We demonstrate a collection of techniques that seek to make the transition between drawings based on two topologically distinct spanning trees of the same graph as clear as possible. As Herman, Melançon, and Marshall note [HMM00], one way to draw a large graph is to extract a spanning tree from it, use a tree layout algorithm [CK95, Ead92, RT81, II90, TM02, GADM04, LY05] to draw the spanning tr...

A dynamic transmembrane voltage field has been suggested as an intrinsic element in voltage sensor (VS) domains. Here, the dynamic field contribution to the VS energetics was analyzed via electrostatic calculations applied to a number of atomistic structures made available recently. We find that the field is largely static along with the molecular motions of the domain, and more importantly, it...

Consider a population consisting of n individuals, each of whom has one of d types (e.g. their blood type, in which case d = 4). We are allowed to query this database by specifying a subset of the population, and in response we observe a noiseless histogram (a d-dimensional vector of counts) of types of the pooled individuals. This measurement model arises in practical situations such as poolin...

We propose a novel framework for deriving approximations for intractable probabilistic models. This framework is based on a free energy (negative log marginal likelihood) and can be seen as a generalization of adaptive TAP [1-3] and expectation propagation (EP) [4,5] The free energy is constructed from two approximating distributions which encode different aspects of the intractable model such ...

Let S be a planar point set in general position, and let $$\mathcal {P}(S)$$ the of all plane straight-line paths with vertex S. A flip on path $$P \in \mathcal is operation replacing an edge e P another f to obtain new valid from . It long-standing open question whether for every given S, can transformed into any other by sequence flips. To achieve better understanding this question, we show t...