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Register a new userLISA: Towards Learned DNA Sequence Search
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Added by
Jialin Ding
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming performance bottlenecks, such as searching for short DNA sequences over long reference sequences. In this paper, we introduce LISA (Learned Indexes for Sequence Analysis), a novel learning-based approach to DNA sequence search. As a first proof of concept, we focus on accelerating one of the most essential flavors of the problem, called exact search. LISA builds on and extends FM-index, which is the state-of-the-art technique widely deployed in genomics tool-chains. Initial experiments with human genome datasets indicate that LISA achieves up to a factor of 4X performance speedup against its traditional counterpart.
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Indexes are models: a B-Tree-Index can be seen as a model to map a key to the position of a record within a sorted array, a Hash-Index as a model to map a key to a position of a record within an unsorted array, and a BitMap-Index as a model to indicate if a data record exists or not. In this exploratory research paper, we start from this premise and posit that all existing index structures can be replaced with other types of models, including deep-learning models, which we term learned indexes. The key idea is that a model can learn the sort order or structure of lookup keys and use this signal to effectively predict the position or existence of records. We theoretically analyze under which conditions learned indexes outperform traditional index structures and describe the main challenges in designing learned index structures. Our initial results show, that by using neural nets we are able to outperform cache-optimized B-Trees by up to 70% in speed while saving an order-of-magnitude in memory over several real-world data sets. More importantly though, we believe that the idea of replacing core components of a data management system through learned models has far reaching implications for future systems designs and that this work just provides a glimpse of what might be possible.
Significant efforts have been expended in the research and development of a database management system (DBMS) that has a wide range of applications for managing an enormous collection of multisource, heterogeneous, complex, or growing data. Besides the primary function (i.e., create, delete, and update), a practical and impeccable DBMS can interact with users through information selection, that is, querying with their targets. Previous querying algorithms, such as frequent itemset querying and sequential pattern querying (SPQ) have focused on the measurement of frequency, which does not involve the concept of utility, which is helpful for users to discover more informative patterns. To apply the querying technology for wider applications, we incorporate utility into target-oriented SPQ and formulate the task of targeted utility-oriented sequence querying. To address the proposed problem, we develop a novel algorithm, namely targeted high-utility sequence querying (TUSQ), based on two novel upper bounds suffix remain utility and terminated descendants utility as well as a vertical Last Instance Table structure. For further efficiency, TUSQ relies on a projection technology utilizing a compact data structure called the targeted chain. An extensive experimental study conducted on several real and synthetic datasets shows that the proposed algorithm outperformed the designed baseline algorithm in terms of runtime, memory consumption, and candidate filtering.
The mining of frequent subgraphs from labeled graph data has been studied extensively. Furthermore, much attention has recently been paid to frequent pattern mining from graph sequences. A method, called GTRACE, has been proposed to mine frequent patterns from graph sequences under the assumption that changes in graphs are gradual. Although GTRACE mines the frequent patterns efficiently, it still needs substantial computation time to mine the patterns from graph sequences containing large graphs and long sequences. In this paper, we propose a new version of GTRACE that enables efficient mining of frequent patterns based on the principle of a reverse search. The underlying concept of the reverse search is a general scheme for designing efficient algorithms for hard enumeration problems. Our performance study shows that the proposed method is efficient and scalable for mining both long and large graph sequence patterns and is several orders of magnitude faster than the original GTRACE.
There is great excitement about learned index structures, but understandable skepticism about the practicality of a new method uprooting decades of research on B-Trees. In this paper, we work to remove some of that uncertainty by demonstrating how a learned index can be integrated in a distributed, disk-based database system: Googles Bigtable. We detail several design decisions we made to integrate learned indexes in Bigtable. Our results show that integrating learned index significantly improves the end-to-end read latency and throughput for Bigtable.
Recent advancements in learned index structures propose replacing existing index structures, like B-Trees, with approximate learned models. In this work, we present a unified benchmark that compares well-tuned implementations of three learned index structures against several state-of-the-art traditional baselines. Using four real-world datasets, we demonstrate that learned index structures can indeed outperform non-learned indexes in read-only in-memory workloads over a dense array. We also investigate the impact of caching, pipelining, dataset size, and key size. We study the performance profile of learned index structures, and build an explanation for why learned models achieve such good performance. Finally, we investigate other important properties of learned index structures, such as their performance in multi-threaded systems and their build times.
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