Bridging Elementary Landscapes and a Geometric Theory of Evolutionary Algorithms: First Steps

This is the author accepted manuscript. The final version is available from Springer via the DOI in this record.Paper to be presented at the Fifteenth International Conference on Parallel Problem Solving from Nature (PPSN XV), Coimbra, Portugal on 8-12 September.Based on a geometric theory of evolutionary algorithms, it was shown that all evolutionary algorithms equipped with a geometric crossover and no mutation operator do the same kind of convex search across representations, and that they are well matched with generalised forms of concave fitness landscapes for which they provably find the optimum in polynomial time. Analysing the landscape structure is essential to understand the relationship between problems and evolutionary algorithms. This paper continues such investigations by considering the following challenge: develop an analytical method to recognise that the fitness landscape for a given problem provably belongs to a class of concave fitness landscapes. Elementary landscapes theory provides analytic algebraic means to study the landscapes structure. This work begins linking both theories to better understand how such method could be devised using elementary landscapes. Examples on well known One Max, Leading Ones, Not-All-Equal Satisfiability and Weight Partitioning problems illustrate the fundamental concepts supporting this approach

A Unifying View on Recombination Spaces and Abstract Convex Evolutionary Search

This is the author accepted manuscript. The final version is available from Springer via the DOI in this record.Proceedings of EvoCOP 2019 - 19th European Conference on Evolutionary Computation, 24-26 April 2019, Leipzig, GermanyPrevious work proposed to unify an algebraic theory of fitness landscapes and a geometric framework of evolutionary algorithms (EAs). One of the main goals behind this unification is to develop an analytical method that verifies if a problem's landscape belongs to certain abstract convex landscapes classes, where certain recombination-based EAs (without mutation) have polynomial runtime performance. This paper advances such unification by showing that: (a) crossovers can be formally classified according to geometric or algebraic axiomatic properties; and (b) the population behaviour induced by certain crossovers in recombination-based EAs can be formalised in the geometric and algebraic theories. These results make a significant contribution to the basis of an integrated geometric-algebraic framework with which analyse recombination spaces and recombination-based EAs

Best match graphs

Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let T be a phylogenetic (gene) tree T and σ an assignment of leaves of T to species. The best match graph (G,σ) is a digraph that contains an arc from x to y if the genes x and y reside in different species and y is one of possibly many (evolutionary) closest relatives of x compared to all other genes contained in the species σ(y). Here, we characterize best match graphs and show that it can be decided in cubic time and quadratic space whether (G,σ) derived from a tree in this manner. If the answer is affirmative, there is a unique least resolved tree that explains (G,σ), which can also be constructed in cubic time

From pairs of most similar sequences to phylogenetic best matches

Background Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This approximation of best matches by best hits becomes exact for ultrametric dissimilarities, i.e., under the Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level of noise into the input data for best-hit-based orthology detection methods. Results If additive distances between genes are known, then evolutionary most closely related pairs can be identified by considering certain quartets of genes provided that in each quartet the outgroup relative to the remaining three genes is known. A priori knowledge of underlying species phylogeny greatly facilitates the identification of the required outgroup. Although the workflow remains a heuristic since the correct outgroup cannot be determined reliably in all cases, simulations with lineage specific biases and rate asymmetries show that nearly perfect results can be achieved. In a realistic setting, where distances data have to be estimated from sequence data and hence are noisy, it is still possible to obtain highly accurate sets of best matches. Conclusion Improvements of tree-free orthology assessment methods can be expected from a combination of the accurate inference of best matches reported here and recent mathematical advances in the understanding of (reciprocal) best match graphs and orthology relations. Availability Accompanying software is available at https://github.com/david-schaller/AsymmeTree

Evolutionary Games with Affine Fitness Functions: Applications to Cancer

We analyze the dynamics of evolutionary games in which fitness is defined as an affine function of the expected payoff and a constant contribution. The resulting inhomogeneous replicator equation has an homogeneous equivalent with modified payoffs. The affine terms also influence the stochastic dynamics of a two-strategy Moran model of a finite population. We then apply the affine fitness function in a model for tumor-normal cell interactions to determine which are the most successful tumor strategies. In order to analyze the dynamics of concurrent strategies within a tumor population, we extend the model to a three-strategy game involving distinct tumor cell types as well as normal cells. In this model, interaction with normal cells, in combination with an increased constant fitness, is the most effective way of establishing a population of tumor cells in normal tissue.Comment: The final publication is available at http://www.springerlink.com, http://dx.doi.org/10.1007/s13235-011-0029-

Understanding Phase Transitions with Local Optima Networks: Number Partitioning as a Case Study

Phase transitions play an important role in understanding search difficulty in combinatorial optimisation. However, previous attempts have not revealed a clear link between fitness landscape properties and the phase transition. We explore whether the global landscape structure of the number partitioning problem changes with the phase transition. Using the local optima network model, we analyse a number of instances before, during, and after the phase transition. We compute relevant network and neutrality metrics; and importantly, identify and visualise the funnel structure with an approach (monotonic sequences) inspired by theoretical chemistry. While most metrics remain oblivious to the phase transition, our results reveal that the funnel structure clearly changes. Easy instances feature a single or a small number of dominant funnels leading to global optima; hard instances have a large number of suboptimal funnels attracting the search. Our study brings new insights and tools to the study of phase transitions in combinatorial optimisation

On RAF Sets and Autocatalytic Cycles in Random Reaction Networks

The emergence of autocatalytic sets of molecules seems to have played an important role in the origin of life context. Although the possibility to reproduce this emergence in laboratory has received considerable attention, this is still far from being achieved. In order to unravel some key properties enabling the emergence of structures potentially able to sustain their own existence and growth, in this work we investigate the probability to observe them in ensembles of random catalytic reaction networks characterized by different structural properties. From the point of view of network topology, an autocatalytic set have been defined either in term of strongly connected components (SCCs) or as reflexively autocatalytic and food-generated sets (RAFs). We observe that the average level of catalysis differently affects the probability to observe a SCC or a RAF, highlighting the existence of a region where the former can be observed, whereas the latter cannot. This parameter also affects the composition of the RAF, which can be further characterized into linear structures, autocatalysis or SCCs. Interestingly, we show that the different network topology (uniform as opposed to power-law catalysis systems) does not have a significantly divergent impact on SCCs and RAFs appearance, whereas the proportion between cleavages and condensations seems instead to play a role. A major factor that limits the probability of RAF appearance and that may explain some of the difficulties encountered in laboratory seems to be the presence of molecules which can accumulate without being substrate or catalyst of any reaction.Comment: pp 113-12

Fitness Landscape Analysis of Automated Machine Learning Search Spaces

The field of Automated Machine Learning (AutoML) has as its main goal to automate the process of creating complete Machine Learning (ML) pipelines to any dataset without requiring deep user expertise in ML. Several AutoML methods have been proposed so far, but there is not a single one that really stands out. Furthermore, there is a lack of studies on the characteristics of the fitness landscape of AutoML search spaces. Such analysis may help to understand the performance of different optimization methods for AutoML and how to improve them. This paper adapts classic fitness landscape analysis measures to the context of AutoML. This is a challenging task, as AutoML search spaces include discrete, continuous, categorical and conditional hyperparameters. We propose an ML pipeline representation, a neighborhood definition and a distance metric between pipelines, and use them in the evaluation of the fitness distance correlation (FDC) and the neutrality ratio for a given AutoML search space. Results of FDC are counter-intuitive and require a more in-depth analysis of a range of search spaces. Results of neutrality, in turn, show a strong positive correlation between the mean neutrality ratio and the fitness value