Computer Science

Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).

We study theta-joins in general and join predicates with conjunctions and disjunctions of inequalities in particular, focusing on ranked enumeration where the answers are returned incrementally in an order dictated by a given ranking function. Our approach achieves strong time and space complexity properties: with n denoting the number of tuples in the database, we guarantee for acyclic full join queries with inequality conditions that for every value of k , the k top-ranked answers are returned in O(npolylogn+klogk) time. This is within a polylogarithmic factor of the best known complexity for equi-joins and even of O(n+k) , the time it takes to look at the input and return k answers in any order. Our guarantees extend to join queries with selections and many types of projections, such as the so-called free-connex queries. Remarkably, they hold even when the entire output is of size n ??for a join of ??relations. The key ingredient is a novel O(npolylogn) -size factorized representation of the query output, which is constructed on-the-fly for a given query and database. In addition to providing the first non-trivial theoretical guarantees beyond equi-joins, we show in an experimental study that our ranked-enumeration approach is also memory-efficient and fast in practice, beating the running time of state-of-the-art database systems by orders of magnitude.

Bitvector filtering is an important query processing technique that can significantly reduce the cost of execution, especially for complex decision support queries with multiple joins. Despite its wide application, however, its implication to query optimization is not well understood. In this work, we study how bitvector filters impact query optimization. We show that incorporating bitvector filters into query optimization straightforwardly can increase the plan space complexity by an exponential factor in the number of relations in the query. We analyze the plans with bitvector filters for star and snowflake queries in the plan space of right deep trees without cross products. Surprisingly, with some simplifying assumptions, we prove that, the plan of the minimal cost with bitvector filters can be found from a linear number of plans in the number of relations in the query. This greatly reduces the plan space complexity for such queries from exponential to linear. Motivated by our analysis, we propose an algorithm that accounts for the impact of bitvector filters in query optimization. Our algorithm optimizes the join order for an arbitrary decision support query by choosing from a linear number of candidate plans in the number of relations in the query. We implement our algorithm in Microsoft SQL Server as a transformation rule. Our evaluation on both industry standard benchmarks and customer workload shows that, compared with the original Microsoft SQL Server, our technique reduces the total CPU execution time by 22%-64% for the workloads, with up to two orders of magnitude reduction in CPU execution time for individual queries.

Data analytics in the cloud has become an integral part of enterprise businesses. Big data analytics systems, however, still lack the ability to take user performance goals and budgetary constraints for a task, collectively referred to as task objectives, and automatically configure an analytic job to achieve these objectives. This paper presents a data analytics optimizer that can automatically determine a cluster configuration with a suitable number of cores as well as other system parameters that best meet the task objectives. At a core of our work is a principled multi-objective optimization (MOO) approach that computes a Pareto optimal set of job configurations to reveal tradeoffs between different user objectives, recommends a new job configuration that best explores such tradeoffs, and employs novel optimizations to enable such recommendations within a few seconds. We present efficient incremental algorithms based on the notion of a Progressive Frontier for realizing our MOO approach and implement them into a Spark-based prototype. Detailed experiments using benchmark workloads show that our MOO techniques provide a 2-50x speedup over existing MOO methods, while offering good coverage of the Pareto frontier. When compared to Ottertune, a state-of-the-art performance tuning system, our approach recommends configurations that yield 26\%-49\% reduction of running time of the TPCx-BB benchmark while adapting to different application preferences on multiple objectives.

Bounded-memory computability continues to be in the focus of those areas of AI and databases that deal with feasible computations over streams---be it feasible arithmetical calculations on low-level streams or feasible query answering for declaratively specified queries on relational data streams or even feasible query answering for high-level queries on streams w.r.t. a set of constraints in an ontology such as in the paradigm of Ontology-Based Data Access (OBDA). In classical OBDA, a high-level query is answered by transforming it into a query on data source level. The transformation requires a rewriting step, where knowledge from an ontology is incorporated into the query, followed by an unfolding step with respect to a set of mappings. Given an OBDA setting it is very difficult to decide, whether and how a query can be answered efficiently. In particular it is difficult to decide whether a query can be answered in bounded memory, i.e., in constant space w.r.t. an infinitely growing prefix of a data stream. This work presents criteria for bounded-memory computability of select-project-join (SPJ) queries over streams with application time. Deciding whether an SPJ query can be answered in constant space is easier than for high-level queries, as neither an ontology nor a set of mappings are part of the input. Using the transformation process of classical OBDA, these criteria then can help deciding the efficiency of answering high-level queries on streams.

