proof of the classic estimate of the expected runtime of the $(1+1)$ evolutionary algorithm on the Needle problem due to Garnier, Kallel, and Schoenauer (1999). We also use this method to analyze the runtime of the $(1+1)$ evolutionary algorithm on a new benchmark consisting of $n/\ell$ plateaus of effective size $2^\ell-1$ which have to be optimized sequentially in a LeadingOnes fashion. Using our new method, we determine the precise expected runtime both for static and fitness-dependent mutation rates. We also determine the asymptotically optimal static and fitness-dependent mutation rates. For $\ell = o(n)$, the optimal static mutation rate is approximately $1.59/n$. The optimal fitness dependent mutation rate, when the first $k$ fitness-relevant bits have been found, is asymptotically $1/(k+1)$. These results, so far only proven for the single-instance problem LeadingOnes, thus hold for a much broader class of problems. We expect similar extensions to be true for other important results on LeadingOnes. We are also optimistic that our Fourier analysis approach can be applied to other plateau problems as well.

Prototyping robotic systems is a time consuming process. Computer aided design, however, might speed up the process significantly. Quality-diversity evolutionary approaches optimise for novelty as well as performance, and can be used to generate a repertoire of diverse designs. This design repertoire could be used as a tool to guide a designer and kick-start the rapid prototyping process. This paper explores this idea in the context of mechanical linkage based robots. These robots can be a good test-bed for rapid prototyping, as they can be modified quickly for swift iterations in design. We compare three evolutionary algorithms for optimising 2D mechanical linkages: 1) a standard evolutionary algorithm, 2) the multi-objective algorithm NSGA-II, and 3) the quality-diversity algorithm MAP-Elites. Some of the found linkages are then realized on a physical hexapod robot through a prototyping process, and tested on two different floors. We find that all the tested approaches, except the standard evolutionary algorithm, are capable of finding mechanical linkages that creates a path similar to a specified desired path. However, the quality-diversity approaches that had the length of the linkage as a behaviour descriptor were the most useful when prototyping. This was due to the quality-diversity approaches having a larger variety of similar designs to choose from, and because the search could be constrained by the behaviour descriptors to make linkages that were viable for construction on our hexapod platform.

Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the most suitable data for a specific study, and specifically for validation studies, remains challenging with respect to scale and access. Therefore, in silico genomics sequence generators have been proposed as a possible solution. However, the current generators produce inferior data using mostly shallow (stochastic) connections, detected with limited computational complexity in the training data. This means they do not take the appropriate biological relations and constraints, that originally caused the observed connections, into consideration. To address this issue, we propose cancer-inspired genomics mapper model (CGMM), that combines genetic algorithm (GA) and deep learning (DL) methods to tackle this challenge. CGMM mimics processes that generate genetic variations and mutations to transform readily available control genomes into genomes with the desired phenotypes. We demonstrate that CGMM can generate synthetic genomes of selected phenotypes such as ancestry and cancer that are indistinguishable from real genomes of such phenotypes, based on unsupervised clustering. Our results show that CGMM outperforms four current state-of-the-art genomics generators on two different tasks, suggesting that CGMM will be suitable for a wide range of purposes in genomic medicine, especially for much-needed validation studies.

Designing protein sequences with desired biological function is crucial in biology and chemistry. Recent machine learning methods use a surrogate sequence-function model to replace the expensive wet-lab validation. How can we efficiently generate diverse and novel protein sequences with high fitness? In this paper, we propose IsEM-Pro, an approach to generate protein sequences towards a given fitness criterion. At its core, IsEM-Pro is a latent generative model, augmented by combinatorial structure features from a separately learned Markov random fields (MRFs). We develop an Monte Carlo Expectation-Maximization method (MCEM) to learn the model. During inference, sampling from its latent space enhances diversity while its MRFs features guide the exploration in high fitness regions. Experiments on eight protein sequence design tasks show that our IsEM-Pro outperforms the previous best methods by at least 55% on average fitness score and generates more diverse and novel protein sequences.

Genetic Algorithm (GA) is a popular meta-heuristic evolutionary algorithm that uses stochastic operators to find optimal solution and has proved its effectiveness in solving many complex optimization problems (such as classification, optimization, and scheduling). However, despite its performance, popularity and simplicity, not much attention has been paid towards reproducibility and reusability of GA. In this paper, we have extended Findable, Accessible, Interoperable and Reusable (FAIR) data principles to enable the reproducibility and reusability of algorithms. We have chosen GA as a usecase to the demonstrate the applicability of the proposed principles. Also we have presented an overview of methodological developments and variants of GA that makes it challenging to reproduce or even find the right source. Additionally, to enable FAIR algorithms, we propose a vocabulary (i.e. $evo$) using light weight RDF format, facilitating the reproducibility. Given the stochastic nature of GAs, this work can be extended to numerous Optimization and machine learning algorithms/methods.

