Ward method of hierarchical clustering for non-Euclidean similarity measures

Author(s):  
Sadaaki Miyamoto ◽  
Ryosuke Abe ◽  
Yasunori Endo ◽  
Jun-ichi Takeshita
2017 ◽  
Vol 14 (1) ◽  
Author(s):  
Zdeněk Šulc ◽  
Martin Matějka ◽  
Jiří Procházka ◽  
Hana Řezanková

This paper thoroughly examines three recently introduced modifications of the Gower coefficient, which were determined for data with mixed-type variables in hierarchical clustering. On the contrary to the original Gower coefficient, which only recognizes if two categories match or not in the case of nominal variables, the examined modifications offer three different approaches to measuring the similarity between categories. The examined dissimilarity measures are compared and evaluated regarding the quality of their clusters measured by three internal indices (Dunn, silhouette, McClain) and regarding their classification abilities measured by the Rand index. The comparison is performed on 810 generated datasets. In the analysis, the performance of the similarity measures is evaluated by different data characteristics (the number of variables, the number of categories, the distance of clusters, etc.) and by different hierarchical clustering methods (average, complete, McQuitty and single linkage methods). As a result, two modifications are recommended for the use in practice.


Solid Earth ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 2159-2209
Author(s):  
Rahul Prabhakaran ◽  
Giovanni Bertotti ◽  
Janos Urai ◽  
David Smeulders

Abstract. Rock fractures organize as networks, exhibiting natural variation in their spatial arrangements. Therefore, identifying, quantifying, and comparing variations in spatial arrangements within network geometries are of interest when explicit fracture representations or discrete fracture network models are chosen to capture the influence of fractures on bulk rock behaviour. Treating fracture networks as spatial graphs, we introduce a novel approach to quantify spatial variation. The method combines graph similarity measures with hierarchical clustering and is applied to investigate the spatial variation within large-scale 2-D fracture networks digitized from the well-known Lilstock limestone pavements, Bristol Channel, UK. We consider three large, fractured regions, comprising nearly 300 000 fractures spread over 14 200 m2 from the Lilstock pavements. Using a moving-window sampling approach, we first subsample the large networks into subgraphs. Four graph similarity measures – fingerprint distance, D-measure, Network Laplacian spectral descriptor (NetLSD), and portrait divergence – that encapsulate topological relationships and geometry of fracture networks are then used to compute pair-wise subgraph distances serving as input for the statistical hierarchical clustering technique. In the form of hierarchical dendrograms and derived spatial variation maps, the results indicate spatial autocorrelation with localized spatial clusters that gradually vary over distances of tens of metres with visually discernable and quantifiable boundaries. Fractures within the identified clusters exhibit differences in fracture orientations and topology. The comparison of graph similarity-derived clusters with fracture persistence measures indicates an intra-network spatial variation that is not immediately obvious from the ubiquitous fracture intensity and density maps. The proposed method provides a quantitative way to identify spatial variations in fracture networks, guiding stochastic and geostatistical approaches to fracture network modelling.


2021 ◽  
Author(s):  
Rahul Prabhakaran ◽  
Giovanni Bertotti ◽  
Janos Urai ◽  
David Smeulders

Abstract. We investigate the spatial variation of 2D fracture networks digitized from the well-known Lilstock limestone pavements, Bristol Channel, UK. By treating fracture networks as spatial graphs, we utilize a novel approach combining graph similarity measures and hierarchical clustering to identify spatial clusters within fracture networks and quantify spatial variation. We use four graph similarity measures: fingerprint distance, D-measure, NetLSD, and portrait divergence to compare fracture graphs. The technique takes into account both topological relationship and geometry of the networks and is applied to three large fractured regions consisting of nearly 300,000 fractures spread over 14,200 sq.m. The results indicates presence of spatial clusters within fracture networks with that vary gradually over distances of tens of metres. One region is not influenced by faulting but still displays variation in background fracturing. Variation in fracture development in the other two regions are interpreted to be primarily influenced by proximity to faults that gradually gives way to background fracturing. Comparative analysis of the graph similarity-derived clusters with fracture persistence measures indicate that there is a general correspondence between patterns; however, additional variations are highlighted that is not obvious from fracture intensity and density plots. The proposed method provides a quantitative way to identify spatial variations in fracture networks which can be used to guide stochastic and geostatistical approaches to fracture network modelling.


Author(s):  
Satoshi Takumi ◽  
◽  
Sadaaki Miyamoto

Algorithms of agglomerative hierarchical clustering using asymmetric similarity measures are studied. Two different measures between two clusters are proposed, one of which generalizes the average linkage for symmetric similarity measures. Asymmetric dendrogram representation is considered after foregoing studies. It is proved that the proposed linkage methods for asymmetric measures have no reversals in the dendrograms. Examples based on real data show how the methods work.


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