The Computational Complexity of Genetic Diversity

A key question in biological systems is whether genetic diversity persists in the long run under evolutionary competition, or whether a single dominant genotype emerges. Classic work by [Kalmus, J. og Genetics, 1945] has established that even in simple diploid species (species with chromosome pairs) diversity can be guaranteed as long as the heterozygous (having different alleles for a gene on two chromosomes) individuals enjoy a selective advantage. Despite the classic nature of the problem, as we move towards increasingly polymorphic traits (e.g., human blood types) predicting diversity (and its implications) is still not fully understood. Our key contribution is to establish complexity theoretic hardness results implying that even in the textbook case of single locus (gene) diploid models, predicting whether diversity survives or not given its fitness landscape is algorithmically intractable. Our hardness results are structurally robust along several dimensions, e.g., choice of parameter distribution, different definitions of stability/persistence, restriction to typical subclasses of fitness landscapes. Technically, our results exploit connections between game theory, nonlinear dynamical systems, and complexity theory and establish hardness results for predicting the evolution of a deterministic variant of the well known multiplicative weights update algorithm in symmetric coordination games; finding one Nash equilibrium is easy in these games. In the process we characterize stable fixed points of these dynamics using the notions of Nash equilibrium and negative semidefiniteness. This as well as hardness results for decision problems in coordination games may be of independent interest. Finally, we complement our results by establishing that under randomly chosen fitness landscapes diversity survives with significant probability. The full version of this paper is available at http://arxiv.org/abs/1411.6322

Evolutionary Metadynamics: a Novel Method to Predict Crystal Structures

A novel method for crystal structure prediction, based on metadynamics and evolutionary algorithms, is presented here. This technique can be used to produce efficiently both the ground state and metastable states easily reachable from a reasonable initial structure. We use the cell shape as collective variable and evolutionary variation operators developed in the context of the USPEX method [Oganov, Glass, \textit{J. Chem. Phys.}, 2006, \textbf{124}, 244704; Lyakhov \textit{et al., Comp. Phys. Comm.}, 2010, \textbf{181}, 1623; Oganov \textit{et al., Acc. Chem. Res.}, 2011, \textbf{44}, 227] to equilibrate the system as a function of the collective variables. We illustrate how this approach helps one to find stable and metastable states for Al$_2$SiO$_5$, SiO$_2$, MgSiO$_3$, and carbon. Apart from predicting crystal structures, the new method can also provide insight into mechanisms of phase transitions.Comment: 7 pages, 7 figures; CrystEngComm 2012, The Royal Society of Chemistr

Classification hardness for supervised learners on 20 years of intrusion detection data

This article consolidates analysis of established (NSL-KDD) and new intrusion detection datasets (ISCXIDS2012, CICIDS2017, CICIDS2018) through the use of supervised machine learning (ML) algorithms. The uniformity in analysis procedure opens up the option to compare the obtained results. It also provides a stronger foundation for the conclusions about the efficacy of supervised learners on the main classification task in network security. This research is motivated in part to address the lack of adoption of these modern datasets. Starting with a broad scope that includes classification by algorithms from different families on both established and new datasets has been done to expand the existing foundation and reveal the most opportune avenues for further inquiry. After obtaining baseline results, the classification task was increased in difficulty, by reducing the available data to learn from, both horizontally and vertically. The data reduction has been included as a stress-test to verify if the very high baseline results hold up under increasingly harsh constraints. Ultimately, this work contains the most comprehensive set of results on the topic of intrusion detection through supervised machine learning. Researchers working on algorithmic improvements can compare their results to this collection, knowing that all results reported here were gathered through a uniform framework. This work's main contributions are the outstanding classification results on the current state of the art datasets for intrusion detection and the conclusion that these methods show remarkable resilience in classification performance even when aggressively reducing the amount of data to learn from

Existence of Evolutionarily Stable Strategies Remains Hard to Decide for a Wide Range of Payoff Values

The concept of an evolutionarily stable strategy (ESS), introduced by Smith and Price, is a refinement of Nash equilibrium in 2-player symmetric games in order to explain counter-intuitive natural phenomena, whose existence is not guaranteed in every game. The problem of deciding whether a game possesses an ESS has been shown to be $\Sigma_{2}^{P}$-complete by Conitzer using the preceding important work by Etessami and Lochbihler. The latter, among other results, proved that deciding the existence of ESS is both NP-hard and coNP-hard. In this paper we introduce a "reduction robustness" notion and we show that deciding the existence of an ESS remains coNP-hard for a wide range of games even if we arbitrarily perturb within some intervals the payoff values of the game under consideration. In contrast, ESS exist almost surely for large games with random and independent payoffs chosen from the same distribution.Comment: 24 pages, 4 figure