Transactions have been a key issue in database management for a long time and there are a plethora of architectures and algorithms to support and implement them. The current state-of-the-art is focused on storage management and is tightly coupled with its design, leading, for instance, to the need for completely new engines to support new features such as Hybrid Transactional Analytical Processing (HTAP). We address this challenge with a proposal to implement transactional logic in a query language such as SQL. This means that our approach can be layered on existing analytical systems but that the retrieval of a transactional snapshot and the validation of update transactions runs in the server and can take advantage of advanced query execution capabilities of an optimizing query engine. We demonstrate our proposal, TiQuE, on MonetDB and obtain an average 500x improvement in transactional throughput while retaining good performance on analytical queries, making it competitive with the state-of-the-art HTAP systems.

There is an increasing demand for stateful edge computing for both complex Virtual Network Functions (VNFs) and application services in emerging 5G networks. Managing a mutable persistent state in the edge does however bring new architectural, performance, and dependability challenges. Not only it has to be integrated with existing cloud-based systems, but also cope with both operational and analytical workloads and be compatible with a variety of SQL and NoSQL database management systems. We address these challenges with AIDA-DB, a polyglot data management architecture for the edge and cloud continuum. It leverages recent development in distributed transaction processing for a reliable mutable state in operational workloads, with a flexible synchronization mechanism for efficient data collection in cloud-based analytical workloads.

BACKGROUND: Gene expression studies are an important tool in biological and biomedical research. The signal carried in expression profiles helps derive signatures for the prediction, diagnosis and prognosis of different diseases. Data science and specifically machine learning have many applications in gene expression analysis. However, as the dimensionality of genomics datasets grows, scalable solutions become necessary. METHODS: In this paper we review the main steps and bottlenecks in machine learning pipelines, as well as the main concepts behind scalable data science including those of concurrent and parallel programming. We discuss the benefits of the Dask framework and how it can be integrated with the Python scientific environment to perform data analysis in computational biology and bioinformatics. RESULTS: This review illustrates the role of Dask for boosting data science applications in different case studies. Detailed documentation and code on these procedures is made available at https://github.com/martaccmoreno/gexp-ml-dask . CONCLUSION: By showing when and how Dask can be used in transcriptomics analysis, this review will serve as an entry point to help genomic data scientists develop more scalable data analysis procedures.

Logs are still the primary resource for debugging distributed systems executions. Complexity and heterogeneity of modern distributed systems, however, make log analysis extremely challenging. First, due to the sheer amount of messages, in which the execution paths of distinct system components appear interleaved. Second, due to unsynchronized physical clocks, simply ordering the log messages by timestamp does not suffice to obtain a causal trace of the execution. To address these issues, we present Horus, a system that enables the refinement of distributed system logs in a causally-consistent and scalable fashion. Horus leverages kernel-level probing to capture events for tracking causality between application-level logs from multiple sources. The events are then encoded as a directed acyclic graph and stored in a graph database, thus allowing the use of rich query languages to reason about runtime behavior. Our case study with TrainTicket, a ticket booking application with 40+ microservices, shows that Horus surpasses current widely-adopted log analysis systems in pinpointing the root cause of anomalies in distributed executions. Also, we show that Horus builds a causally-consistent log of a distributed execution with much higher performance (up to 3 orders of magnitude) and scalability than prior state-of-the-art solutions. Finally, we show that Horus' approach to query causality is up to 30 times faster than graph database built-in traversal algorithms.

Encrypted databases systems and searchable encryption schemes still leak critical information (e.g.: access patterns) and require a choice between privacy and efficiency. We show that using ORAM schemes as a black-box is not a panacea and that optimizations are still possible by improving the data structures. We design an ORAM-based secure database that is built from the ground up: we replicate the typical data structure of a database system using different optimized ORAM constructions and derive a new solution for oblivious searches on databases. Our construction has a lower bandwidth overhead than state-of-the-art ORAM constructions by moving client-side computations to a proxy with an intermediate (rigorously defined) level of trust, instantiated as a server-side isolated execution environment. We formally prove the security of our construction and show that its access patterns depend only on public information. We also provide an implementation compatible with SQL databases (PostgresSQL). Our system is 1.2 times to 4 times faster than state-of-the-art ORAM-based solutions.

