Vertex Clustering of Augmented Graph Streams

In this paper we propose a graph stream clustering algorithm with a unied similarity measure on both structural and attribute properties of vertices, with each attribute being treated as a vertex. Unlike others, our approach does not require an input parameter for the number of clusters, instead, it dynamically creates new sketch-based clusters and periodically merges existing similar clusters. Experiments on two publicly available datasets reveal the advantages of our approach in detecting vertex clusters in the graph stream. We provide a detailed investigation into how parameters affect the algorithm performance. We also provide a quantitative evaluation and comparison with a well-known offline community detection algorithm which shows that our streaming algorithm can achieve comparable or better average cluster purity.

General, PDB-based collective variables for protein folding

New, automated forms of data-analysis are required in order to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that different sets of coordinates are required for each different chemical systems under study precisely because the coordinates are constructed using information from the trajectory. In this paper we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank (PDB). We show that the resulting coordinates are as useful for analysing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

Objects of Transcendence: Scots Protestantism and an Anthropology of Things

This anthropological essay takes as its ethnographic point of departure two apparently contrasting deployments of the Bible within contemporary Scotland, one as observed among Brethren and Presbyterian fisher-families in Gamrie, coastal Aberdeenshire, and the other as observed among the Orange Order, a Protestant marching fraternity, in Airdrie and Glasgow. By examining how and with what effects the Bible and other objects (plastic crowns, ‘Sunday clothes’, Orange regalia) enter into and extend beyond the everyday practices of fishermen and Orangemen, my aim is to sketch different aspects of the material life of Scottish Protestantism. By offering a critique of Bruno Latour’s early writing on ‘quasi-objects’ via Alfred Gell’s notion of ‘distributed personhood’, I seek to undermine the sociological assumption that modernity and enchantment are mutually exclusive.