CLIPPER+: A Fast Maximal Clique Algorithm for Robust Global Registration

We present CLIPPER+, an algorithm for finding maximal cliques in unweighted graphs for outlier-robust global registration. The registration problem can be formulated as a graph and solved by finding its maximum clique. This formulation leads to extreme robustness to outliers; however, finding the maximum clique is an NP-hard problem, and therefore approximation is required in practice for large-size problems. The performance of an approximation algorithm is evaluated by its computational complexity (the lower the runtime, the better) and solution accuracy (how close the solution is to the maximum clique). Accordingly, the main contribution of CLIPPER+ is outperforming the state-of-the-art in accuracy while maintaining a relatively low runtime. CLIPPER+ builds on prior work (CLIPPER [1] and PMC [2]) and prunes the graph by removing vertices that have a small core number and cannot be a part of the maximum clique. This will result in a smaller graph, on which the maximum clique can be estimated considerably faster. We evaluate the performance of CLIPPER+ on standard graph benchmarks, as well as synthetic and real-world point cloud registration problems. These evaluations demonstrate that CLIPPER+ has the highest accuracy and can register point clouds in scenarios where over $99\%$ of associations are outliers. Our code and evaluation benchmarks are released at https://github.com/ariarobotics/clipperp

On maximizing clique, clique-Helly and hereditary clique-Helly induced subgraphs

Clique-Helly and hereditary clique-Helly graphs are polynomial-time recognizable. Recently, we presented a proof that the clique graph recognition problem is NP-complete [L. Alcón, L. Faria, C.M.H. de Figueiredo, M. Gutierrez, Clique graph recognition is NP-complete, in: Proc. WG 2006, in: Lecture Notes in Comput. Sci., vol. 4271, Springer, 2006, pp. 269-277]. In this work, we consider the decision problems: given a graph G = (V, E) and an integer k ≥ 0, we ask whether there exists a subset V ′ ⊆ V with | V ′ | ≥ k such that the induced subgraph G [V ′ ] of G is, variously, a clique, clique-Helly or hereditary clique-Helly graph. The first problem is clearly NP-complete, from the above reference; we prove that the other two decision problems mentioned are NP-complete, even for maximum degree 6 planar graphs. We consider the corresponding maximization problems of finding a maximum induced subgraph that is, respectively, clique, clique-Helly or hereditary clique-Helly. We show that these problems are Max SNP-hard, even for maximum degree 6 graphs. We show a general polynomial-time frac(1, Δ + 1)-approximation algorithm for these problems when restricted to graphs with fixed maximum degree Δ. We generalize these results to other graph classes. We exhibit a polynomial 6-approximation algorithm to minimize the number of vertices to be removed in order to obtain a hereditary clique-Helly subgraph.Facultad de Ciencias Exacta

On maximizing clique, clique-Helly and hereditary clique-Helly induced subgraphs

Clique-Helly and hereditary clique-Helly graphs are polynomial-time recognizable. Recently, we presented a proof that the clique graph recognition problem is NP-complete [L. Alcón, L. Faria, C.M.H. de Figueiredo, M. Gutierrez, Clique graph recognition is NP-complete, in: Proc. WG 2006, in: Lecture Notes in Comput. Sci., vol. 4271, Springer, 2006, pp. 269-277]. In this work, we consider the decision problems: given a graph G = (V, E) and an integer k ≥ 0, we ask whether there exists a subset V ′ ⊆ V with | V ′ | ≥ k such that the induced subgraph G [V ′ ] of G is, variously, a clique, clique-Helly or hereditary clique-Helly graph. The first problem is clearly NP-complete, from the above reference; we prove that the other two decision problems mentioned are NP-complete, even for maximum degree 6 planar graphs. We consider the corresponding maximization problems of finding a maximum induced subgraph that is, respectively, clique, clique-Helly or hereditary clique-Helly. We show that these problems are Max SNP-hard, even for maximum degree 6 graphs. We show a general polynomial-time frac(1, Δ + 1)-approximation algorithm for these problems when restricted to graphs with fixed maximum degree Δ. We generalize these results to other graph classes. We exhibit a polynomial 6-approximation algorithm to minimize the number of vertices to be removed in order to obtain a hereditary clique-Helly subgraph.Facultad de Ciencias Exacta

