GPGPU microbenchmarking for irregular application optimization

Irregular applications, such as unstructured mesh operations, do not easily map onto the typical GPU programming paradigms endorsed by GPU manufacturers, which mostly focus on maximizing concurrency for latency hiding. In this work, we show how alternative techniques focused on latency amortization can be used to control overall latency while requiring less concurrency. We used a custom-built microbenchmarking framework to test several GPU kernels and show how the GPU behaves under relevant workloads. We demonstrate that coalescing is not required for efficacious performance; an uncoalesced access pattern can achieve high bandwidth - even over 80% of the theoretical global memory bandwidth in certain circumstances. We also make other further observations on specific relevant behaviors of GPUs. We hope that this study opens the door for further investigation into techniques that can exploit latency amortization when latency hiding does not achieve sufficient performance

A Formal Account of the Open Provenance Model

On the Web, where resources such as documents and data are published, shared, transformed, and republished, provenance is a crucial piece of metadata that would allow users to place their trust in the resources they access. The Open Provenance Model (OPM) is a community data model for provenance that is designed to facilitate the meaningful interchange of provenance information between systems. Underpinning OPM is a notion of directed graph, where nodes represent data products and processes involved in past computations, and edges represent dependencies between them; it is complemented by graphical inference rules allowing new dependencies to be derived. Until now, however, the OPM model was a purely syntactical endeavor. The present paper extends OPM graphs with an explicit distinction between precise and imprecise edges. Then a formal semantics for the thus enriched OPM graphs is proposed, by viewing OPM graphs as temporal theories on the temporal events represented in the graph. The original OPM inference rules are scrutinized in view of the semantics and found to be sound but incomplete. An extended set of graphical rules is provided and proved to be complete for inference. The paper concludes with applications of the formal semantics to inferencing in OPM graphs, operators on OPM graphs, and a formal notion of refinement among OPM graphs

Beyond Volume: The Impact of Complex Healthcare Data on the Machine Learning Pipeline

From medical charts to national census, healthcare has traditionally operated under a paper-based paradigm. However, the past decade has marked a long and arduous transformation bringing healthcare into the digital age. Ranging from electronic health records, to digitized imaging and laboratory reports, to public health datasets, today, healthcare now generates an incredible amount of digital information. Such a wealth of data presents an exciting opportunity for integrated machine learning solutions to address problems across multiple facets of healthcare practice and administration. Unfortunately, the ability to derive accurate and informative insights requires more than the ability to execute machine learning models. Rather, a deeper understanding of the data on which the models are run is imperative for their success. While a significant effort has been undertaken to develop models able to process the volume of data obtained during the analysis of millions of digitalized patient records, it is important to remember that volume represents only one aspect of the data. In fact, drawing on data from an increasingly diverse set of sources, healthcare data presents an incredibly complex set of attributes that must be accounted for throughout the machine learning pipeline. This chapter focuses on highlighting such challenges, and is broken down into three distinct components, each representing a phase of the pipeline. We begin with attributes of the data accounted for during preprocessing, then move to considerations during model building, and end with challenges to the interpretation of model output. For each component, we present a discussion around data as it relates to the healthcare domain and offer insight into the challenges each may impose on the efficiency of machine learning techniques.Comment: Healthcare Informatics, Machine Learning, Knowledge Discovery: 20 Pages, 1 Figur

Context-Aware Personalized Activity Modeling in Concurrent Environment

Activity recognition, having endemic impact on smart homes, faces one of the biggest challenges in learning a personalized activity model completely by using a generic model especially for parallel and interleaved activities. Furthermore, inhabitant’s mistaken object interaction may entail in another spurious activity at smart homes. Identifying and removing such spurious activities is another challenging task. Knowledge driven techniques used for recognizing activity models are static in nature, lack contextual representation and may not comprehend spurious actions for parallel/interleaved activities. In this paper, a novel approach for completing the personalized model specific to each inhabitant at smart homes using generic model (incomplete) is presented that can recognize the sequential, parallel, and interleaved activities dynamically while removing the spurious activities semantically. A comprehensive set of experiments and results based upon number of correct (true positivity) or incorrect (false negativity) recognition of activities assert effectiveness of presented approach within a smart hom

Leveraging Pre-trained Language Models for Time Interval Prediction in Text-Enhanced Temporal Knowledge Graphs

Most knowledge graph completion (KGC) methods learn latent representations of entities and relations of a given graph by mapping them into a vector space. Although the majority of these methods focus on static knowledge graphs, a large number of publicly available KGs contain temporal information stating the time instant/period over which a certain fact has been true. Such graphs are often known as temporal knowledge graphs. Furthermore, knowledge graphs may also contain textual descriptions of entities and relations. Both temporal information and textual descriptions are not taken into account during representation learning by static KGC methods, and only structural information of the graph is leveraged. Recently, some studies have used temporal information to improve link prediction, yet they do not exploit textual descriptions and do not support inductive inference (prediction on entities that have not been seen in training). We propose a novel framework called TEMT that exploits the power of pre-trained language models (PLMs) for text-enhanced temporal knowledge graph completion. The knowledge stored in the parameters of a PLM allows TEMT to produce rich semantic representations of facts and to generalize on previously unseen entities. TEMT leverages textual and temporal information available in a KG, treats them separately, and fuses them to get plausibility scores of facts. Unlike previous approaches, TEMT effectively captures dependencies across different time points and enables predictions on unseen entities. To assess the performance of TEMT, we carried out several experiments including time interval prediction, both in transductive and inductive settings, and triple classification. The experimental results show that TEMT is competitive with the state-of-the-art.Comment: 10 pages, 3 figure