Bregman distances (also known as Bregman divergences) are widely used in machine learning, speech recognition and signal processing, and kNN searches with Bregman distances have become increasingly important with the rapid advances of multimedia applications. Data in multimedia applications such as images and videos are commonly transformed into space of hundreds of dimensions. Such high-dimensional space has posed significant challenges for existing kNN search algorithms with Bregman distances, which could only handle data of medium dimensionality (typically less than 100). This paper addresses the urgent problem of high-dimensional kNN search with Bregman distances. We propose a novel partition-filter-refinement framework. Specifically, we propose an optimized dimensionality partitioning scheme to solve several non-trivial issues. First, an effective bound from each partitioned subspace to obtain exact kNN results is derived. Second, we conduct an in-depth analysis of the optimized number of partitions and devise an effective strategy for partitioning. Third, we design an efficient integrated index structure for all the subspaces together to accelerate the search processing. Moreover, we extend our exact solution to an approximate version by a trade-off between the accuracy and efficiency. Experimental results on four real-world datasets and two synthetic datasets show the clear advantage of our method in comparison to state-of-the-art algorithms.

Log-Structured Merge-trees (LSM-trees) have been widely used in modern NoSQL systems. Due to their out-of-place update design, LSM-trees have introduced memory walls among the memory components of multiple LSM-trees and between the write memory and the buffer cache. Optimal memory allocation among these regions is non-trivial because it is highly workload-dependent. Existing LSM-tree implementations instead adopt static memory allocation schemes due to their simplicity and robustness, sacrificing performance. In this paper, we attempt to break down these memory walls in LSM-based storage systems. We first present a memory management architecture that enables adaptive memory management. We then present a partitioned memory component structure with new flush policies to better exploit the write memory to minimize the write cost. To break down the memory wall between the write memory and the buffer cache, we further introduce a memory tuner that tunes the memory allocation between these two regions. We have conducted extensive experiments in the context of Apache AsterixDB using the YCSB and TPC-C benchmarks and we present the results here.

In many Big Data applications today, information needs to be actively shared between systems managed by different organizations. To enable sharing Big Data at scale, developers would have to create dedicated server programs and glue together multiple Big Data systems for scalability. Developing and managing such glued data sharing services requires a significant amount of work from developers. In our prior work, we developed a Big Active Data (BAD) system for enabling Big Data subscriptions and analytics with millions of subscribers. Based on that, we introduce a new mechanism for enabling the sharing of Big Data at scale declaratively so that developers can easily create and provide data sharing services using declarative statements and can benefit from an underlying scalable infrastructure. We show our implementation on top of the BAD system, explain the data sharing data flow among multiple systems, and present a prototype system with experimental results.

With the prevalence of online platforms, today, data is being generated and accessed by users at a very high rate. Besides, applications such as stock trading or high frequency trading require guaranteed low delays for performing an operation on a database. It is consequential to design databases that guarantee data insertion and query at a consistently high rate without introducing any long delay during insertion. In this paper, we propose Nested B-trees (NB-trees), an index that can achieve a consistently high insertion rate on large volumes of data, while providing asymptotically optimal query performance that is very efficient in practice. Nested B-trees support insertions at rates higher than LSM-trees, the state-of-the-art index for insertion-intensive workloads, while avoiding their long insertion delays and improving on their query performance. They approach the query performance of B-trees when complemented with Bloom filters. In our experiments, NB-trees had worst-case delays up to 1000 smaller than LevelDB, RocksDB and bLSM, commonly used LSM-tree data-stores, could perform queries more than 4 times faster than LevelDB and 1.5 times faster than bLSM and RocksDB, while also outperforming them in terms of average insertion rate.

In this extended abstract, we propose a new technique for query scheduling with the explicit goal of reducing disk reads and thus implicitly increasing query performance. We introduce \system, a learned scheduler that leverages overlapping data reads among incoming queries and learns a scheduling strategy that improves cache hits. \system relies on deep reinforcement learning to produce workload-specific scheduling strategies that focus on long-term performance benefits while being adaptive to previously-unseen data access patterns. We present results from a proof-of-concept prototype, demonstrating that learned schedulers can offer significant performance improvements over hand-crafted scheduling heuristics. Ultimately, we make the case that this is a promising research direction in the intersection of machine learning and databases.