Nathaniel Osgood

Nathaniel Osgood - Professor
Email: osgood@cs.usask.ca
Office : 254.4 Thorvaldson (Computational Epidemiology and Public Health Informatics Lab)
Phone: (306) 966 6102
Fax: (306) 966 4884 Email: osgood 'at' cs.usask.ca

BS EECS (MIT), MS EECS (MIT), PhD CS (MIT)



Professor, Department of Computer Science

Associate Faculty, Department of Community Health & Epidemiology

Associate Faculty, Bioengineering Division

(CV) (Google Scholar) (LinkedIn) (Youtube) (Selected dynamic models pubs) (Selected combos of dynamic modeling & machine learning) (Ethica & iEpi)


Research Interests -- Combining Data Science, Systems Science, Computational Science and Applied Math to improve decision making in health and healthcare

My research is focused on providing cross-linked system simulation, mobile data collection, and theory-informed machine learning/artificial intelligence tools, and Category Theory-informed metalinguistic abstraction to inform decision making in health. Such tools can, for example, aid public health decision makers in putting into place cost-effective preventive policies, design more effective screening or treatment strategies for an illness, help support epidemiological models that learn from incoming evidence and are kept perpetually up-to-date with the latest evidence so as to provide for more reliable policy planning. Such tools can further enable insight into the causes underlying changes in the number of cases of a disease reported, and react more quickly to an outbreak of infectious disease when it occurs.

Tools of choice include supplementing system science dynamic models (particularly Agent-Based models, System Dynamics, and discrete event simulation) with particle filtering and particle MCMC with such system science models, systems for visualizing state space reconstruction and for Convergent Cross Mapping (CCM), existing and novel machine learning and dynamic modeling toolsets, GPU-based computational statistics algorithms (PMCMC and Particle Filtering) and CCM. Of late, I have a particularly strong focus on leveraging understanding from Applied Category Theory -- an area I find to offer compelling alignment with the systems science perspective, synergies with systems science techniques, the requisite power to deliver compelling insight, and an outstanding foundation for more powerful tools for study of complex systems.

All such tools are applied within the health sphere, as this is our elected point of focus and dedication. We further make extensive investment in machine learning to sharpen and broaden the health surveillance, including using our Ethica epidemiological smartphone and wearable-based data collection system, time series of search volumes, time series of machine-learning-classifed Twitter messages, web-scraped data, and other mechanisms. For example, as part of our strategy of using twitter for health surveillance in Canada, we have amassed more than 200M tweets. The types of data we obtain through surveillance data are classified using machine learning tools (including more traditional tools through to deep learning) to flag tweets of relevance and inform our particle-filtered and PMCMC-regrounded models.

Various Internal and External Summaries of Aspects of my Work

I list here some relevant links to varied summaries of our work.

Here is a list of selected elements of my dynamic models (Agent-Based models, System Dynamics models, Hybrid Models, etc.) in Health.

Background on examples of our work combining dynamic modeling (Agent-Based Models and System Dynamics modeling) and machine learning/artificial intelligence/computational statistics tools

Particularly because I use it to disseminate updates on our work, and because there are others who share my name on LinkedIn, I note that my LinkedIn page can be found here

Similarly, while I put a great deal of emphasis on making a difference in diverse ways that are not captured in publications and citations, my Google Scholar page can be found here

Visitors interested in my innovations in contributing platforms for collection of big data and those interested my latest and entrepreneurial contributions may find of interest this link to the Ethica Data Services company for which I serve as co-founder and an ongoing contributor

Those who enjoy video-based learning may be interested in the 1000's of videos of my lectures that I maintain on my Youtube Channel

Spheres of Research: Further information

Our work includes both application and methodological components.

Health Applications

On the application side, our research involves collaborating with cross-disciplinary teams to create tools to inform the design of health interventions that are high leverage, robust, and cost-effective. Such applications are almost always pursued in close collaboration with broader teams, frequently including those with close clinical familiarity of the diseases and/or pathogens involved (particularly doctors and nurses), epidemiologists, biostatisticians, public health nurses, and researchers or others involved in data collection and surveillance.

Please see our applications page for more information on this work.

Data sources that we tap in this area include smartphone and wearable based data collection (particularly via the Ethica epidemiological data collection system, which emerged from our iEpi project), social media and search mining.

To help make sense of such data and make it actionable at policy, health services and clinical levels, we use a variety of tools, including Agent-Based modeling and ODE (System Dynamics, particularly when leveraged by Particle Filtering) and Discrete Event modeling & hybrids, MCMC, and PMCMC, deep learning for symptom and health-behaviour recognition, additional types of Machine Learning tools (e.g., HMMs and Bayesian Networks), CCM and State-Space Reconstruction. Much recent work has focused on fully homomorphic encryption and privacy-preserving technologies for health and social data. Where they fill a key gap, we also develop apps for smartphone and web platforms.

Methodological Research

Our methodological work reflects the fact that practitioners of dynamic modelling for public health currently face many hurdles and challenges in building, validating, executing, modifying and understanding their models.

