Structural Matching of 2D Electrophoresis Gels using Graph Models

Abstract

2D electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. Each spot in the image represents a protein accumulation and the goal is to perform a differential analysis between pairs of images to study changes in protein content. It is thus necessary to register two images by finding spot correspondences. Although it may seem a simple task, generally, the manual processing of this kind of images is very cumbersome. The complete task of individual spot matching and gel registration is a complex and time consuming process when strong variations between corresponding sets of spots are expected. Besides, because an oneto-one mapping is expected between the two images, missing spots there may exist on both images (i.e. spots without correspondence). In order to solve this problem, this paper proposes a new distance together with a correspondence estimation algorithm based on graph matching which takes into account the structural information between the detected spots. Each image is represented by a graph and the task is to find an isomorphism between subgraphs. Successful experimental results using real data are presented, including a comparative performance evaluation.

A Computer-Assisted Colorization Approach Based on Efficient Belief Propagation and Graph Matching

“…After T iterations, the BP approach computes the belief vector for each vertex, representing the costs of each label, and assigns a label with minimum cost to obtain a homomorphism. In order to obtain a MCS and to guarantee that the mapping is bijective between subsets of V i and V m , we applied the same post-processing as described in [8]: for each model vertex, we kept the cheapest input vertex, and the remaining input vertices were associated to a NULL label, indicating they are not classified, leaving ambiguous cases for the animator to decide which color must be used to the unclassified (uncolored) regions.…”

“…Here, we propose a simple approach based on area, contour length and point locations used to encode the spatial relations as described in [5] and [8]. The objetive of the proposed general framework based on MRF is to overcome the main difficulty in graph matching problems, expressed by the following question.…”

Duas abordagens para casamento de padrões de pontos usando relações espaciais e casamento entre grafos

“…• casamento entre gels de eletroforese 2D [65,66] [78,85] e propagação de crenças (BP) [36]. Nossa segunda contribuição segue esta tendência, baseada em um algoritmo eficiente baseado em BP [39] (veja Capítulo 3).…”

“…Esta parte foi desenvolvida com o professor Alvaro Pardo, que nos proporcionou uma importante aplicação para o nosso método baseado em DGs. Graças a sua dedicação e competência, obtivemos nossas primeiras publicações durante o doutorado em conferência[66] e em revista[65].…”