This note introduces Bute-Plus, an exact solver for the treedepth problem. The core of the solver is a positive-instance driven dynamic program that constructs an elimination tree of minimum depth in a bottom-up fashion. Three features greatly improve the algorithm's run time. The first of these is a specialised trie data structure. The second is a domination rule. The third is a heuristic presolve step can quickly find a treedepth decomposition of optimal depth for many instances.

This paper introduces Tweed-Plus, a heuristic solver for the treedepth problem. The solver uses two well-known algorithms to create an initial elimination tree: nested dissection (making use of the Metis library) and the minimum-degree heuristic. After creating an elimination tree of the entire input graph, the solver continues to apply nested dissection and the minimum-degree heuristic to parts of the graph with the aim of replacing subtrees of the elimination tree with alternatives of lower depth.

We present a novel algorithm for the minimum-depth elimination tree problem, which is equivalent to the optimal treedepth decomposition problem. Our algorithm makes use of two cheaply-computed lower bound functions to prune the search tree, along with symmetry-breaking and domination rules. We present an empirical study showing that the algorithm outperforms the current state-of-the-art solver (which is based on a SAT encoding) by orders of magnitude on a range of graph classes.

The subgraph isomorphism problem involves deciding whether a copy of a pattern graph occurs inside a larger target graph. The non-induced version allows extra edges in the target, whilst the induced version does not. Although both variants are NP-complete, algorithms inspired by constraint programming can operate comfortably on many real-world problem instances with thousands of vertices. However, they cannot handle arbitrary instances of this size. We show how to generate "really hard" random instances for subgraph isomorphism problems, which are computationally challenging with a couple of hundred vertices in the target, and only twenty pattern vertices. For the non-induced version of the problem, these instances lie on a satisfiable / unsatisfiable phase transition, whose location we can predict; for the induced variant, much richer behaviour is observed, and constrainedness gives a better measure of difficulty than does proximity to a phase transition. These results have practical consequences: we explain why the widely researched "filter / verify" indexing technique used in graph databases is founded upon a misunderstanding of the empirical hardness of NP-complete problems, and cannot be beneficial when paired with any reasonable subgraph isomorphism algorithm.

We introduce a new branch and bound algorithm for the maximum common subgraph and maximum common connected subgraph problems which is based around vertex labelling and partitioning. Our method in some ways resembles a traditional constraint programming approach, but uses a novel compact domain store and supporting inference algorithms which dramatically reduce the memory and computation requirements during search, and allow better dual viewpoint ordering heuristics to be calculated cheaply. Experiments show a speedup of more than an order of magnitude over the state of the art, and demonstrate that we can operate on much larger graphs without running out of memory.

A kidney exchange is an organized barter market where patients in need of a kidney swap willing but incompatible donors. Determining an optimal set of exchanges is theoretically and empirically hard. Traditionally, exchanges took place in cycles, with each participating patient-donor pair both giving and receiving a kidney. The recent introduction of chains, where a donor without a paired patient triggers a sequence of donations without requiring a kidney in return, increased the efficacy of fielded kidney exchanges---while also dramatically raising the empirical computational hardness of clearing the market in practice. While chains can be quite long, unbounded-length chains are not desirable: planned donations can fail before transplant for a variety of reasons, and the failure of a single donation causes the rest of that chain to fail, so parallel shorter chains are better in practice.