Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Efficient Document Re-Ranking for Transformers by Precomputing Term Representations

Deep pretrained transformer networks are effective at various ranking tasks, such as question answering and ad-hoc document ranking. However, their computational expenses deem them cost-prohibitive in practice. Our proposed approach, called PreTTR (Precomputing Transformer Term Representations), considerably reduces the query-time latency of deep transformer networks (up to a 42x speedup on web document ranking) making these networks more practical to use in a real-time ranking scenario. Specifically, we precompute part of the document term representations at indexing time (without a query), and merge them with the query representation at query time to compute the final ranking score. Due to the large size of the token representations, we also propose an effective approach to reduce the storage requirement by training a compression layer to match attention scores. Our compression technique reduces the storage required up to 95% and it can be applied without a substantial degradation in ranking performance.Comment: Accepted at SIGIR 2020 (long

A Compression Technique Exploiting References for Data Synchronization Services

Department of Computer Science and EngineeringIn a variety of network applications, there exists significant amount of shared data between two end hosts. Examples include data synchronization services that replicate data from one node to another. Given that shared data may have high correlation with new data to transmit, we question how such shared data can be best utilized to improve the efficiency of data transmission. To answer this, we develop an encoding technique, SyncCoding, that effectively replaces bit sequences of the data to be transmitted with the pointers to their matching bit sequences in the shared data so called references. By doing so, SyncCoding can reduce data traffic, speed up data transmission, and save energy consumption for transmission. Our evaluations of SyncCoding implemented in Linux show that it outperforms existing popular encoding techniques, Brotli, LZMA, Deflate, and Deduplication. The gains of SyncCoding over those techniques in the perspective of data size after compression in a cloud storage scenario are about 12.4%, 20.1%, 29.9%, and 61.2%, and are about 78.3%, 79.6%, 86.1%, and 92.9% in a web browsing scenario, respectively.ope