Privacy sensitive applications that store confidential information such as personal identifiable data or medical records have strict security concerns. These concerns hinder the adoption of the cloud. With cloud providers under the constant threat of malicious attacks, a single successful breach is sufficient to exploit any valuable information and disclose sensitive data. Existing privacy-aware databases mitigate some of these concerns, but sill leak critical information that can potently compromise the entire system's security. This paper proposes d'Artagnan, the first privacy-aware multi-cloud NoSQL database framework that renders database leaks worthless. The framework stores data as encrypted secrets in multiple clouds such that i) a single data breach cannot break the database's confidentiality and ii) queries are processed on the server-side without leaking any sensitive information. d'Artagnan is evaluated with industry-standard benchmark on market-leading cloud providers.

The blooming of different cloud data stores has turned polystore systems to a major topic in the nowadays cloud landscape. Especially, as the amount of processed data grows rapidly each year, much attention is being paid on taking advantage of the parallel processing capabilities of the underlying data stores. To provide data federation, a typical polystore solution defines a common data model and query language with translations to API calls or queries to each data store. However, this may lead to losing important querying capabilities. The polyglot approach of the CloudMdsQL query language allows data store native queries to be expressed as inline scripts and combined with regular SQL statements in ad-hoc integration queries. Moreover, efficient optimization techniques, such as bind join, can still take place to improve the performance of selective joins. In this paper, we introduce the distributed architecture of the LeanXcale query engine that processes polyglot queries in the CloudMdsQL query language, yet allowing native scripts to be handled in parallel at data store shards, so that efficient and scalable parallel joins take place at the query engine level. The experimental evaluation of the LeanXcale parallel query engine on various join queries illustrates well the performance benefits of exploiting the parallelism of the underlying data management technologies in combination with the high expressivity provided by their scripting/querying frameworks.

The increasing demand for real-time analytics requires the fusion of Transactional (OLTP) and Analytical (OLAP) systems, eschewing ETL processes and introducing a plethora of proposals for the so-called Hybrid Analytical and Transactional Processing (HTAP) systems.

Window functions are a sub-class of analytical operators that allow data to be handled in a derived view of a given relation, while taking into account their neighboring tuples. We propose a technique that can be used in the parallel execution of this operator when data is naturally partitioned. The proposed method benefits the cases where the required partitioning is not the natural partitioning employed. Preliminary evaluation shows that we are able to limit data transfer among parallel workers to 14% of the registered transfer when using a naive approach.

In order to attain the promises of the Cloud Computing paradigm, systems need to be able to transparently adapt to environment changes. Such behavior benefits from the ability to predict those changes in order to handle them seamlessly. In this paper, we present a mechanism to accurately predict the resource usage of distributed key-value datastores. Our mechanism requires offline training but, in contrast with other approaches, it is sufficient to run it only once per hardware configuration and subsequently use it for online prediction of database performance under any circumstance. The mechanism accurately estimates the database resource usage for any request distribution with an average accuracy of 94 %, only by knowing two parameters: (i) cache hit ratio; and (ii) incoming throughput. Both input values can be observed in real time or synthesized for request allocation decisions. This novel approach is sufficiently simple and generic, while simultaneously being suitable for other practical applications. These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

NoSQL databases opt not to offer important abstractions traditionally found in relational databases in order to achieve high levels of scalability and availability: transactional guarantees and strong data consistency. In this work we propose pH1, a generic middleware layer over NoSQL databases that offers transactional guarantees with Snapshot Isolation. This is achieved in a non-intrusive manner, requiring no modifications to servers and no native support for multiple versions. Instead, the transactional context is achieved by means of a multiversion distributed cache and an external transaction certifier, exposed by extending the client's interface with transaction bracketing primitives. We validate and evaluate pH1 with Apache Cassandra and Hyperdex. First, using the YCSB benchmark, we show that the cost of providing ACID guarantees to these NoSQL databases amounts to 11% decrease in throughput. Moreover, using the transaction intensive TPC-C workload, pH1 presented an impact of 22% decrease in throughput. This contrasts with OMID, a previous proposal that takes advantage of HBase's support for multiple versions, with a throughput penalty of 76% in the same conditions.

