A cloud‐based, multi‐modal, cognitive ophthalmic imaging platform for enhanced clinical trial design and personalized medicine in blinding eye disease
Age Related Macular Degeneration is the leading cause of irreversible blindness in Canada and the industrialized world, yet there are no treatments for the vast majority of patients. Led by Tracery Ophthalmics inc, and working with Translatum Medicus inc (TMi) and academic partners at the Robarts Research Institute, Western University, and the “High Risk Dry AMD Clinic” of St Michael’s Hospital, we will engage SOSCIP’s Cloud Analytics platform, including servers, software and human resources, to accelerate the search for new treatments.
Specifically, Tracery has developed a novel functional imaging method, “AMD Imaging” (AMDI) that has already generated unprecedented pictures of the retina (the film of the eye) that include both known and unknown “flavours” of disease (the phenotype). These complex images will be compared against an individual’s genetic makeup (their genotype) and their concurrent illnesses, medications, and lifestyle history (their epigenetics). Further, Tracery’s imaging will help identify particular patients that will benefit from TMi’s drug development program, and ultimately help doctors choose which treatment will work best. Over the course of two years, we will involve increasing numbers of medical experts and their patients to generate and amass AMDI images, evaluating them over time and against other modalities.
Ultimately, through the “I3” program, we will work with IBM to train Watson and the Medical Sieve to recognize and co‐analyse complex disease patterns in the context of the ever‐expanding scientific literature. In short, we will leverage cloud‐based computing, to integrate image‐based and structured data, genomics and large data analytic to unite global users. We anticipate that this approach will significantly accelerate drug development, providing personalized treatment for the right patient at the right time.
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.
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.
Big cardiac data
We propose to develop a cloud based image centered informatics system powered by newly developed big data analytics from our group for automatic diagnosis and prognosis of heart failure (HF). HF is a leading cause of morbidity and mortality in Ontario and around the world. There is no cure. Therefore early diagnosis and accurate prediction is very critical before the symptoms appears. However, previously lack of efficient image analytics tool has been the major pitfall to have an accurate prognosis and early diagnosis system. The system will greatly improve the clinical accuracy and enables accurate early diagnosis and prediction by intelligently analyzing all associated historical images and clinical reports. The final system will not only greatly reduce the sudden death and irreversible cardiac conditions, but also offers a great optimization of decision system in current healthcare. This project is based on strength built upon one successful SOSCIP project and two OCE projects.
Cloud Native Big Data Engineering and Automation
XLScout is a startup engaged in democratizing Innovation and connecting research and development with intellectual property (IP) departments across the world. The company is investing in developing proprietary algorithms, using Artificial Intelligence and Machine learning, to mimic the behaviour of an expert searcher. XLScout focus is on creating a sustainable and adaptive text mining framework that will provide natural Language Processing (NLP)based research outputs for IP in different domains. Various data points have been secured for our solution and they include patent data, litigation data, corporate data, reassignment data, examination data, and other patient-related data. XLScout hosts a data vault of about 130+ million patent documents which occupies approximately 8TB of storage. Document searching, in general ,is a cumbersome process, and specifically, searching the patent-related documents requires advanced strategies that a novice searcher might not be aware of. Therefore, this type of search requires extensive effort and time. The main objective of this project is to automate the patent and non-patent search effectively by allowing machines to understand users’ queries and thus, creating a sustainable and adaptive text mining framework that will provide NLP-based research outputs for IP search in different domains. Furthermore, this project aims to develop scalable solutions for XLScout’s data vault on which the company will run proprietary AI and ML models and generate high-value analytic solutions to help the customers make informed decisions.
