Combinatorial optimization problems implicitly define fitness landscapes that combine the numeric structure of the 'fitness' function to be maximized with the combinatorial structure of which assignments are 'adjacent'. Local search starts at an assignment in this landscape and successively moves assignments until no further improvement is possible among the adjacent assignments. Classic analyses of local search algorithms have focused more on the question of effectiveness ("did we find a good solution?") and often implicitly assumed that there are no doubts about their efficiency ("did we find it quickly?"). But there are many reasons to doubt the efficiency of local search. Even if we focus on fitness landscapes on the hypercube that are single peaked on every subcube (i.e., semismooth fitness landscapes) where effectiveness is obvious, many local search algorithms are known to be inefficient. Since fitness landscapes are unwieldy exponentially large objects, we focus on their polynomial-sized representations by instances of valued constraint satisfaction problems (VCSP). We define a "direction" for valued constraints such that directed VCSPs generate semismooth fitness landscapes. We call VCSPs oriented if they do not have any pair of variables with arcs in both directions. Since recognizing if a VCSP-instance is directed or oriented is coNP-complete, we generalized oriented VCSPs as conditionally-smooth fitness landscapes that are recognizable in polynomial time for a VCSP-instance. We prove that many popular local search algorithms like random ascent, simulated annealing, history-based rules, jumping rules, and the Kernighan-Lin heuristic are very efficient on conditionally-smooth landscapes. But conditionally-smooth landscapes are still expressive enough so that algorithms like steepest ascent and random facet require a super-polynomial number of steps to find the fitness peak.

Greedy local search is especially popular for solving valued constraint satisfaction problems (VCSPs). Since any method will be slow for some VCSPs, we ask: what is the simplest VCSP on which greedy local search is slow? We construct a VCSP on 6n Boolean variables for which greedy local search takes 7(2ⁿ - 1) steps to find the unique peak. Our VCSP is simple in two ways. First, it is very sparse: its constraint graph has pathwidth 2 and maximum degree 3. This is the simplest VCSP on which some local search could be slow. Second, it is "oriented" – there is an ordering on the variables such that later variables are conditionally-independent of earlier ones. Being oriented allows many non-greedy local search methods to find the unique peak in a quadratic number of steps. Thus, we conclude that - among local search methods - greed is particularly slow.

SUMMARY: Evolutionary game theory describes frequency-dependent selection for fixed, heritable strategies in a population of competing individuals using a payoff matrix. We present a software package to aid in the construction, analysis and visualization of three-strategy matrix games. The IsoMaTrix package computes the isoclines (lines of zero growth) of matrix games, and facilitates direct comparison of well-mixed dynamics to structured populations on a lattice grid. IsoMaTrix computes fixed points, phase flow, trajectories, (sub)velocities and uncertainty quantification for stochastic effects in spatial matrix games. We describe a result obtained via IsoMaTrix's spatial games functionality, which shows that the timing of competitive release in a cancer model (under continuous treatment) critically depends on the initial spatial configuration of the tumor. AVAILABILITY AND IMPLEMENTATION: The code is available at: https://github.com/mathonco/isomatrix. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Local search is widely used to solve combinatorial optimisation problems and to model biological evolution, but the performance of local search algorithms on different kinds of fitness landscapes is poorly understood. Here we introduce a natural approach to modelling fitness landscapes using valued constraints. This allows us to investigate minimal representations (normal forms) and to consider the effects of the structure of the constraint graph on the tractability of local search. First, we show that for fitness landscapes representable by binary Boolean valued constraints there is a minimal necessary constraint graph that can be easily computed. Second, we consider landscapes as equivalent if they allow the same (improving) local search moves; we show that a minimal normal form still exists, but is NP-hard to compute. Next we consider the complexity of local search on fitness landscapes modelled by valued constraints with restricted forms of constraint graph. In the binary Boolean case, we prove that a tree-structured constraint graph gives a tight quadratic bound on the number of improving moves made by any local search; hence, any landscape that can be represented by such a model will be tractable for local search. We build two families of examples to show that both the conditions in our tractability result are essential. With domain size three, even just a path of binary constraints can model a landscape with an exponentially long sequence of improving moves. With a treewidth two constraint graph, even with a maximum degree of three, binary Boolean constraints can model a landscape with an exponentially long sequence of improving moves.