An Extensible Timing Infrastructure for Adaptive Large-scale Applications

Real-time access to accurate and reliable timing information is necessary to profile scientific applications, and crucial as simulations become increasingly complex, adaptive, and large-scale. The Cactus Framework provides flexible and extensible capabilities for timing information through a well designed infrastructure and timing API. Applications built with Cactus automatically gain access to built-in timers, such as gettimeofday and getrusage, system-specific hardware clocks, and high-level interfaces such as PAPI. We describe the Cactus timer interface, its motivation, and its implementation. We then demonstrate how this timing information can be used by an example scientific application to profile itself, and to dynamically adapt itself to a changing environment at run time

Learned Cardinalities: Estimating Correlated Joins with Deep Learning

We describe a new deep learning approach to cardinality estimation. MSCN is a multi-set convolutional network, tailored to representing relational query plans, that employs set semantics to capture query features and true cardinalities. MSCN builds on sampling-based estimation, addressing its weaknesses when no sampled tuples qualify a predicate, and in capturing join-crossing correlations. Our evaluation of MSCN using a real-world dataset shows that deep learning significantly enhances the quality of cardinality estimation, which is the core problem in query optimization.Comment: CIDR 2019. https://github.com/andreaskipf/learnedcardinalitie

Estimating Cardinalities with Deep Sketches

We introduce Deep Sketches, which are compact models of databases that allow us to estimate the result sizes of SQL queries. Deep Sketches are powered by a new deep learning approach to cardinality estimation that can capture correlations between columns, even across tables. Our demonstration allows users to define such sketches on the TPC-H and IMDb datasets, monitor the training process, and run ad-hoc queries against trained sketches. We also estimate query cardinalities with HyPer and PostgreSQL to visualize the gains over traditional cardinality estimators.Comment: To appear in SIGMOD'1

Integrated Assessment and Prediction of Transcription Factor Binding

Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of chromatin binding does not necessarily imply regulation, and binding may be difficult to detect if it is condition or cofactor dependent. To address these challenges, we present an approach for reliably assigning transcription factors (TFs) to target genes that integrates many lines of direct and indirect evidence into a single probabilistic model. Using this approach, we analyze publicly available chIP-chip binding profiles measured for yeast TFs in standard conditions, showing that our model interprets these data with significantly higher accuracy than previous methods. Pooling the high-confidence interactions reveals a large network containing 363 significant sets of factors (TF modules) that cooperate to regulate common target genes. In addition, the method predicts 980 novel binding interactions with high confidence that are likely to occur in so-far untested conditions. Indeed, using new chIP-chip experiments we show that predicted interactions for the factors Rpn4p and Pdr1p are observed only after treatment of cells with methyl-methanesulfonate, a DNA-damaging agent. We outline the first approach for consistently integrating all available evidences for TF–target interactions and we comprehensively identify the resulting TF module hierarchy. Prioritizing experimental conditions for each factor will be especially important as increasing numbers of chIP-chip assays are performed in complex organisms such as humans, for which “standard conditions” are ill defined

Integrating Web 2.0 technologies with scientific simulation codes for real-time collaboration

Abstract—This paper motivates how collaborative tools are needed to support modern computational science, using the case study of a distributed team of numerical relativists developing and running codes to model black holes and other astrophysical objects. We describe a summary of previous tools developed within the collaboration, and how they are integrated and used with their simulation codes which are built using the Cactus Framework. We also describe new Cactus tools which use the Twitter and Flickr services. These tools are fundamentally integrated with the code base as Cactus modules and provide reliable, real-time information about simulations that can be easily shared across a collaboration. I

Ice Formation in Gas-Diffusion Layers

Under sub-freezing conditions, ice forms in the gas-diffusion layer (GDL) of a proton exchange membrane fuel cell (PEMFC) drastically reducing cell performance. Although a number of strategies exist to prevent ice formation, there is little fundamental understanding of the mechanisms of freezing within PEMFC components. Differential scanning calorimetry (DSC) is used to elucidate the effects of hydrophobicity (Teflon® loading) and water saturation on the rate of ice formation within three commercial GDLs. We find that as the Teflon® loading increases, the crystallization temperature decreases due to a change in internal ice/substrate contact angle, as well as the attainable level of water saturation. Classical nucleation theory predicts the correct trend in freezing temperature with Teflon® loading

Learned cardinalities: Estimating correlated joins with deep learning

We describe a new deep learning approach to cardinality estimation. MSCN is a multi-set convolutional network, tailored to representing relational query plans, that employs set semantics to capture query features and true cardinalities. MSCN builds on sampling-based estimation, addressing its weaknesses when no sampled tuples qualify a predicate, and in capturing join-crossing correlations. Our evaluation of MSCN using a real-world dataset shows that deep learning signiicantly enhances the quality of cardinality estimation, which is the core problem in query optimization

Estimating cardinalities with deep sketches

We introduce Deep Sketches, which are compact models of databases that allow us to estimate the result sizes of SQL queries. Deep Sketches are powered by a new deep learning approach to cardinality estimation that can capture correlations between columns, even across tables. Our demonstration allows users to define such sketches on the TPC-H and IMDb datasets, monitor the training process, and run ad-hoc queries against trained sketches. We also estimate query cardinalities with HyPer and PostgreSQL to visualize the gains over traditional cardinality estimators