The ability to access and query data stored in multiple versions is an important asset for many applications, such as Web graph analysis, collaborative editing platforms, data forensics, or correlation mining. The storage and retrieval of versioned data requires a specific API and support from the storage layer. The choice of the data structures used to maintain versioned data has a fundamental impact on the performance of insertions and queries. The appropriate data structure also depends on the nature of the versioned data and the nature of the access patterns. In this paper we study the design and implementation space for providing versioning support on top of a distributed key-value store (KVS). We define an API for versioned data access supporting multiple writers and show that a plain KVS does not offer the necessary synchronization power for implementing this API. We leverage the support for listeners at the KVS level and propose a general construction for implementing arbitrary types of data structures for storing and querying versioned data. We explore the design space of versioned data storage ranging from a flat data structure to a distributed sharded index. The resulting system, ALEPH, is implemented on top of an industrial-grade open-source KVS, Infinispan. Our evaluation, based on real-world Wikipedia access logs, studies the performance of each versioning mechanisms in terms of load balancing, latency and storage overhead in the context of different access scenarios.

Very large scale distributed systems provide some of the most interesting research challenges while at the same time being increasingly required by nowadays applications. The escalation in the amount of connected devices and data being produced and exchanged, demands new data management systems. Although new data stores are continuously being proposed, they are not suitable for very large scale environments. The high levels of churn and constant dynamics found in very large scale systems demand robust, proactive and unstructured approaches to data management. In this paper we propose a novel data store solely based on epidemic (or gossip-based) protocols. It leverages the capacity of these protocols to provide data persistence guarantees even in highly dynamic, massive scale systems. We provide an open source prototype of the data store and correspondent evaluation.

Recently, tuple-stores have become pivotal structures in many information systems. Their ability to handle large datasets makes them important in an era with unprecedented amounts of data being produced and exchanged. However, these tuple-stores typically rely on structured peer-to-peer protocols which assume moderately stable environments. Such assumption does not always hold for very large scale systems sized in the scale of thousands of machines. In this paper we present a novel approach to the design of a tuple-store. Our approach follows a stratified design based on an unstructured substrate. We focus on this substrate and how the use of epidemic protocols allow reaching high dependability and scalability.

NoSQL databases manage the bulk of data produced by modern Web applications such as social networks. This stems from their ability to partition and spread data to all available nodes, allowing NoSQL systems to scale. Unfortunately, current solutions' scale out is oblivious to the underlying data access patterns, resulting in both highly skewed load across nodes and suboptimal node configurations.

Database clusters based on share-nothing replication techniques are currently widely accepted as a practical solution to scalability and availability of the data tier. A key issue when planning such systems is the ability to meet service level agreements when load spikes occur or cluster nodes fail. This translates into the ability to provision and deploy additional nodes. Many current research efforts focus on designing autonomic controllers to perform such reconfiguration, tuned to quickly react to system changes and spawn new replicas based on resource usage and performance measurements. In contrast, we are concerned about the inherent impact of deploying an additional node to an online cluster, considering both the time required to finish such an action as well as the impact on resource usage and performance of the cluster as a whole. If noticeable, such impact hinders the practicability of self-management techniques, since it adds an additional dimension that has to be accounted for. Our approach is to systematically benchmark a number of different reconfiguration scenarios to assess the cost of bringing a new replica online. We consider factors such as: workload characteristics, incremental and parallel recovery, flow control and outdatedness of the recovering replica. As a result, we show that research should be refocused from optimizing the capture and transmition of changes to applying them, which in a realistic setting dominates the cost of the recovery operation.

Database replication has been a common feature in database management systems (DBMSs) for a long time. In particular, asynchronous or lazy propagation of updates provides a simple yet efficient way of increasing performance and data availability and is widely available across the DBMS product spectrum. High end systems additionally offer sophisticated conflict resolution and data propagation options as well as, synchronous replication based on distributed locking and two-phase commit protocols. This paper presents GORDA architecture and programming interface (GAPI), that enables different replication strategies to be implemented once and deployed in multiple DBMSs. This is achieved by proposing a reflective interface to transaction processing instead of relying on-client interfaces or ad-hoc server extensions. The proposed approach is thus cost-effective, in enabling reuse of replication protocols or components in multiple DBMSs, as well as potentially efficient, as it allows close coupling with DBMS internals.