Efficient Projection onto the Perfect Phylogeny Model
Efficient Projection onto the Perfect Phylogeny Model
复制标题
DOI：
--
复制
发表时间：
2018-11
期刊：
影响因子：
--
通讯作者：
Bei Jia;Surjyendu Ray;S. Safavi;José Bento
中科院分区：
文献类型：
--
作者：
Bei Jia;Surjyendu Ray;S. Safavi;José Bento
一些算法建立在完美的系统发育模型上来推断进化树。当进化树是从在不同位置、不同样本中有突变的基因组部分推断出来的时候，这个问题就特别困难了。现有的算法可能会对可能的树空间进行广泛的搜索。这些算法的核心是一个为系统发育树分配适应度代价的投影问题。为了在树的空间中进行广泛的搜索，快速解决这个投影问题是至关重要的。在本文中，我们使用莫罗分解的近端算子和树约简方案，开发了一个新的算法来计算这个投影。我们的算法在有限的步骤中得到一个精确的解，并且非常快。特别是，它可以在大约2小时内搜索所有少于11个节点的进化树，这个节点的大小与几个生物学问题（超过20亿棵树）有关。
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across different samples. Existing algorithms might do extensive searches over the space of possible trees. At the center of these algorithms is a projection problem that assigns a fitness cost to phylogenetic trees. In order to perform a wide search over the space of the trees, it is critical to solve this projection problem fast. In this paper, we use Moreau's decomposition for proximal operators, and a tree reduction scheme, to develop a new algorithm to compute this projection. Our algorithm terminates with an exact solution in a finite number of steps, and is extremely fast. In particular, it can search over all evolutionary trees with fewer than 11 nodes, a size relevant for several biological problems (more than 2 billion trees) in about 2 hours.