(FoRCE): Powering clinical trials research through a secure and integrated data management platform
Critical care units are one of the most data-rich environments in clinical settings, with data being generated by advanced patient monitoring, frequent laboratory and radiologic tests, and around-the-clock evaluation. There are substantial opportunities in linking data that are collected as a part of such clinical practice with data collected in a research setting, such as genome wide studies or comprehensive imaging protocols. However, security and privacy issues have historically been a significant barrier to the storage, analysis, and linkage of such biomedical data. Further, disparate technologies hinder collaboration across teams, most of which lack the secure systems required to enable federation and sharing of these data. This is particularly true when clinical practice or research designs require close to real time analysis and timely feedback, such as when dealing with streamed medical data or output from clinical laboratories. Current commercial and research solutions often fail to integrate different data types, are incapable of handling streaming data, and rely solely on the security measures put in place by the organizations that deploy them.
This proposal seeks to build FoRCE (Focus on Research and Clinical Evaluation), a scalable and adaptable add-on module to the existing Indoc Informatics platform that will address the critical gaps in cybersecurity and privacy infrastructure within shared clinical and research settings, while fulfilling important unmet needs for both the clinical and research communities. FoRCE will provide the secure architecture and processes to support the collection, federation and sharing of data from distributed clinical settings, including critical care units, clinical laboratories, and imaging facilities. The proposed platform will address several key issues including security considerations, infrastructure and software requirements for linkage, and solutions for handling streaming real time medical data, and ensuring regulatory and ethics compliance when linking diverse medical data modalities in a clinical setting.
FoRCE will be designed and developed with broad applicability in mind, and will therefore allow the different data types from numerous technologies and across multiple disease states to utilize the platform. The long term impact of FoRCE on improving the health of Ontarians is of course dependent on its utilization within research and clinical settings. An initial project which will utilize the platform as part of the testing and validation of FoRCE includes Dr. Maslove’s integrated approach to merging genomic and physiologic data streams from the ICU in the context of clinical research. FoRCE will enable Dr. Maslove’s team of critical care researchers to move beyond predictors of survival to focus on predictors of response to therapy, so that clinical trials in the ICU can be optimized to produce actionable evidence and personalized results. This will lead to better allocation of ICU resources, which in Canada cost nearly $3,000 per patient per day – $3.72 billion per year.
A parallel algorithm for quantum circuit synthesis
Quantum circuit synthesis is an important step in the process of quantum compilation. Given an arbitrary unitary operation, quantum circuit synthesis is the process that constructs a quantum circuit using only gates from a universal gate set which is either exactly, or approximately equivalent to the original operation. The currently known algorithms for multi-qubit circuit synthesis run in exponential time and rely on the generation of databases many GBs in size to complete the search; synthesis of circuits of more than 3 qubits up to a certain length is infeasible using current methods due to this exponential scaling. We have developed a framework and accompanying software that uses time/memory tradeoffs and parallel collision finding techniques to synthesize circuits. A simple implementation using 16 OpenMP threads found that this approach can increase the speed of synthesis over previous algorithms, as well as synthesize larger circuits. In order to fully reap the benefits offered by this algorithm, we are developing a hybrid OpenMP/MPI algorithm, with the hopes of scaling up this method to thousands of cores or more.
Advancing microarray analysis with GPU-based image analysis
Multiplexed tests detect multiple analytes from a single biological specimen in an automated fashion using microarrays. These can be used to determine patient immune response with minimal invasiveness and to better quantify biomarkers for advanced biological tests. To do this, microarrays require the printing of biological and chemical materials onto an optically transparent substrate (this require dispensing, curing, putting down a protective coating that is then dried to create a plate). Each well contains multiple spots (sensors) to detect different proteins. The proposed work improves analytical tools with a focus on accuracy, significantly decreased time to results and advanced image analysis using capability provided by SOSCIP. The SOSCIP platforms allow testing new approaches using cloud-based analysis as well as develop tools necessary for in-house analysis. The work will enhance the performance of current assay designs and inform the next generation of assays to support the partner’s technology leadership position. The results will be implemented immediately by the industry partner – as has been done in the previous work. The impact will be to place SQI in a unique market position in the diagnostics market. Ultimately, this work aligns with the partner’s goal of “cheaper, better, faster”.
Advancing sustainable aerodynamic solutions with improved modeling
Within current aerospace design, it is necessary to over-engineer features to ensure stability and safety under emergency conditions. It would be ideal to develop capabilities to reduce the size of large elements of commercial aircraft with reliable technologies that ensure safe operation under hazardous conditions. A key advantage of the synthetic jet is that no bulky air source and supply system is required to provide actuation to the flow. The planned changes to the aircraft structure that increase fuel economy and reduce weight will ensure the success of the economically important Canadian aerospace industry.
