Parallelising wavefront applications on general-purpose GPU devices

Pipelined wavefront applications form a large portion of the high performance scientific computing workloads at supercomputing centres. This paper investigates the viability of graphics processing units (GPUs) for the acceleration of these codes, using NVIDIA's Compute Unified Device Architecture (CUDA). We identify the optimisations suitable for this new architecture and quantify the characteristics of those wavefront codes that are likely to experience speedups

SPRINT: Ultrafast protein-protein interaction prediction of the entire human interactome

Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods have been proposed among which sequence-based ones are very promising. However, so far no such method is able to predict effectively the entire human interactome: they require too much time or memory. We present SPRINT (Scoring PRotein INTeractions), a new sequence-based algorithm and tool for predicting protein-protein interactions. We comprehensively compare SPRINT with state-of-the-art programs on seven most reliable human PPI datasets and show that it is more accurate while running orders of magnitude faster and using very little memory. SPRINT is the only program that can predict the entire human interactome. Our goal is to transform the very challenging problem of predicting the entire human interactome into a routine task. The source code of SPRINT is freely available from github.com/lucian-ilie/SPRINT/ and the datasets and predicted PPIs from www.csd.uwo.ca/faculty/ilie/SPRINT/

Context Trees: Augmenting Geospatial Trajectories with Context

Exposing latent knowledge in geospatial trajectories has the potential to provide a better understanding of the movements of individuals and groups. Motivated by such a desire, this work presents the context tree, a new hierarchical data structure that summarises the context behind user actions in a single model. We propose a method for context tree construction that augments geospatial trajectories with land usage data to identify such contexts. Through evaluation of the construction method and analysis of the properties of generated context trees, we demonstrate the foundation for understanding and modelling behaviour afforded. Summarising user contexts into a single data structure gives easy access to information that would otherwise remain latent, providing the basis for better understanding and predicting the actions and behaviours of individuals and groups. Finally, we also present a method for pruning context trees, for use in applications where it is desirable to reduce the size of the tree while retaining useful information

Improving Image Classification with Location Context

With the widespread availability of cellphones and cameras that have GPS capabilities, it is common for images being uploaded to the Internet today to have GPS coordinates associated with them. In addition to research that tries to predict GPS coordinates from visual features, this also opens up the door to problems that are conditioned on the availability of GPS coordinates. In this work, we tackle the problem of performing image classification with location context, in which we are given the GPS coordinates for images in both the train and test phases. We explore different ways of encoding and extracting features from the GPS coordinates, and show how to naturally incorporate these features into a Convolutional Neural Network (CNN), the current state-of-the-art for most image classification and recognition problems. We also show how it is possible to simultaneously learn the optimal pooling radii for a subset of our features within the CNN framework. To evaluate our model and to help promote research in this area, we identify a set of location-sensitive concepts and annotate a subset of the Yahoo Flickr Creative Commons 100M dataset that has GPS coordinates with these concepts, which we make publicly available. By leveraging location context, we are able to achieve almost a 7% gain in mean average precision

Understanding language-elicited EEG data by predicting it from a fine-tuned language model

Electroencephalography (EEG) recordings of brain activity taken while participants read or listen to language are widely used within the cognitive neuroscience and psycholinguistics communities as a tool to study language comprehension. Several time-locked stereotyped EEG responses to word-presentations -- known collectively as event-related potentials (ERPs) -- are thought to be markers for semantic or syntactic processes that take place during comprehension. However, the characterization of each individual ERP in terms of what features of a stream of language trigger the response remains controversial. Improving this characterization would make ERPs a more useful tool for studying language comprehension. We take a step towards better understanding the ERPs by fine-tuning a language model to predict them. This new approach to analysis shows for the first time that all of the ERPs are predictable from embeddings of a stream of language. Prior work has only found two of the ERPs to be predictable. In addition to this analysis, we examine which ERPs benefit from sharing parameters during joint training. We find that two pairs of ERPs previously identified in the literature as being related to each other benefit from joint training, while several other pairs of ERPs that benefit from joint training are suggestive of potential relationships. Extensions of this analysis that further examine what kinds of information in the model embeddings relate to each ERP have the potential to elucidate the processes involved in human language comprehension.Comment: To appear in Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistic

Compiler analysis for trace-level speculative multithreaded architectures

Trace-level speculative multithreaded processors exploit trace-level speculation by means of two threads working cooperatively. One thread, called the speculative thread, executes instructions ahead of the other by speculating on the result of several traces. The other thread executes speculated traces and verifies the speculation made by the first thread. In this paper, we propose a static program analysis for identifying candidate traces to be speculated. This approach identifies large regions of code whose live-output values may be successfully predicted. We present several heuristics to determine the best opportunities for dynamic speculation, based on compiler analysis and program profiling information. Simulation results show that the proposed trace recognition techniques achieve on average a speed-up close to 38% for a collection of SPEC2000 benchmarks.Peer ReviewedPostprint (published version

CFD applications: The Lockheed perspective

The Numerical Aerodynamic Simulator (NAS) epitomizes the coming of age of supercomputing and opens exciting horizons in the world of numerical simulation. An overview of supercomputing at Lockheed Corporation in the area of Computational Fluid Dynamics (CFD) is presented. This overview will focus on developments and applications of CFD as an aircraft design tool and will attempt to present an assessment, withing this context, of the state-of-the-art in CFD methodology