Deep Learning with Big Data for Innovation Acceleration
Presently, XLScout hosts data of over 130 million patents and 200+ million research publications occupying approximately 8TB of storage. Searching such a massive database using basic, mostly keyword-based search is very cumbersome and time-consuming. Moreover, it requires domain-specific knowledge about patents. With this project, XLScout aims to alleviate the pain of searching this massive system by employing machine learning (ML) and natural language processing(NL)techniques.Text autocompletion and recommendation will provide a better and smarter way for the end-users to search thismassive database. The auto-completion will be based on the corpus of patent documents and research publication to provide suggestions ofrelevant content. The MLmodel will be trained on that massive corpus taking into consideration language semantics. Techniques such as BERT and GPT 2/3 will be considered together with various pre-processing techniques. The size of the document database, document diversity, together with the subjectivity of desired results will make it challenging to evaluate such a system. We will employ both human-centric and automated evaluation approaches.Document categorization will also be based on the semantics, and it will group documents into labeled categories. Unsupervised techniques will be examined in their ability to do this categorization. However, different companies, XLScout clients, have different preferences in respect to this categorization. Therefore, an approach will be developed for the end-users to express their preferences by providing sample categories. Then, the model will learn from those preferences and carry out categorization. The challenge in this categorization is to enable unsupervised categorizationwhile supporting semi-supervision and customization. This categorization will be client-company specific and the modelwill have to learn from a limited number of example classes identified by the end-user.
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.
High performance computing for assessing and mitigating the effect of extreme wind on building and cities
As the second largest country in the world, Canada’s diverse geography and climate increases our cities exposure to different types of natural hazards, such as snow storms, hurricanes, tornadoes and floods. The insurance industry estimates that insured catastrophic losses in North America average $80B per year. In Toronto (2005), for example. a single tornado event resulted in $500M loss. This is further compounded by changes in climate, population growth and aging infrastructure.
To maintain the prosperity of our communities, it is imperative that a comprehensive framework be developed to assess and mitigate the impacts of extreme climate on cities. The current project aims to develop a multi-scale climate responsive design framework that accounts for the complex interaction between buildings and wind (including hurricane and tornado). This computational framework, at neighborhood scale, models urban micro-climate necessary to assess the impact of changing city topology on the pedestrian level wind, air quality and to generate boundary conditions for small-scale simulations. At building scale, it develops a full numerical aeroealstic model (e.g. building model that flex) immersed in turbulent city flows, for the first time. This frame work when integrated with artificial intelligence based optimization procedures, allow optimizing tall building aerodynamics (shape) and dynamics (structural systems) appropriate for current era of booming tall building construction.
As a result, Ontario will save materials and energy in one of the most resource intensive sector, while enhancing the safety of Ontarians during extreme climate. For successful implementation of the framework, a high performance computing environment and experimental validations are necessary, which will be enabled by two unique research facilities in Ontario, Blue Gene Q and WindEEE Dome, respectively.
Machine Learning Methods for Behavioural Biometrics
The project will focus on creating a Data architecture that will be composed of models, policies, rules and standards that will monitor which data is collected, and how it is stored, arranged and integrated into the system. The task of the professor and the student will be to create a data architecture and a machine learning algorithm that will help build a robust user-profile system that will help extract, store, build and analyse up to 1 million user profiles. This profile system will also be in charge of generating at least 50 behavioral data or 64 bytes of data per second. Simultaneously, the given data architecture will provide over 5 million user-profile recognitions per day through the use of predictive modeling and the given REST API call. This will help detect suspicious activities and anomalies without the use of browser cookies, location, and hardware information. For this project, the professor and the student will be given access to a part of F8th’s repository and must work together as a team to build a user-profile system that will help extract the given user profiles. This data architecture will help tolerate the behavioral data noise caused by the modification of input devices such as a mouse, keyboard, mobile and laptop. As F8th IDaaS is an Identity as a Service Solution (as described above), it is necessary to provide predictions on the given trained models (also known as behavioral biometrics). The market requires the predictions of the models to be done in less than 1 second (something that will be discussed later on when the project is being worked on by the professor and the student). The service must be provided at a reasonable cost and time; hence, it is very important to monitor the data as well as the resource consumption continuously. Lastly, as the project is to be worked on between the professor and the student as a team-constant discussions, comparisons, and decisions regarding the quality and the affordability of the solution will have to be done by the student and the professor.