Agile real time radio signal processing
Canadian VLBI capability has been missing for a decade. Jointly with Thoth Technology Inc we propose to restore domestic and international VLBI infrastructure that will be commercialized by Thoth Technology Inc. This project will implement and optimize multi-telescope correlation and analysis software on the SOSCIP BGQ, Agile and LMS platforms. The resulting pipeline package will allow commercial turnkey VLBI delivery by Thoth Technology Inc to domestic and international customers into a market of about $10 million/year
An Integrated Risk Assessment Framework for Compound Flooding in Canadian Urban Environments
The simultaneous or subsequent occurrence different flood drivers including heavy rainfall, river overflow, storm tides, among others threaten Canadian communities and infrastructure especially in coastal environments. Analysis of drivers of flooding in isolation without proper characterization of their interrelationships can lead to a significant underestimation of flood risk. This can severely undermine resilience measures and lead to the misallocation of investment in flood protection. In this project, we will develop an integrated statistical and physically-based modelling framework to simulate and predict compound flood risks under climate change in Canadian coastal zones to develop effective mitigation plans. The proposed approach will quantifythe dependencies between multiple flood hazards and identify/characterize compound events using a novel multivariate statistical approach. We will set up and calibrate a land surface modelcoupled to a hydrodynamic model to characterize the multivariate behaviour of flooding. The resulting framework will assess the impacts of compound flooding and characterize the contribution of each driver to the impacted areas under future scenarios considering the effects of more intense hydroclimatic events and sea-level rise in a changing climate. In collaboration with the Institute for Catastrophic Loss Reduction (ICLR), we will disseminate the results from the proposed project directly to insurance industry involved in the management of urban flood risks. This project will provide river forecast centres, conservation authorities, insurance industries, municipalities, among other stakeholders with data, rigorous methodology, and personnel to analyze and predict compound flooding and will significantly contribute to improved resilience of Canadian cities and communities.
An intelligent immersive content creation platform for the non-programmer for training, maintenance and assembly using AR and VR.
OVA’s StellarX is an uncompromisingly good virtual and augmented reality software. Purpose-built for teams that want to collaborate and create in those new paradigms.
Application of Data Analytics in Industrial CFD
The long-term objective of this project is to develop an efficient interface between the large data sets generated by industrial-level computational fluid dynamics (CFD) simulations and the latest tools that are available for data analytics. Industrial-level CFD is very compute-intensive. This project capitalizes on the experience of the industrial partner (SOTAES) and the CFD group at the University of Windsor, which is currently running large-scale simulations using STAR-CCM+ software on Compute Canada resources for many fundamental studies to understand the evolution of bluff body flow field characteristics.
Assessment and adaptation strategies for a changing climate: future wind loading on buildings in Toronto
Maintaining resiliency of Canada’s built environment against extreme wind hazard is necessary to sustain the prosperity of our communities. Buildings are becoming more complex, lighter and taller making them more prone to wind effects. This is further aggravated by the long-term effects of climate change, and the associated uncertainty of future wind load characteristics. Historical climate data is no longer enough for long-term planning and adaptation in urban environments. The formulation of adaptation strategies to mitigate the effects of climate change in cities will require a collaborative effort that draws on expertise, tools, and approaches from a variety of disciplines.
This project will investigate the response of selected tall, highly flexible structures together with their surroundings in downtown Toronto under the new wind conditions due to climate change. Structures that are currently safe and serviceable under wind loading may experience issues (large accelerations, member failures) when the wind loading characteristics change with the changing climate. The multi-disciplinary project team will capitalize on the availability of large archives of climate model output, new tools of downscaling, and extensive computational resources. This technical expertise and infrastructure will enable the translation of knowledge of global climate change into actionable knowledge useful to practitioners in the area of urban building design. This project will deliver sustainability and resiliency-focused design, as well as retrofit recommendations for practitioners and decision makers with a direct benefit to the residents of Toronto.
Assessment of Active and Passive Methods to Reduce Pressure Fluctuations in Gas Turbine Testing Facilities
The R&D problem that the larger collaborative project has undertaken is focused on the problem that very large mass flow rates of air through newer engines (and thus the testing facilities) can result in large-amplitude, low-frequency unsteady pressure fluctuations in the exhaust portion of the testing facility. These can lead to unacceptable environmental noise emissions and/or excessively high fatigue loading on facility components. The engine exhaust flow entrains additional airflow through the facility, leading to a confined jet in the augmenter tube. The partially mixed jet impinges on the cone downstream after being decelerated in the diffuser. Thus, the problem is one of high Mach number jet impingement on a conical surface in a confined, diffusing internal flow. Jet impingement has been widely studied but the physical mechanisms at play in the confined geometry of interest here are not well understood. The main challenges are that the detailed flow physics within the facility are not known and that anything done to mitigate the problem must be sufficiently robust to survive in the test facility environment.
