The Minimum Quartet Tree Cost problem is to construct an optimal weight tree from the 3 (

The hierarchical clustering methods based on vertex similarity have the advantage that global evaluation can be incorporated for community discovery. Vertex similarity metric is the most important part of these methods. However, the existing methods do not perform well for community discovery compared with the state-ofthe-art algorithms. In this paper, we propose a new vertex similarity metric ...

Modern day science presentsmany challenges to data analysts. Advances in data collection provide very large (number of observations and number of dimensions) data sets. In many areas of data analysis an informative task is to find natural separations of data into homogeneous groups, i.e. clusters. In this paper we study the asymptotic behavior of hierarchical clustering in situations where both...

We consider the problem of constructing an an optimal-weight tree from the 3 `

This work draws its inspiration from three important sources of research on dissimilarity-based clustering and intertwines those three threads into a consistent principled functorial theory of clustering. Those three are the overlapping clustering of Jardine and Sibson, the functorial approach of Carlsson and Mémoli to partition-based clustering, and the Isbell/Dress school’s study of injective...

In this paper we show that diversity-driven widening, the parallel exploration of the model space with focus on developing diverse models, can improve hierarchical agglomerative clustering. Depending on the selected linkage method, the model that is found through the widened search achieves a better silhouette coefficient than its sequentially built counterpart.

We have completed an exhaustive search for the common spatial arrangements of backbone fragments (SARFs) in nonhomologous proteins. This type of local structural similarity, incorporating short fragments of backbone atoms, arranged not necessarily in the same order along the polypeptide chain, appears to be important for protein function and stability. To estimate the statistical significance o...

The Hybrid Cellular Automata (HCA) modelling framework can be an efficient approach to a number of biological problems, particularly those which involve the integration of multiple spatial and temporal scales. As such, HCA may become a key modelling tool in the development of the so-called integrative biology. In this paper, we first discuss HCA on a general level and then present results obtai...