We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment—previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches—yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/.

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Flash solid-state drives (SSDs) are changing the I/O landscape, which has largely been dominated by traditional hard disk drives (HDDs) for the last 50 years. In this paper we propose and systematically explore designs for using an SSD to improve the performance of a DBMS buffer manager. We propose three alternatives that differ mainly in the way that they deal with the dirty pages evicted from the buffer pool. We implemented these alternatives, as well another recently proposed algorithm for this task (TAC), in SQL Server, and ran experiments using a variety of benchmarks (TPC-C, E and H) at multiple scale factors. Our empirical evaluation shows significant performance improvements of our methods over the default HDD configuration (up to 9.4X), and up to a 6.8X speedup over TAC.

The growing volume of data produced continuously in the Cloud and at the Edge poses significant challenges for large-scale AI applications to extract and learn useful information from the data in a timely and efficient way. The goal of this article is to explore the use of computational storage to address such challenges by distributed near-data processing. We describe Newport, a high-performance and energy-efficient computational storage developed for realizing the full potential of in-storage processing. To the best of our knowledge, Newport is the first commodity SSD that can be configured to run a server-like operating system, greatly minimizing the effort for creating and maintaining applications running inside the storage. We analyze the benefits of using Newport by running complex AI applications such as image similarity search and object tracking on a large visual dataset. The results demonstrate that data-intensive AI workloads can be efficiently parallelized and offloaded, even to a small set of Newport drives with significant performance gains and energy savings. In addition, we introduce a comprehensive taxonomy of existing computational storage solutions together with a realistic cost analysis for high-volume production, giving a good big picture of the economic feasibility of the computational storage technology.

Data storage devices are getting "smarter." Smart Flash storage devices (a.k.a. "Smart SSD") are on the horizon and will package CPU processing and DRAM storage inside a Smart SSD, and make that available to run user programs inside a Smart SSD. The focus of this paper is on exploring the opportunities and challenges associated with exploiting this functionality of Smart SSDs for relational analytic query processing. We have implemented an initial prototype of Microsoft SQL Server running on a Samsung Smart SSD. Our results demonstrate that significant performance and energy gains can be achieved by pushing selected query processing components inside the Smart SSDs. We also identify various changes that SSD device manufacturers can make to increase the benefits of using Smart SSDs for data processing applications, and also suggest possible research opportunities for the database community.