Bordered Floer homology and the spectral sequence of a branched double cover II: the spectral sequences agree

Given a link in the three-sphere, Ozsv\'ath and Szab\'o showed that there is a spectral sequence starting at the Khovanov homology of the link and converging to the Heegaard Floer homology of its branched double cover. The aim of this paper is to explicitly calculate this spectral sequence in terms of bordered Floer homology. There are two primary ingredients in this computation: an explicit calculation of bimodules associated to Dehn twists, and a general pairing theorem for polygons. The previous part (arXiv:1011.0499) focuses on computing the bimodules; this part focuses on the pairing theorem for polygons, in order to prove that the spectral sequence constructed in the previous part agrees with the one constructed by Ozsv\'ath and Szab\'o.Comment: 85 pages, 19 figures, v3: Version to appear in Journal of Topolog

A Novel Approach to Finding Near-Cliques: The Triangle-Densest Subgraph Problem

Many graph mining applications rely on detecting subgraphs which are near-cliques. There exists a dichotomy between the results in the existing work related to this problem: on the one hand the densest subgraph problem (DSP) which maximizes the average degree over all subgraphs is solvable in polynomial time but for many networks fails to find subgraphs which are near-cliques. On the other hand, formulations that are geared towards finding near-cliques are NP-hard and frequently inapproximable due to connections with the Maximum Clique problem. In this work, we propose a formulation which combines the best of both worlds: it is solvable in polynomial time and finds near-cliques when the DSP fails. Surprisingly, our formulation is a simple variation of the DSP. Specifically, we define the triangle densest subgraph problem (TDSP): given $G(V,E)$, find a subset of vertices $S^*$ such that $\tau(S^*)=\max_{S \subseteq V} \frac{t(S)}{|S|}$, where $t(S)$ is the number of triangles induced by the set $S$. We provide various exact and approximation algorithms which the solve the TDSP efficiently. Furthermore, we show how our algorithms adapt to the more general problem of maximizing the $k$-clique average density. Finally, we provide empirical evidence that the TDSP should be used whenever the output of the DSP fails to output a near-clique.Comment: 42 page

The polytope of non-crossing graphs on a planar point set

For any finite set \A of $n$ points in $\R^2$, we define a $(3n-3)$-dimensional simple polyhedron whose face poset is isomorphic to the poset of ``non-crossing marked graphs'' with vertex set \A, where a marked graph is defined as a geometric graph together with a subset of its vertices. The poset of non-crossing graphs on \A appears as the complement of the star of a face in that polyhedron. The polyhedron has a unique maximal bounded face, of dimension $2n_i +n -3$ where $n_i$ is the number of points of \A in the interior of \conv(\A). The vertices of this polytope are all the pseudo-triangulations of \A, and the edges are flips of two types: the traditional diagonal flips (in pseudo-triangulations) and the removal or insertion of a single edge. As a by-product of our construction we prove that all pseudo-triangulations are infinitesimally rigid graphs.Comment: 28 pages, 16 figures. Main change from v1 and v2: Introduction has been reshape

Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page

The geometry of flip graphs and mapping class groups

The space of topological decompositions into triangulations of a surface has a natural graph structure where two triangulations share an edge if they are related by a so-called flip. This space is a sort of combinatorial Teichm\"uller space and is quasi-isometric to the underlying mapping class group. We study this space in two main directions. We first show that strata corresponding to triangulations containing a same multiarc are strongly convex within the whole space and use this result to deduce properties about the mapping class group. We then focus on the quotient of this space by the mapping class group to obtain a type of combinatorial moduli space. In particular, we are able to identity how the diameters of the resulting spaces grow in terms of the complexity of the underlying surfaces.Comment: 46 pages, 23 figure