Finding the interacting pairs of proteins between two different protein families whose members are known to interact is an important problem in molecular biology. We developed and tested an algorithm that finds optimal matches between two families of proteins by comparing their distance matrices. A distance matrix provides a measure of the sequence similarity of proteins within a family. Since ...

In network topology discovery, it is often necessary to collect measurements between network elements without injecting large amounts of traffic into the network. A possible solution to this problem is to actively query the network for some measurements and use these to infer the remaining ones. We frame this as a particular version of the Noisy Matrix Completion problem where the entries refle...

however, it is not always clear what ‘near’ means in this context. The simplest definition, if the data being analysed consists of spatial point data, is to work with Euclidean (or straight line) distances however this is not always a reliable indicator of proximity. A number of alternative measures of proximity are possible for example travel times or travel distances based on routes on roads ...

In this paper we use the Gray code representation of the genetic code C=00, U=10, G=11 and A=01 (C pairs with G, A pairs with U) to generate a sequence of genetic code-based matrices. In connection with these code-based matrices, we use the Hamming distance to generate a sequence of numerical matrices. We then further investigate the properties of the numerical matrices and show that they are d...

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Exchange matrices represent spatial weights as symmetric probability distributions on pairs of regions, whose margins yield regional weights, generally well-specified and known in most contexts. This contribution proposes a mechanism for constructing exchange matrices, derived from quite general symmetric proximity matrices, in such a way that the margin of the exchange matrix coincides with th...

In this work, we explore the problem of aligning two time-ordered point clouds which are spatially transformed and re-parameterized versions of each other. This has a diverse array of applications such as cross modal time series synchronization (e.g. MOCAP to video) and alignment of discretized curves in images. Most other works that address this problem attempt to jointly uncover a spatial ali...