Maximum common subgraph isomorphism algorithms for the matching of chemical structures

The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks

Large induced subgraphs via triangulations and CMSO

We obtain an algorithmic meta-theorem for the following optimization problem. Let \phi\ be a Counting Monadic Second Order Logic (CMSO) formula and t be an integer. For a given graph G, the task is to maximize |X| subject to the following: there is a set of vertices F of G, containing X, such that the subgraph G[F] induced by F is of treewidth at most t, and structure (G[F],X) models \phi. Some special cases of this optimization problem are the following generic examples. Each of these cases contains various problems as a special subcase: 1) "Maximum induced subgraph with at most l copies of cycles of length 0 modulo m", where for fixed nonnegative integers m and l, the task is to find a maximum induced subgraph of a given graph with at most l vertex-disjoint cycles of length 0 modulo m. 2) "Minimum \Gamma-deletion", where for a fixed finite set of graphs \Gamma\ containing a planar graph, the task is to find a maximum induced subgraph of a given graph containing no graph from \Gamma\ as a minor. 3) "Independent \Pi-packing", where for a fixed finite set of connected graphs \Pi, the task is to find an induced subgraph G[F] of a given graph G with the maximum number of connected components, such that each connected component of G[F] is isomorphic to some graph from \Pi. We give an algorithm solving the optimization problem on an n-vertex graph G in time O(#pmc n^{t+4} f(t,\phi)), where #pmc is the number of all potential maximal cliques in G and f is a function depending of t and \phi\ only. We also show how a similar running time can be obtained for the weighted version of the problem. Pipelined with known bounds on the number of potential maximal cliques, we deduce that our optimization problem can be solved in time O(1.7347^n) for arbitrary graphs, and in polynomial time for graph classes with polynomial number of minimal separators

Finding Induced Subgraphs via Minimal Triangulations

Potential maximal cliques and minimal separators are combinatorial objects which were introduced and studied in the realm of minimal triangulations problems including Minimum Fill-in and Treewidth. We discover unexpected applications of these notions to the field of moderate exponential algorithms. In particular, we show that given an n-vertex graph G together with its set of potential maximal cliques Pi_G, and an integer t, it is possible in time |Pi_G| * n^(O(t)) to find a maximum induced subgraph of treewidth t in G; and for a given graph F of treewidth t, to decide if G contains an induced subgraph isomorphic to F. Combined with an improved algorithm enumerating all potential maximal cliques in time O(1.734601^n), this yields that both problems are solvable in time 1.734601^n * n^(O(t)).Comment: 14 page

From Gap-ETH to FPT-Inapproximability: Clique, Dominating Set, and More

We consider questions that arise from the intersection between the areas of polynomial-time approximation algorithms, subexponential-time algorithms, and fixed-parameter tractable algorithms. The questions, which have been asked several times (e.g., [Marx08, FGMS12, DF13]), are whether there is a non-trivial FPT-approximation algorithm for the Maximum Clique (Clique) and Minimum Dominating Set (DomSet) problems parameterized by the size of the optimal solution. In particular, letting $\text{OPT}$ be the optimum and $N$ be the size of the input, is there an algorithm that runs in $t(\text{OPT})\text{poly}(N)$ time and outputs a solution of size $f(\text{OPT})$, for any functions $t$ and $f$ that are independent of $N$ (for Clique, we want $f(\text{OPT})=\omega(1)$)? In this paper, we show that both Clique and DomSet admit no non-trivial FPT-approximation algorithm, i.e., there is no $o(\text{OPT})$-FPT-approximation algorithm for Clique and no $f(\text{OPT})$-FPT-approximation algorithm for DomSet, for any function $f$ (e.g., this holds even if $f$ is the Ackermann function). In fact, our results imply something even stronger: The best way to solve Clique and DomSet, even approximately, is to essentially enumerate all possibilities. Our results hold under the Gap Exponential Time Hypothesis (Gap-ETH) [Dinur16, MR16], which states that no $2^{o(n)}$-time algorithm can distinguish between a satisfiable 3SAT formula and one which is not even $(1 - \epsilon)$-satisfiable for some constant $\epsilon > 0$. Besides Clique and DomSet, we also rule out non-trivial FPT-approximation for Maximum Balanced Biclique, Maximum Subgraphs with Hereditary Properties, and Maximum Induced Matching in bipartite graphs. Additionally, we rule out $k^{o(1)}$-FPT-approximation algorithm for Densest $k$-Subgraph although this ratio does not yet match the trivial $O(k)$-approximation algorithm.Comment: 43 pages. To appear in FOCS'1