Pairwise Compatibility Graphs (Invited Talk)

Pairwise Compatibility Graphs (PCG) are graphs introduced in relation to the biological problem of reconstructing phylogenetic trees. Without demanding to be exhaustive, in this note we take a quick look at what is known in the literature for these graphs. The evolutionary history of a set of organisms is usually represented by a tree-like structure called phylogenetic tree, where the leaves are the known species and the internal nodes are the possible ancestors that might have led, through evolution, to this set of species. Edges are evolutionary relationships between species, while the edge weights represent evolutionary distances among species (evolutionary times). The phylogenetic tree reconstruction problem consists in finding a fully labeled phylogenetic tree that'best' explains the evolution of given species, where'best' means that it optimizes a specific target function. Tree reconstruction problem is proved to be NP-hard under many criteria of optimality, so the performance of the heuristics for this problem is usually experimentally evaluated by comparing the output trees with the partial trees that are unanimously recognized as sure by biologists. But real data consist of a huge number of species, and it is unfeasible to compare trees with such a number of leaves, so it is common to exploit sample techniques. The idea is to find efficient ways to sample subsets of species from a large set in order to test the heuristics on the smaller sub-trees induced by the sample. The constraints on the sample attempt to ensure that the behavior of the heuristics will not be biased by the fact it is applied on the sample instead of on the whole tree. Since very close or very distant taxa can create problems for phylogenetic reconstruction heuristics [9], the following definition of Pairwise Compatibility Graphs [12] appears natura

Exploring Context with Deep Structured models for Semantic Segmentation

State-of-the-art semantic image segmentation methods are mostly based on training deep convolutional neural networks (CNNs). In this work, we proffer to improve semantic segmentation with the use of contextual information. In particular, we explore `patch-patch' context and `patch-background' context in deep CNNs. We formulate deep structured models by combining CNNs and Conditional Random Fields (CRFs) for learning the patch-patch context between image regions. Specifically, we formulate CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied in order to avoid repeated expensive CRF inference during the course of back propagation. For capturing the patch-background context, we show that a network design with traditional multi-scale image inputs and sliding pyramid pooling is very effective for improving performance. We perform comprehensive evaluation of the proposed method. We achieve new state-of-the-art performance on a number of challenging semantic segmentation datasets including $NYUDv2$, $PASCAL$-$VOC2012$, $Cityscapes$, $PASCAL$-$Context$, $SUN$-$RGBD$, $SIFT$-$flow$, and $KITTI$ datasets. Particularly, we report an intersection-over-union score of $77.8$ on the $PASCAL$-$VOC2012$ dataset.Comment: 16 pages. Accepted to IEEE T. Pattern Analysis & Machine Intelligence, 2017. Extended version of arXiv:1504.0101

Extended modular operad

This paper is a sequel to [LoMa] where moduli spaces of painted stable curves were introduced and studied. We define the extended modular operad of genus zero, algebras over this operad, and study the formal differential geometric structures related to these algebras: pencils of flat connections and Frobenius manifolds without metric. We focus here on the combinatorial aspects of the picture. Algebraic geometric aspects are treated in [Ma2].Comment: 38 pp., amstex file, no figures. This version contains additional references and minor change

Nonspecific Networking

A new model of strategic network formation is developed and analyzed, where an agent's investment in links is nonspecific. The model comprises a large class of games which are both potential and super- or submodular games. We obtain comparative statics results for Nash equilibria with respect to investment costs for supermodular as well as submodular networking games. We also study logit-perturbed best-response dynamics for supermodular games with potentials. We find that the associated set of stochastically stable states forms a sublattice of the lattice of Nash equilibria and derive comparative statics results for the smallest and the largest stochastically stable state. Finally, we provide a broad spectrum of applications from social interaction to industrial organization. Models of strategic network formation typically assume that each agent selects his direct links to other agents in which to invest. Nonspecific networking means that an agent cannot select a specific subset of feasible links which he wants to establish or strengthen. Rather, each agent chooses an effort level or intensity of networking. In the simplest case, the agent faces a binary choice: to network or not to network. If an agent increases his networking effort, all direct links to other agents are strengthened to various degrees. We assume that benefits accrue only from direct links. The set of agents or players is finite. Each agent has a finite strategy set consisting of the networking levels to choose from. For any pair of agents, their networking levels determine the individual benefits which they obtain from interacting with each other. An agent derives an aggregate benefit from the pairwise interactions with all others. In addition, the agent incurs networking costs, which are a function of the agent's own networking level. The agent's payoff is his aggregate benefit minus his cost.Network Formation, Potential Games, Supermodular Games

Noncommutative algebras related with Schubert calculus on Coxeter groups

For any finite Coxeter system $(W,S)$ we construct a certain noncommutative algebra, so-called {\it bracket algebra}, together with a familiy of commuting elements, so-called {\it Dunkl elements.} Dunkl elements conjecturally generate an algebra which is canonically isomorphic to the coinvariant algebra of the group $W.$ We prove this conjecture for classical Coxeter groups and $I_2(m)$. We define a ``quantization'' and a multiparameter deformation of our construction and show that for Lie groups of classical type and $G_2,$ the algebra generated by Dunkl elements in the quantized bracket algebra is canonically isomorphic to the small quantum cohomology ring of the corresponding flag variety, as described by B. Kim. For crystallographic Coxeter systems we define {\it quantum Bruhat representation} of the corresponding bracket algebra. We study in more detail relations and structure of $B_n$-, $D_n$- and $G_2$-bracket algebras, and as an application, discover {\it Pieri type formula} in the $B_n$-bracket algebra. As a corollary, we obtain Pieri type formula for multiplication of arbitrary $B_n$-Schubert classes by some special ones. Our Pieri type formula is a generalization of Pieri's formulas obtained by A. Lascoux and M.-P. Sch\"utzenberger for flag varieties of type $A.$ We also introduce a super-version of the bracket algebra together with a family of pairwise anticommutative elements which describes ``noncommutative differential geometry on a finite Coxeter group'' in a sense of S. Majid

Neighbourhood-consensus message passing and its potentials in image processing applications

In this paper, a novel algorithm for inference in Markov Random Fields (MRFs) is presented. Its goal is to find approximate maximum a posteriori estimates in a simple manner by combining neighbourhood influence of iterated conditional modes (ICM) and message passing of loopy belief propagation (LBP). We call the proposed method neighbourhood-consensus message passing because a single joint message is sent from the specified neighbourhood to the central node. The message, as a function of beliefs, represents the agreement of all nodes within the neighbourhood regarding the labels of the central node. This way we are able to overcome the disadvantages of reference algorithms, ICM and LBP. On one hand, more information is propagated in comparison with ICM, while on the other hand, the huge amount of pairwise interactions is avoided in comparison with LBP by working with neighbourhoods. The idea is related to the previously developed iterated conditional expectations algorithm. Here we revisit it and redefine it in a message passing framework in a more general form. The results on three different benchmarks demonstrate that the proposed technique can perform well both for binary and multi-label MRFs without any limitations on the model definition. Furthermore, it manifests improved performance over related techniques either in terms of quality and/or speed