Machine Learning Methods for Behavioural Biometrics
The project will focus on creating a Data architecture that will be composed of models, policies, rules and standards that will monitor which data is collected, and how it is stored, arranged and integrated into the system. The task of the professor and the student will be to create a data architecture and a machine learning algorithm that will help build a robust user-profile system that will help extract, store, build and analyze up to 1 million user profiles. This profile system will also be in charge of generating at least 50 behavioural data or 64 bytes of data per second. Simultaneously, the given data architecture will provide over 5 million user-profile recognitions per day through the use of predictive modelling and the given REST API call. This will help detect suspicious activities and anomalies without the use of browser cookies, location, and hardware information. For this project, the professor and the student will be given access to a part of F8th’s repository and must work together as a team to build a user-profile system that will help extract the given user profiles. This data architecture will help tolerate the behavioural data noise caused by the modification of input devices such as a mouse, keyboard, mobile and laptop. As F8th IDaaS is an Identity as a Service Solution (as described above), it is necessary to provide predictions on the given trained models (also known as behavioural biometrics). The market requires the predictions of the models to be done in less than 1 second (something that will be discussed later on when the project is being worked on by the professor and the student). The service must be provided at a reasonable cost and time; hence, it is very important to monitor the data as well as the resource consumption continuously. Lastly, as the project is to be worked on between the professor and the student as team-constant discussions, comparisons, and decisions regarding the quality and the affordability of the solution will have to be done by the student and the professor.
Modeling of urban wind flow and its interaction with buildings and their components
The design challenge is that as city populations rapidly increase, urban densification through vertical design will demand highly efficient, optimized and safe built environments to suit a changing climate. Therefore building and urban designers in the Architecture and Engineering (A&E) industry can benefit greatly from having access to robust, accurate, fast and cost effective wind modelling processes to assist in building and urban design performance simulation. However, urban wind flows are highly complex due to the time and spatial characteristics of the wind, its turbulence characteristics, and its interaction with the urban environment. Computational wind simulations therefore require very advanced modelling processes and demand enormous computational resources to replicate this phenomena. A validated and trusted computational wind simulation process, developed through this partnership, will offer new ways through which design practitioners can improve design, make buildings safer, more efficient and reduce building construction costs and materials through concept optimization. This research collaboration will allow the Ontario business and research community to continue to play its global and leading role in the application and export of its resources and expertise in physical testing and computational wind engineering.
Novel approaches and architecture for survivable smart grid
The term smart grid refers to a power grid in which the electricity distribution and management is upgraded by incorporating advanced two-way communications and pervasive computing capabilities for improved control, efficiency, reliability and safety [6]. Today’s power grid systems lack the ability to detect failure in ‘the last mile’ (i.e., in the power line between the user and the last transmission point). For example, during any power outage event, if the problem is within the last mile then the utility company’s operations center is unaware of the outage until notified by customers. Also, inside the power grid core systems, although the operations centre has the ability to detect a failure, their current systems lack the ability to provide an automated power backup facility. This means that when there is a core grid systems failure, their current fault notification systems can identify the failure, technicians are dispatched to diagnose and repair the fault. From the time the systems fails to the time it gets restored, the affected area/community experience power outage. In order to have (a) an automated failure notification systems in the last mile, and (b) a smart resilient system inside the grid’s core, today’s smart grid will require the ability to failure detection in the last mile, and a failure protection ability inside the core.
Our research will develop (a) an automatic fault notification systems for the last mile so that the operations center get real time notification of any failure in the last mile and can take measures to restore the outage; and (b) a new smart resilient system which would (during a power outage) automatically re-route its power to an alternate route bypassing the failed components of the grid so that it doesn’t lead to a power outage during a grid failure.
Quantitative analysis of Parkinson’s disease symptoms using whole-body kinematic technology for optimizing deep brain stimulation
Parkinson’s disease (PD) is a degenerative and progressive neurological disorder that can severely affect the mobility, particularly in advanced stages. Deep brain stimulation (DBS) is a surgical procedure used to treat the motor symptoms of Parkinson disease patients by implanting electrodes into the brain. Motor symptoms of PD like slowness of movement, tremor, walking and speech difficulty, and dyskinesia, are the key parameters that are taken into consideration by clinicians to program the DBS device. These motor symptoms differ across the body and are unique to each patient. Moreover, patient variability in terms of medication and non-motor symptoms like sleep and mood makes programming DBS electrode setting a significant challenge. On the other hand, the biomechanics of the whole-body are too complex to accurately assess visually due to the multitude of simultaneous movements. Therefore, a detailed, quantitative method of assessment needs to be employed to make the DBS setting optimization as accurate as possible.
