Homological Region Adjacency Tree for a 3D Binary Digital Image via HSF Model

Given a 3D binary digital image I, we define and compute an edge-weighted tree, called Homological Region Tree (or Hom-Tree, for short). It coincides, as unweighted graph, with the classical Region Adjacency Tree of black 6-connected components (CCs) and white 26- connected components of I. In addition, we define the weight of an edge (R, S) as the number of tunnels that the CCs R and S “share”. The Hom-Tree structure is still an isotopic invariant of I. Thus, it provides information about how the different homology groups interact between them, while preserving the duality of black and white CCs. An experimentation with a set of synthetic images showing different shapes and different complexity of connected component nesting is performed for numerically validating the method.Ministerio de Economía y Competitividad MTM2016-81030-

Computing the Component-Labeling and the Adjacency Tree of a Binary Digital Image in Near Logarithmic-Time

Connected component labeling (CCL) of binary images is one of the fundamental operations in real time applications. The adjacency tree (AdjT) of the connected components offers a region-based representation where each node represents a region which is surrounded by another region of the opposite color. In this paper, a fully parallel algorithm for computing the CCL and AdjT of a binary digital image is described and implemented, without the need of using any geometric information. The time complexity order for an image of m × n pixels under the assumption that a processing element exists for each pixel is near O(log(m+ n)). Results for a multicore processor show a very good scalability until the so-called memory bandwidth bottleneck is reached. The inherent parallelism of our approach points to the direction that even better results will be obtained in other less classical computing architectures.Ministerio de Economía y Competitividad MTM2016-81030-PMinisterio de Economía y Competitividad TEC2012-37868-C04-0

Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies

The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Following the approach pioneered by Sturmfels and Pachter, we describe how to modify the DeCo dynamic programming algorithm to identify classes of cost schemes that generates similar parsimonious evolutionary scenarios for gene adjacencies, as well as the robustness to changes to the cost scheme of evolutionary events of the presence or absence of specific ancestral gene adjacencies. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes to cost schemes provides new and interesting insights on the evolution of gene adjacencies and the DeCo model.Comment: Accepted, to appear in ISBRA - 11th International Symposium on Bioinformatics Research and Applications - 2015, Jun 2015, Norfolk, Virginia, United State

On the Topological Disparity Characterization of Square-Pixel Binary Image Data by a Labeled Bipartite Graph

Given an nD digital image I based on cubical n-xel, to fully characterize the degree of internal topological dissimilarity existing in I when using different adjacency relations (mainly, comparing 2n or 2n −1 adjacency relations) is a relevant issue in current problems of digital image processing relative to shape detection or identification. In this paper, we design and implement a new self-dual representation for a binary 2D image I, called {4, 8}-region adjacency forest of I ({4, 8}-RAF, for short), that allows a thorough analysis of the differences between the topology of the 4-regions and that of the 8-regions of I. This model can be straightforwardly obtained from the classical region adjacency tree of I and its binary complement image Ic, by a suitable region label identification. With these two labeled rooted trees, it is possible: (a) to compute Euler number of the set of foreground (resp. background) pixels with regard to 4-adjacency or 8-adjacency; (b) to identify new local and global measures and descriptors of topological dissimilarity not only for one image but also between two or more images. The parallelization of the algorithms to extract and manipulate these structures is complete, thus producing efficient and unsophisticated codes with a theoretical computing time near the logarithm of the width plus the height of an image. Some toy examples serve to explain the representation and some experiments with gray real images shows the influence of the topological dissimilarity when detecting feature regions, like those returned by the MSER (maximally stable extremal regions) method.Ministerio de Economía, Industria y Competitividad PID2019-110455GB-I00 (Par-HoT)Junta de Andalucía US-138107

Maximal Entropy Random Walk: solvable cases of dynamics

We focus on the study of dynamics of two kinds of random walk: generic random walk (GRW) and maximal entropy random walk (MERW) on two model networks: Cayley trees and ladder graphs. The stationary probability distribution for MERW is given by the squared components of the eigenvector associated with the largest eigenvalue \lambda_0 of the adjacency matrix of a graph, while the dynamics of the probability distribution approaching to the stationary state depends on the second largest eigenvalue \lambda_1. Firstly, we give analytic solutions for Cayley trees with arbitrary branching number, root degree, and number of generations. We determine three regimes of a tree structure that result in different statics and dynamics of MERW, which are due to strongly, critically, and weakly branched roots. We show how the relaxation times, generically shorter for MERW than for GRW, scale with the graph size. Secondly, we give numerical results for ladder graphs with symmetric defects. MERW shows a clear exponential growth of the relaxation time with the size of defective regions, which indicates trapping of a particle within highly entropic intact region and its escaping that resembles quantum tunneling through a potential barrier. GRW shows standard diffusive dependence irrespective of the defects.Comment: 13 pages, 6 figures, 24th Marian Smoluchowski Symposium on Statistical Physics (Zakopane, Poland, September 17-22, 2011

A graph-based mathematical morphology reader

This survey paper aims at providing a "literary" anthology of mathematical morphology on graphs. It describes in the English language many ideas stemming from a large number of different papers, hence providing a unified view of an active and diverse field of research

Graph Refinement based Airway Extraction using Mean-Field Networks and Graph Neural Networks

Graph refinement, or the task of obtaining subgraphs of interest from over-complete graphs, can have many varied applications. In this work, we extract trees or collection of sub-trees from image data by, first deriving a graph-based representation of the volumetric data and then, posing the tree extraction as a graph refinement task. We present two methods to perform graph refinement. First, we use mean-field approximation (MFA) to approximate the posterior density over the subgraphs from which the optimal subgraph of interest can be estimated. Mean field networks (MFNs) are used for inference based on the interpretation that iterations of MFA can be seen as feed-forward operations in a neural network. This allows us to learn the model parameters using gradient descent. Second, we present a supervised learning approach using graph neural networks (GNNs) which can be seen as generalisations of MFNs. Subgraphs are obtained by training a GNN-based graph refinement model to directly predict edge probabilities. We discuss connections between the two classes of methods and compare them for the task of extracting airways from 3D, low-dose, chest CT data. We show that both the MFN and GNN models show significant improvement when compared to one baseline method, that is similar to a top performing method in the EXACT'09 Challenge, and a 3D U-Net based airway segmentation model, in detecting more branches with fewer false positives.Comment: Accepted for publication at Medical Image Analysis. 14 page

Cluster adjacency beyond MHV

We explore further the notion of cluster adjacency, focussing on non-MHV amplitudes. We extend the notion of adjacency to the BCFW decomposition of tree-level amplitudes. Adjacency controls the appearance of poles, both physical and spurious, in individual BCFW terms. We then discuss how this notion of adjacency is connected to the adjacency already observed at the level of symbols of scattering amplitudes which controls the appearance of branch cut singularities. Poles and symbols become intertwined by cluster adjacency and we discuss the relation of this property to the $\bar{Q}$-equation which imposes constraints on the derivatives of the transcendental functions appearing in loop amplitudes.Comment: 51 pages, 25 figures, 4 table