论文标题

Bloom折纸分析:实用小组测试

Bloom Origami Assays: Practical Group Testing

论文作者

Abraham, Louis, Becigneul, Gary, Coleman, Benjamin, Scholkopf, Bernhard, Shrivastava, Anshumali, Smola, Alexander

论文摘要

我们研究了在Covid-19的背景下通常称为小组测试的问题。鉴于从患者那里收集的N样品,我们应该如何选择和测试样品混合物以最大化信息并最大程度地减少测试数量?小组测试是一些有吸引力的解决方案的一个充分研究的问题,但是最近的生物学研究对COVID-19构成了与传统方法不相容的实用限制。此外,现有方法使用不必要的限制性解决方案,该解决方案是为具有内存和计算限制更多的设置而设计的,而不是手头的问题。这导致效用差。在新的环境中,我们使用进化策略为N的少量值获得了强大的解决方案。然后,我们开发了一种新方法,将Bloom过滤器与信念传播相结合,以扩展到较大的N值(超过100),并获得良好的经验结果。我们还提出了一种针对特定的Covid-19设置量身定制的更准确的解码算法。这项工作证明了专用算法与众所周知的通用解决方案之间的实际差距。我们的努力导致了一种新的实用多路复用方法,可产生强大的经验表现,而没有将所选的患者数量多于相同的探针混合在一起。最后,我们简要讨论自适应方法,将其投入到适应性亚模型的框架中。

We study the problem usually referred to as group testing in the context of COVID-19. Given n samples collected from patients, how should we select and test mixtures of samples to maximize information and minimize the number of tests? Group testing is a well-studied problem with several appealing solutions, but recent biological studies impose practical constraints for COVID-19 that are incompatible with traditional methods. Furthermore, existing methods use unnecessarily restrictive solutions, which were devised for settings with more memory and compute constraints than the problem at hand. This results in poor utility. In the new setting, we obtain strong solutions for small values of n using evolutionary strategies. We then develop a new method combining Bloom filters with belief propagation to scale to larger values of n (more than 100) with good empirical results. We also present a more accurate decoding algorithm that is tailored for specific COVID-19 settings. This work demonstrates the practical gap between dedicated algorithms and well-known generic solutions. Our efforts results in a new and practical multiplex method yielding strong empirical performance without mixing more than a chosen number of patients into the same probe. Finally, we briefly discuss adaptive methods, casting them into the framework of adaptive sub-modularity.

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