Smart computing for tornado and downburst resilient cities
High intensity wind storms such as tornadoes and downbursts significantly impact the livelihood and the economy of Southern Ontario communities. According to the Insurance Bureau of Canada, the 2005 tornado outbreak in Southern Ontario cost more than 500 million Canadian dollars in insured loss. During tornado or downburst events, the built-environment sustains severe damages from the strong vertical vortexes of tornadoes or the horizontal winds that move outward from a central location during a downburst. These wind events have complex interactions with building components that can cause cascading failures and result in flying wind-born debris. The state-of-the-art on the assessment of tornadic wind effects is limited to rating the intensity of tornadoes based on surveying the damage following the disaster and involves inferring the aerodynamics from straight wind flows that are not representative of tornadoes.
This project aims to develop a combined mechanics based and data-driven approach for high resolution numerical simulations of realistic tornado/downburst and building-cluster interactions for cities. Incorporating physics-based tornado and downburst data into structural models will improve the design of structures and allow them to withstand the most commonly observed tornadoes and downbursts. A method for estimating the damage from high intensity wind assisted by simulations of tornado/downburst interactions in user-selected urban regions will uncover the potential hazards cities are exposed to. Furthermore, the developed computational models enabled by SOSCIP’s blue gene super computer will ensure that Western University and the partner organization, RWDI Inc. (an Ontario based consulting firm focusing on the microclimate and science of buildings) will deliver optimal and innovative high intensity wind engineering solutions around the world.
Spinal data analytics for computer aided diagnosis and prediction
A vast amount of information associated with spinal patient diagnosis, treatment and follow-up are generated every day. The application of multiple imaging tools (e.g. CT and MRI) has offered a great tool to diagnose and track diseases but at the same time poses significant challenges to human perception. One such challenge is the huge amount of information (a single Spinal Magnetic Resonance Imaging (MRI) is about 300M) associated with each scan. Often, a typical diagnosis and treatment of one spinal patient would involve multiple spinal imaging modalities and multiple follow-ups.
The ability to analyze changes in those data over time (longitudinal analysis) of all those data would provide much more accurate diagnosis and prediction. Despite the available data, there is a lack of automated tools to analyze the data to support physicians’ diagnosis, prognosis, and treatment. There is an urgent need of semi and fully-automated intelligent tools to help physicians with their quantitative measurement, longitudinal analysis, and population studies. To provide a comprehensive solution for the above challenges, we propose to develop a new generation of computer aided spinal data analytics system to improve the efficiency and accuracy of spinal patient care. This will be the first comprehensive cloud-based spinal diagnosis and prediction system, which will handle multiple spinal imaging modalities to facilitate detection, segmentation, direct historical diagnostic parameter extractions and medical records analytics. The automated data analytics will allow healthcare providers to manage the ever-growing amount of spinal data more effectively and positively contribute to immediate and long-term Canadian healthcare.
Using brain fMRI machine learning as a predictor of PTSD treatment outcomes for Canadian Military
Approximately 13% of Canadian Armed Forces (CAF) members and veterans deployed to Afghanistan are diagnosed with a deployment-related mental disorder, such as post-traumatic stress disorder (PTSD) and many will experience comorbid major depressive disorder. The proposed study will utilize brain imaging data (fMRI) to determine if neurobiological machine learning algorithms can predict treatment outcomes and psychiatric symptomatology in CAF members and veterans. This research will benefit CAF members and veterans through the identification and clinical application of novel avenues to personalized medicine; namely, using neuroimaging data to predict probable treatment outcomes and aid in the selection of appropriate treatment methodologies. The proposed research requires making data linkages and generalizing datasets by combining imaging and clinical outcomes data; however, by overcoming these challenges, we anticipate developing a tool that can aid in the diagnosis of PTSD and its various subtypes as well as inform treatment guidelines.