Model comparison games can be used not only to decide whether two specific models are equivalent or not, but also to establish a measurement of difference among a whole class of models. We show how this is possible in the case of the spatial modal logic S4u of Bennett. The approach results in a spatial similarity measure based on topological model comparison games. After establishing the theore...

MOTIVATION There recently has been great interest in aligning protein-protein interaction (PPI) networks to identify potentially orthologous proteins between species. It is thought that the topological information contained in these networks will yield better orthology predictions than sequence similarity alone. Recent work has found that existing aligners have difficulty making use of both top...

In biology, similarity in structure or sequence between molecules is often used as evidence of functional similarity. In protein interaction networks, structural similarity of nodes (i.e., proteins) is often captured by comparing node signatures (vectors of topological properties of neighborhoods surrounding the nodes). In this paper, we ask how well such topological signatures predict protein ...

In recent years, many algorithms have been developed to narrow down the set of candidate disease genes implicated by genome wide association studies (GWAS), using knowledge on protein-protein interactions (PPIs). All of these algorithms are based on a common principle; functional association between proteins is correlated with their connectivity/proximity in the PPI network. However, recent res...

The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approac...

Conceptual neighborhood graphs are similarity-based schemata of spatial/temporal relations. This paper proposes a semi-automated method for deriving a conceptual neighborhood graph of topological relations, which shows all pairs of relations between which a smooth transformation can be performed. The method is applicable to various sets of topological relations distinguished by the 9-intersecti...

The aspect graph (AG) has been proposed as a viewer-centered tool for object recognition. Although the aspects could be used for recognition from one image,the full information stored in the AG (aspects and visual events) suggests a multiple views, possibly active, approach. The topological nature of the AG also suggests a topological match of images of the unknown object and stored aspects. In...

The aspect graph (AG) has been proposed as a viewer-centered tool for object recognition. Although the aspects could be used for recognition from one image, the full information stored in the AG (aspects and visual events) suggests a multiple views, possibly active, approach. The topological nature of the AG also suggests a topological match of images of the unknown object and stored aspects. I...

This paper aims at presenting a topological model of motivic structure and analysis, and its application, via the implementation, to Schumann’s Of Foreign Lands and People in Scenes from Childhood. Our immanent approach importantly includes the concept of contour similarity for different motif lengths making then possible to formalize the germinal motif (or leitmotif) concept. Based on motif, c...