Assise: Performance and Availability via NVM Colocation in a Distributed File System

The adoption of very low latency persistent memory modules (PMMs) upends the long-established model of disaggregated file system access. Instead, by colocating computation and PMM storage, we can provide applications much higher I/O performance, sub-second application failover, and strong consistency. To demonstrate this, we built the Assise distributed file system, based on a persistent, replicated coherence protocol for managing a set of server-colocated PMMs as a fast, crash-recoverable cache between applications and slower disaggregated storage, such as SSDs. Unlike disaggregated file systems, Assise maximizes locality for all file IO by carrying out IO on colocated PMM whenever possible and minimizes coherence overhead by maintaining consistency at IO operation granularity, rather than at fixed block sizes. We compare Assise to Ceph/Bluestore, NFS, and Octopus on a cluster with Intel Optane DC PMMs and SSDs for common cloud applications and benchmarks, such as LevelDB, Postfix, and FileBench. We find that Assise improves write latency up to 22x, throughput up to 56x, fail-over time up to 103x, and scales up to 6x better than its counterparts, while providing stronger consistency semantics. Assise promises to beat the MinuteSort world record by 1.5x

Distinguishing Provenance Equivalence of Earth Science Data

Reproducibility of scientific research relies on accurate and precise citation of data and the provenance of that data. Earth science data are often the result of applying complex data transformation and analysis workflows to vast quantities of data. Provenance information of data processing is used for a variety of purposes, including understanding the process and auditing as well as reproducibility. Certain provenance information is essential for producing scientifically equivalent data. Capturing and representing that provenance information and assigning identifiers suitable for precisely distinguishing data granules and datasets is needed for accurate comparisons. This paper discusses scientific equivalence and essential provenance for scientific reproducibility. We use the example of an operational earth science data processing system to illustrate the application of the technique of cascading digital signatures or hash chains to precisely identify sets of granules and as provenance equivalence identifiers to distinguish data made in an an equivalent manner

Indexing methods for web archives

There have been numerous efforts recently to digitize previously published content and preserving born-digital content leading to the widespread growth of large text reposi- tories. Web archives are such continuously growing text collections which contain ver- sions of documents spanning over long time periods. Web archives present many op- portunities for historical, cultural and political analyses. Consequently there is a grow- ing need for tools which can efficiently access and search them. In this work, we are interested in indexing methods for supporting text-search work- loads over web archives like time-travel queries and phrase queries. To this end we make the following contributions: • Time-travel queries are keyword queries with a temporal predicate, e.g., “mpii saarland” @ [06/2009], which return versions of documents in the past. We in- troduce a novel index organization strategy, called index sharding, for efficiently supporting time-travel queries without incurring additional index-size blowup. We also propose index-maintenance approaches which scale to such continuously growing collections. • We develop query-optimization techniques for time-travel queries called partition selection which maximizes recall at any given query-execution stage. • We propose indexing methods to support phrase queries, e.g., “to be or not to be that is the question”. We index multi-word sequences and devise novel query- optimization methods over the indexed sequences to efficiently answer phrase queries. We demonstrate the superior performance of our approaches over existing methods by extensive experimentation on real-world web archives.In der jüngsten Vergangenheit gab es zahlreiche Bemühungen zuvor veröffentlichte Inhalte zu digitalisieren und elektronisch erstellte Inhalte zu erhalten. Dies führte zu einem weit verbreitenden Anstieg großer Textdatenbestände. Webarchive sind eine solche Art konstant ansteigender Textdatensammlung. Sie enthalten mehrere Versionen von Dokumenten, welche sich über längere Zeiträume erstrecken. Darüber hinaus bieten sie viele Möglichkeiten für historische, kulturelle und politische Analysen. Infolgedessen gibt es einen wachsenden Bedarf an Werkzeugen, die eine effiziente Suche in Webarchiven und einen effizienten Zugriff auf die Daten erlauben. Der Fokus dieser Arbeit liegt auf Indexierungsverfahren, um die Arbeitslast von Textsuche auf Webarchiven zu unterstützen, wie zum Beispiel time-travel queries oder phrase queries. Zu diesem Zweck leisten wir folgende Beiträge: • Time-travel queries sind Suchwortanfragen mit einem temporalen Prädikat. Zum Beispiel liefert die Anfrage “mpii saarland” @ [06/2009] Versionen des Dokuments aus der Vergangenheit als Ergebnis. Zur effizienten Unterstützung solcher Anfragen ohne die Indexgröße aufzublasen, stellen wir eine neue Strategie zur Organisation von Indizes dar, so genanntes index sharding. Des Weiteren schlagen wir Wartungsverfahren für Indizes vor, die für solch konstant wachsende Datensätze skalieren. • WirentwickelnTechnikenzurAnfrageoptimierungvontime-travelqueries, nachstehend partition selection genannt. Diese maximieren den Recall in jeder Phase der Anfrageverarbeitung. • Wir stellen Indexierungsmethoden vor, die phrase queries unterstützen, z. B. “Sein oder Nichtsein, das ist hier die Frage”. Wir indexieren Sequenzen bestehend aus mehreren Wörtern und entwerfen neue Optimierungsverfahren für die indexierten Sequenzen, um phrase queries effizient zu beantworten. Die Performanz dieser Verfahren wird anhand von ausführlichen Experimenten auf realen Webarchiven demonstriert