CAREER: Scalable and Flexible Indexing of Compressed Sequences

无损数据压缩是一项经典且普遍存在的任务，它减少了数据的大小，从而降低了传输或存档的成本。然而，现代应用程序需要的不仅仅是压缩。在计算生物学等领域，以越来越快的速度生成tb级的高度可压缩数据。为了充分利用这些数据，它不仅需要存储在一个小空间中，而且需要可访问和可搜索。近年来出现了一种名为“压缩索引”的数据结构，它可以完成这项任务。然而，到目前为止的研究主要集中在静态索引上，而忽略了支持更新和高效构建等重要方面。这个项目的总体目标是开发功能强大的动态压缩索引，这些索引能够处理一组通用的查询和各种表示，而且可以高效地构建。这将使存储和共享高度可压缩的数据集（如DNA收集）变得更便宜、更快、更节能，从而充分释放DNA测序的进步潜力。该项目的进展也将被整合到代表性不足的学生的研究经验中，并扩展到非计算机科学的学生。本项目的主要研究目标大致可分为以下三个方向。首先，该项目将产生用于构造压缩索引的新的高效算法。新方法首先使用轻微次优压缩对输入进行预处理，然后在压缩时间内构建最终索引，即与预压缩文本成比例的时间。其次，该项目旨在利用和改进现代后缀采样技术来设计新的强大的索引，这些索引既压缩又能够支持强大的查询，包括多字符串表示。最后，本项目将研究压缩指数下界的欠发达景观。目前，只有最基本的查询，如随机访问，被很好地理解，而对更通用表示的下界或压缩计算的下界知之甚少。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Lossless data compression is a classical and ubiquitous task that reduces the size of data, leading to a decreased cost of transfer or archival. Modern applications, however, require more than compression. In domains such as computational biology, terabytes of highly compressible data are generated at an increasing rate. To fully take advantage of this data, it needs to be not only stored in a small space but also accessible and searchable. Recent years have witnessed the birth of data structures called "compressed indexes" that can accomplish this task. The research so far, however, has mostly focused on static indexes, leaving out important aspects such as support for updates and efficient construction. This project's overarching goal is to develop powerful, dynamic compressed indexes capable of handling a versatile set of queries and various representations, that can moreover be efficiently constructed. This will make it significantly cheaper, faster, and more energy-efficient to store and share highly compressible datasets such as DNA collections, thereby fully unlocking the potential of advances in DNA sequencing. The advances of this project will also be integrated into research experience for underrepresented students, as well as outreach to non-computer science students.The main research goals of this project can be broadly classified into the following three directions. First, the project will lead to new efficient algorithms for constructing compressed indexes. The new approach lies in first preprocessing the input using lightly sub-optimal compression and then constructing the final index in compressed time, i.e., time proportional to the precompressed text. Second, the project aims to utilize and improve modern suffix sampling techniques to design new and powerful indexes that are both compressed and able to support powerful queries, including multi-string representations. Finally, the project will study the underdeveloped landscape of lower bounds for compressed indexes. Currently, only the most basic queries, such as random access, are well-understood, and much less is known about lower bounds on more versatile representations or lower bounds for compressed computation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.