论文标题

距离几何形状的基于周期的配方

Cycle-based formulations in Distance Geometry

论文作者

Liberti, Leo, Iommazzo, Gabriele, Lavor, Carlile, Maculan, Nelson

论文摘要

距离几何问题要求在给定尺寸K的欧几里得空间中找到给定简单的边缘加权图的实现,其中边缘被实现为长度的直段相等(或尽可能接近)。该问题通常被建模为一种数学编程公式,涉及决策变量,这些变量决定了给定欧几里得空间中顶点的位置。通常使用局部或全局非线性优化技术构建解决方案算法。我们提出了一种针对此问题的新建模技术,在该技术中,配方不用决定顶点位置,而是确定代表图中每个周期中边缘的片段的长度,并在每个维度上投影。我们提出了基于欧拉循环的精确配方和放松。然后,我们比较了用随机全局优化技术获得的蛋白质构象实例的计算结果,这些技术在新的基于周期的公式和现有的基于边缘的配方上。尽管基于边缘的配方需要更少的时间才能达到终止,但基于周期的配方通常在解决方案质量措施上更好。

The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension K, where the edges are realized as straight segments of lengths equal (or as close as possible) to the edge weights. The problem is often modelled as a mathematical programming formulation involving decision variables that determine the position of the vertices in the given Euclidean space. Solution algorithms are generally constructed using local or global nonlinear optimization techniques. We present a new modelling technique for this problem where, instead of deciding vertex positions, formulations decide the length of the segments representing the edges in each cycle in the graph, projected in every dimension. We propose an exact formulation and a relaxation based on a Eulerian cycle. We then compare computational results from protein conformation instances obtained with stochastic global optimization techniques on the new cycle-based formulation and on the existing edge-based formulation. While edge-based formulations take less time to reach termination, cycle-based formulations are generally better on solution quality measures.

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