Assessment of Prototype Scour Data
Scour is the removal of riverbed sediment which can be induced due to the presence of channel contraction, hydraulic structures, natural fluctuations in discharge, or changes in sediment supply in a fluvial environment. Scour and erosion have been identified as the primary cause of the majority of bridge failures in North America. Several investigators have concluded that about 50% of all bridge collapses occur due to scour-related complications. The prevalence of scour-induced bridge collapses is indicative of the criticality of scour estimation in the interest of public safety as well as mitigation of infrastructure costs, as this type of collapse often requires significant investment for design and construction of replacement bridges, fault analysis and potential rehabilitation. The available bridge design codes are mostly extracted from estimates of scour at the laboratory scale (experiments in reduced-scale physical models), acquired under highly controlled conditions. Some sources of model inaccuracy include scale effects in physical hydraulic modelling; a lack of understanding of the flow physics of the phenomenon; and the limitations of current computational methods used to model sediment transport. A way to improve the prediction ability of current scour methodologies could be using observed scour values in real rivers to verify/correct such methods, as this proposed research intends to do. The aim of the present project is to study prototype scour data at various field site as well as to use computational tools to assess the efficacy of scour estimation methods for investigating the possible improvements to existing approaches.
Atomic-scale modeling of halide perovskites for optoelectronics and photovoltaics
The proposed applied research is of strategic importance to Ontario. The government of Ontario has repeatedly affirmed its commitment to creating a culture of environmental sustainability in the province, most recently via the Long-Term Energy Plan (2012). The Long-Term Energy Plan sets a 20-year course for Ontario’s clean energy future, and its priorities include the continued development of a diverse supply mix, including more renewable energy sources, fostering a culture of energy-efficiency, and encouraging the development of a clean energy economy. It specifically “encourages the development of renewable sources of energy such as wind, solar, hydro and bio-energy.” Efficient and economical photovoltaic systems such as those that will be facilitated via this project will play a very important role in realizing this objective. The proposed research will further support Ontario’s economy by generating new opportunities in the advanced materials and solar technology sectors, and by training a cadre of highly qualified personnel who will be poised to assume positions of global leadership in these industries.
Automated Assessment of Forest Fire Hazards
The proposed project is to develop a Deep Reinforcement Learning (DRL) model capable of using Light Detection and Ranging (LiDAR) data to automatically analyze whether there is a risk of forest fire due to vegetation management around electric equipment. The model automatically classifies points in a LiDAR scan to determine whether there is direct contact between vegetation and electric equipment and outputs control actions for an Unmanned Aerial Vehicle (UAV) that can autonomously inspect infrastructure as needed. Our research will focus on the solution of two different but complementary machine learning problems that the DRL model will have to solve to allow for a UAV to autonomously acquire data with sufficient quality for fire risk assessment. Firstly, there is the problem of perception, i.e., to analyze raw LiDAR data and deduce classifications of individual objects and their shape and orientation. Secondly, there is the problem of control, i.e., to use the perceived state of the environment as determined by the first stage to adequately navigate through the environment until a complete scan has been obtained of the region that we are conducting a fire risk assessment for. Solving these two problems in a harmonious way that allows for an efficient, accurate and a complete scan of the environment is an open research problem in the domain of DRL that we aim to address.
Automated cytogenetic dosimetry as a public health emergency medical countermeasure
Biodosimetry is a useful tool for assessing the radiation dose received by an individual when no reliable physical dosimetry is available. Our Automated Dicentric Chromosome Identifier software (ADCI) has been developed to automate dose estimation of gamma and X-ray radiation exposures. Biodosimetry laboratories currently process these data manually, and the capacity to handle more than a few samples at the same time would quickly overwhelm the laboratories. The software has been developed to handle radiation exposure estimation in mass casualty or moderate scale radiation events. Federal biodosimetry and clinical cytogenetic laboratories have automated systems to collect digital chromosome images of cells with and without chromosomes exposed to radiation. We have developed advanced image segmentation and artificial intelligence methods to analyze these images. ADCI identifies dicentric chromosomes (DCC), a widely recognized, gold standard hallmark of radiation damage. The number and distribution of DCCs are determined and compared with a calibration curve of known radiation dose. Our ADCI software can also generate these calibration curves. Our software computes the dose received of one or more test samples and generates a report for the user. The desktop version of ADCI contains an easy-to-use graphical user interface to perform all of these functions. The supercomputer version of this software proposed here will be optimized to determine the dose for many samples simultaneously, which would be essential in the event of a mass casualty.