A great deal of research has been conducted in the consideration of meta-heuristic optimisation methods that are able to find global optima in settings that gradient based optimisers have traditionally struggled. Of these, so-called particle swarm optimisation (PSO) approaches have proven to be highly effective in a number of application areas. Given the maturity of the PSO field, it is likely that novel variants of the PSO algorithm stand to offer only marginal gains in terms of performance -- there is, after all, no free lunch. Instead of only chasing performance on suites of benchmark optimisation functions, it is argued herein that research effort is better placed in the pursuit of algorithms that also have other useful properties. In this work, a highly-general, interpretable variant of the PSO algorithm -- particle attractor algorithm (PAO) -- is proposed. Furthermore, the algorithm is designed such that the transition densities (describing the motions of the particles from one generation to the next) can be computed exactly in closed form for each step. Access to closed-form transition densities has important ramifications for the closely-related field of Sequential Monte Carlo (SMC). In order to demonstrate that the useful properties do not come at the cost of performance, PAO is compared to several other state-of-the art heuristic optimisation algorithms in a benchmark comparison study.

Diabetes mellitus is a disease that affects to hundreds of millions of people worldwide. Maintaining a good control of the disease is critical to avoid severe long-term complications. In recent years, several artificial pancreas systems have been proposed and developed, which are increasingly advanced. However there is still a lot of research to do. One of the main problems that arises in the (semi) automatic control of diabetes, is to get a model explaining how glycemia (glucose levels in blood) varies with insulin, food intakes and other factors, fitting the characteristics of each individual or patient. This paper proposes the application of evolutionary computation techniques to obtain customized models of patients, unlike most of previous approaches which obtain averaged models. The proposal is based on a kind of genetic programming based on grammars known as Grammatical Evolution (GE). The proposal has been tested with in-silico patient data and results are clearly positive. We present also a study of four different grammars and five objective functions. In the test phase the models characterized the glucose with a mean percentage average error of 13.69\%, modeling well also both hyper and hypoglycemic situations.

The convective heat transfer in a turbulent boundary layer (TBL) on a flat plate is enhanced using an artificial intelligence approach based on linear genetic algorithms control (LGAC). The actuator is a set of six slot jets in crossflow aligned with the freestream. An open-loop optimal periodic forcing is defined by the carrier frequency, the duty cycle and the phase difference between actuators as control parameters. The control laws are optimised with respect to the unperturbed TBL and to the actuation with a steady jet. The cost function includes the wall convective heat transfer rate and the cost of the actuation. The performance of the controller is assessed by infrared thermography and characterised also with particle image velocimetry measurements. The optimal controller yields a slightly asymmetric flow field. The LGAC algorithm converges to the same frequency and duty cycle for all the actuators. It is noted that such frequency is strikingly equal to the inverse of the characteristic travel time of large-scale turbulent structures advected within the near-wall region. The phase difference between multiple jet actuation has shown to be very relevant and the main driver of flow asymmetry. The results pinpoint the potential of machine learning control in unravelling unexplored controllers within the actuation space. Our study furthermore demonstrates the viability of employing sophisticated measurement techniques together with advanced algorithms in an experimental investigation.

Ensoul is a framework proposed for the purpose of creating technologies that create more technologies through the combined use of networks, and nests, of energy homeostatic (enerstatic) loops and open-ended evolutionary techniques. Generative technologies developed by such an approach serve as both simple, yet insightful models of thermodynamically driven complex systems and as powerful sources of novel technologies. "Self Organizing intelligent Ultra Low power Systems" (SOULS) is a term that well describes the technologies produced by such a generative technology, as well as the generative technology itself. The term is meant to capture the abstract nature of such technologies as being independent of the substrate in which they are embedded. In other words, SOULS can be biological, artificial or hybrid in form.

Black-box optimization (BBO) has a broad range of applications, including automatic machine learning, experimental design, and database knob tuning. However, users still face challenges when applying BBO methods to their problems at hand with existing software packages in terms of applicability, performance, and efficiency. This paper presents OpenBox, an open-source BBO toolkit with improved usability. It implements user-friendly inferfaces and visualization for users to define and manage their tasks. The modular design behind OpenBox facilitates its flexible deployment in existing systems. Experimental results demonstrate the effectiveness and efficiency of OpenBox over existing systems. The source code of OpenBox is available at https://github.com/PKU-DAIR/open-box.