Solving Maximum Clique Problem for Protein Structure Similarity

A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same ancestor. Computing the similarity between two protein structures is therefore a crucial task and has been extensively investigated. Evaluating the similarity of two proteins can be done by finding an optimal one-to-one matching between their components, which is equivalent to identifying a maximum weighted clique in a specific "alignment graph". In this paper we present a new integer programming formulation for solving such clique problems. The model has been implemented using the ILOG CPLEX Callable Library. In addition, we designed a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST (Vector Alignment Search Tool) - a software for aligning protein 3D structures largely used in NCBI (National Center for Biotechnology Information). The original VAST clique solver uses the well known Bron and Kerbosh algorithm (BK). Our computational results on real life protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK for the largest proteins

A structure theorem for graphs with no cycle with a unique chord and its consequences

We give a structural description of the class C of graphs that do not contain a cycle with a unique chord as an induced subgraph. Our main theorem states that any connected graph in C is a either in some simple basic class or has a decomposition. Basic classes are cliques, bipartite graphs with one side containing only nodes of degree two and induced subgraph of the famous Heawood or Petersen graph. Decompositions are node cutsets consisting of one or two nodes and edge cutsets called 1-joins. Our decomposition theorem actually gives a complete structure theorem for C, i.e. every graph in C can be built from basic graphs that can be explicitly constructed, and gluing them together by prescribed composition operations ; and all graphs built this way are in C. This has several consequences : an O(nm)-time algorithm to decide whether a graph is in C, an O(n+m)-time algorithm that finds a maximum clique of any graph in C and an O(nm)-time coloring algorithm for graphs in C. We prove that every graph in C is either 3-colorable or has a coloring with ω colors where ω is the size of a largest clique. The problem of finding a maximum stable set for a graph in C is known to be NP-hard.Cycle with a unique chord, decomposition, structure, detection, recognition, Heawood graph, Petersen graph, coloring.

Maximum Cliques in Graphs with Small Intersection Number and Random Intersection Graphs

In this paper, we relate the problem of finding a maximum clique to the intersection number of the input graph (i.e. the minimum number of cliques needed to edge cover the graph). In particular, we consider the maximum clique problem for graphs with small intersection number and random intersection graphs (a model in which each one of $m$ labels is chosen independently with probability $p$ by each one of $n$ vertices, and there are edges between any vertices with overlaps in the labels chosen). We first present a simple algorithm which, on input $G$ finds a maximum clique in $O(2^{2^m + O(m)} + n^2 \min\{2^m, n\})$ time steps, where $m$ is an upper bound on the intersection number and $n$ is the number of vertices. Consequently, when $m \leq \ln{\ln{n}}$ the running time of this algorithm is polynomial. We then consider random instances of the random intersection graphs model as input graphs. As our main contribution, we prove that, when the number of labels is not too large ($m=n^{\alpha}, 0< \alpha <1$), we can use the label choices of the vertices to find a maximum clique in polynomial time whp. The proof of correctness for this algorithm relies on our Single Label Clique Theorem, which roughly states that whp a "large enough" clique cannot be formed by more than one label. This theorem generalizes and strengthens other related results in the state of the art, but also broadens the range of values considered. As an important consequence of our Single Label Clique Theorem, we prove that the problem of inferring the complete information of label choices for each vertex from the resulting random intersection graph (i.e. the \emph{label representation of the graph}) is \emph{solvable} whp. Finding efficient algorithms for constructing such a label representation is left as an interesting open problem for future research