Characterization and Optimization of Heat Transfer from GRIP Metal Enhanced Surfaces
NUCAP specializes in brake pads and while improving their manufacturing process, they developed an innovative way to enhance the surface of metals in the form of small metal hooks (GRIP Metal). The raised features offer both increased surface and increased turbulence and flow mixing which can also greatly enhance convective heat transfer. The main objective of this project is to develop models which can accurately predict convective heat transfer and associated pressure drop for GRIP Metal enhanced surfaces. These will ultimately be used to optimize GRIP Metal surfaces for a wide range of heat exchange applications.
Computational high-throughput screening of catalyst materials for renewable fuel and feedstock generation
According to a World Energy Council Report, population growth and rising standards of living across the world will at least double global energy demand by 2050. Simultaneously, carbon dioxide emissions must be reduced significantly to prevent a catastrophic rise in global temperatures. Clean and abundant renewable energy sources are available; unfortunately, the intermittency of solar and wind power is a prevailing problem which is limiting the potential for widespread use. Our project seeks to address both of these issues through development of novel catalysts to electrochemically convert CO2 captured from power plants into fuels and other higher value chemical feedstocks using renewable electricity. This innovative strategy will (1) provide a long term storage solution by converting renewable electricity into a stable chemical fuel, (2) provide a means to intelligently recycle CO2 rather than storing it in deep underground aquifers, and (3) provide a cleaner and cheaper pathway for production of industrial chemical feedstocks and fuels. This could be a truly disruptive technology which would allow Canadian led manufacturing of high value chemicals and fuels in a low-cost and low-carbon fashion. Additionally, there are large benefits to Canada’s energy sector by facilitating the dispatchability of renewable power.
FinTech Deep Learning in Financial Modeling
The last four decades saw the development of the financial derivatives valuation technology. Only a few practical models, however, can be solved in closed form, and as most utilize numerical methods such as finite-difference partial differential equation solvers, discrete-time trees, or Monte-Carlo simulators, these traditional methods are quite slow. Running book valuation and risk processes on hundreds of CPU cores requires an overnight process to comply with regulatory and accounting standards. This creates a huge cost(~$10 million/year) and a commensurate environmental and carbon impact. Similar issues are now facing the Insurance industry due to the accounting standard IFRS 17. The key goal of the partnership is to develop deep learning, and more generally machine and reinforcement learning, models to accelerate these processes, and to provide efficient simulation engines for asset prices, volatility surfaces, derivative valuation, and hedging.
Design of OLED materials for manufacturing and improved product quality
Organic light emitting diodes (OLEDs) present a unique opportunity to produce thinner and more efficient lighting and displays. This will change the way we interact with light. The main barrier to mass adoption of OLEDs is the manufacturing process, due to the need for high throughput while maintaining nanoscale precision. High throughput operation requires materials that can undergo elevated temperature without decomposing. Our objective is to use computational chemistry to model innovative materials that can withstand these elevated temperatures while still providing high performing OLEDs. We will simulate targeted compounds using SOSCIP’s computer cluster examining properties relevant to OLED manufacturing processes. Promising materials will be synthesized and their properties experimentally measured then compared to the simulation results. The most promising materials will then be integrated into OLEDs and characterized by OTI Lumionics in their pilot scale manufacturing line located in Toronto, ON.
Detailed computational fluid dynamics modeling of UV-AOPs photoreactors for micropollutants oxidation in water and wastewater
Micropollutants such as bisphenol-A and N-nitrosodimethylamine pose a significant threat to aquatic life, animals, and humans beings due to their persistent and potentially carcinogenic nature. While most conventional water treatment methods cannot remove these contaminants, ultraviolet-driven (UV) advanced oxidation processes (AOPs) are effective in degrading micropollutants. As UV-AOPs require electrical energy to enable the treatment, energy costs present a barrier to the widespread adoption of this technology. In this project, we focus on the optimization of UV-AOPs-based reactors to enhance their degradation performance while reducing their energy consumption. In this respect, we will develop a detailed numerical model that integrates hydraulics, optics and chemistry to investigate UV-AOP photoreactors in a comprehensive manner.
The resulting information will then be utilized to design the next-generation of UV-AOP photoreactors commercialized by Trojan Technologies. The design space will be explored by high-performance computer simulations of full-scale photoreactors rather than simplified or scaled-down models. This will be accomplished by leveraging opensource software, artificial-intelligence optimization techniques and the second-to-none parallel-computing capabilities offered by Blue Gene/Q. Once the optimization of UVAOPs-based reactors is complete, the advanced modeling results generated using Blue Gene/Q will be utilized in the development of a simplified model for sizing purposes. This will be accomplished through combined use of metamodeling techniques and cloud computing. In brief, the concept is to simplify the detailed model developed earlier so that it can be simulated using hand-held mobile devices, which will allow the company’s sales personnel to market the optimized reactors. Consequently, it will allow the company to increase its competitiveness on global scale as well as to increase the rate of adoption of advanced water treatment technologies by water utilities and end-users.