Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces
复制标题
用于大型化学空间精确聚类的分块倒排索引
DOI：
10.1021/ci500150t
复制
发表时间：
2014
影响因子：
5.6
通讯作者：
Kohlbacher O
中科院分区：
文献类型：
--
作者：
Thiel P;Sach-Peltason L;Ottmann C;Kohlbacher O
基于指纹图谱的化合物相似度计算是化学信息学的基本任务之一。有效计算复合相似度的方法对于相似性搜索或库聚类等各种应用至关重要。随着公共复合数据库规模的增加，这些数据库的精确聚类是可取的，但往往计算昂贵。我们提出了一个优化的倒排索引算法，用于计算给定数据集的二维指纹的所有成对相似性。与其他算法相比，它既不需要GPU计算，也不产生聚类的随机近似。该算法已被设计为多核架构工作良好，并表现出良好的并行加速比。作为该算法的一个应用实例，我们实现了一个确定性聚类应用程序，该应用程序被设计为在当前硬件上在短时间内分解包含数千万化合物的虚拟库。我们的研究结果表明，我们的实现实现每秒超过400万Tanimoto相似性计算上一个常见的桌面CPU。因此，可用化学空间的确定性聚类可以在现代多核机器上在几天内完成。
The calculation of pairwise compound similarities based on fingerprints is one of the fundamental tasks in chemoinformatics. Methods for efficient calculation of compound similarities are of the utmost importance for various applications like similarity searching or library clustering. With the increasing size of public compound databases, exact clustering of these databases is desirable, but often computationally prohibitively expensive. We present an optimized inverted index algorithm for the calculation of all pairwise similarities on 2D fingerprints of a given data set. In contrast to other algorithms, it neither requires GPU computing nor yields a stochastic approximation of the clustering. The algorithm has been designed to work well with multicore architectures and shows excellent parallel speedup. As an application example of this algorithm, we implemented a deterministic clustering application, which has been designed to decompose virtual libraries comprising tens of millions of compounds in a short time on current hardware. Our results show that our implementation achieves more than 400 million Tanimoto similarity calculations per second on a common desktop CPU. Deterministic clustering of the available chemical space thus can be done on modern multicore machines within a few days.
使用倒排索引加速 LINGO 计算
影响因子：
5.6
作者：
T. Kristensen;J. Nielsen;Christian N. S. Pedersen
通讯作者：
Christian N. S. Pedersen