The Euclidean Algorithm for Generalized Minimum Distance Decoding of Reed-Solomon Codes

This paper presents a method to merge Generalized Minimum Distance decoding of Reed-Solomon codes with the extended Euclidean algorithm. By merge, we mean that the steps taken to perform the Generalized Minimum Distance decoding are similar to those performed by the extended Euclidean algorithm. The resulting algorithm has a complexity of O(n^2)

An ETH-Tight Exact Algorithm for Euclidean TSP

We study exact algorithms for {\sc Euclidean TSP} in $\mathbb{R}^d$. In the early 1990s algorithms with $n^{O(\sqrt{n})}$ running time were presented for the planar case, and some years later an algorithm with $n^{O(n^{1-1/d})}$ running time was presented for any $d\geq 2$. Despite significant interest in subexponential exact algorithms over the past decade, there has been no progress on {\sc Euclidean TSP}, except for a lower bound stating that the problem admits no $2^{O(n^{1-1/d-\epsilon})}$ algorithm unless ETH fails. Up to constant factors in the exponent, we settle the complexity of {\sc Euclidean TSP} by giving a $2^{O(n^{1-1/d})}$ algorithm and by showing that a $2^{o(n^{1-1/d})}$ algorithm does not exist unless ETH fails.Comment: To appear in FOCS 201

Euclidean algorithm and polynomial equations after Labatie

We recall Labatie's effective method of solving polynomial equations with two unknowns by using the Euclidean algorithm

Fitting a geometric graph to a protein-protein interaction network

Finding a good network null model for protein-protein interaction (PPI) networks is a fundamental issue. Such a model would provide insights into the interplay between network structure and biological function as well as into evolution. Also, network (graph) models are used to guide biological experiments and discover new biological features. It has been proposed that geometric random graphs are a good model for PPI networks. In a geometric random graph, nodes correspond to uniformly randomly distributed points in a metric space and edges (links) exist between pairs of nodes for which the corresponding points in the metric space are close enough according to some distance norm. Computational experiments have revealed close matches between key topological properties of PPI networks and geometric random graph models. In this work, we push the comparison further by exploiting the fact that the geometric property can be tested for directly. To this end, we develop an algorithm that takes PPI interaction data and embeds proteins into a low-dimensional Euclidean space, under the premise that connectivity information corresponds to Euclidean proximity, as in geometric-random graphs.We judge the sensitivity and specificity of the fit by computing the area under the Receiver Operator Characteristic (ROC) curve. The network embedding algorithm is based on multi-dimensional scaling, with the square root of the path length in a network playing the role of the Euclidean distance in the Euclidean space. The algorithm exploits sparsity for computational efficiency, and requires only a few sparse matrix multiplications, giving a complexity of O(N2) where N is the number of proteins.The algorithm has been verified in the sense that it successfully rediscovers the geometric structure in artificially constructed geometric networks, even when noise is added by re-wiring some links. Applying the algorithm to 19 publicly available PPI networks of various organisms indicated that: (a) geometric effects are present and (b) two-dimensional Euclidean space is generally as effective as higher dimensional Euclidean space for explaining the connectivity. Testing on a high-confidence yeast data set produced a very strong indication of geometric structure (area under the ROC curve of 0.89), with this network being essentially indistinguishable from a noisy geometric network. Overall, the results add support to the hypothesis that PPI networks have a geometric structure