Please see our methodological work page for additional information.

iEpi and Ethica

Our most recent contribution here comes in terms of the Ethica epidemiological data collection system, which provides a powerful platform for quickly defining , refining, running and monitoring, and analyzing and reporting on epidemiological data. This platform can tap into the exceptional power of smartphones as a health/mHealth data collection platform, but also leverages wearable devices and web-based data collection from consenting respondents. All of this work is undertaken in the context of strong privacy guarantees, including the capacity to pause data collection at any point, and (for many studies) the capacity for a respondent to retroactively delete previously collected data.

For information on earlier versions of our smartphone-based Ethica/iEpi epidemiological monitoring system, please see information on the Ethica epidemiological data collection system used globally and my iEpi page.

Bootcamp on Combining Data Science and Systems Science (Big Data and Dynamic Modeling) for Health

Registration and information for our coming 2019 bootcamp on Combining Data Science and Systems Science (Big Data and Dynamic Modeling) for Health 2019 (Jul 29-Aug 2, 2019)

Click here to see videos from our 2018 bootcamp on combining Data Science and System Science.

Selected Recent Publications

Please see my publications page and Curriculum Vitae for lists of some recent publications.

Model libraries and information

You can find my recent free library of public health agent-based and hybrid model at these materials from my August 2018 bootcamp. Look in the "Example Models" folder.

Videos & Screencasts

Classes & Tutorials

2019 University of Saskatchewan Bootcamps

For added information on the below, please write christine.hillis@usask.ca

2019 Bootcamp & Incubator on Understanding Health Behavior using Smartphones and Wearables

June 24-26, 2019

This tutorial introduces researchers & practitioners to tools, practical skills and the conceptual background required to define,deploy, monitor & analyze mHealth studies with no programming, and assists participants in getting started in applying such techniques to studies and applications of their specific interest. This tutorial will include hands-on work with the popular Ethica Health data collection system, which has been used by researchers across 4 continents (between it and predecessors, in approximately 100 studies).

Incubator participants will create first versions of mHealth studies in their areas of specific interest, including to build & test out custom study designs, survey instruments (sensor-triggered EMAs, image/audio&video reporting questions), Bluetooth Beacons to detect proximity to actors & resources, wearable technologies, crowdsourcing mechanisms, and sensor-triggered data collection mechanisms, and study data analysis via Apache Kibana.

Combining Data Science and Systems Science (Big Data and Dynamic Modeling) for Health

Jul 29-Aug 2, 2019

Will provide a particularly notable coverage of Particle Filtering and Particle MCMC methods for combining dynamic modeling with incoming data (especially streaming Big Data complementing traditional data), and diversity of case studies. Additional hands-on exercises, templates provided.

Agent-Based and Hybrid Modeling Bootcamp and Incubator for Health Researchers 2019

Aug 19-24, 2019

An intensive, hands-on tutorial offering health science researchers with a practical & accessible introduction to agent-based & hybrid system science modeling for health, together w/an Incubator to give most participants the opportunity to leave with a well-crafted exploratory ABM/hybrid model for their areas of custom interest. This intensive course provides in-class exercises, step-by-step written exercises and challenge problems, guest lectures on application & methodological topics, and distributed many example models not otherwise included with AnyLogic. Most videos, screencasts, and audio are available on my Youtube Channel. Please consult this course for my most refined materials on Agent-based modeling in AnyLogic

Other courses

I teach a graduate course that provides an introduction to dynamic (simulation) modeling for public health (CMPT 858). This course provides a basic hands-on introduction to the theory and practice of Agent-Based and System Dynamics modeling in the context of health issues. Two versions of this course are available, one focusing on Agent-Based modeling and the other on System Dynamics modeling. Screencasts and presentations from the lectures & tutorials of this class are available below. I hope that this material will be of value for those seeking to learn more about simulation modeling.

I have also taught a variety of smaller, tutorial-style courses related to modeling for Public Health. These sessions are taught using Vensim and AnyLogic software.

I further teach undergraduate courses in Software Project Management (CMPT 371) and co-located undergraduate & graduate courses on Advanced Software Engineering (CMPT 470 & CMPT 816).

I am glad to share the materials for these courses with interested parties.

Talks and Selected Tutorials

Videos of some of my talks and selected tutorials can be found here.

Trained Students Available

I currently supervise a broad set of students trained in Agent-Based Modeling, System Dynamics Modeling, and in the use of ubiquitous portable, wireless sensor systems for health insight and decision-making. These students operate at the undergraduate, M.Sc. and Ph.D. levels, and offer a wide range of skill levels in the health sciences, Computer Science, Information Technology and mathematics. Many such students value internship opportunities and knowing about post-graduation career opportunities. Some students are also interested in consulting options. Please be encouraged to write if you have opportunities available, as my students may be interested in learning about them.

Student Supervision and Traineeship Opportunities

Please see my page on student supervision.

In order to ensure that I continue to offer quality supervision to existing trainees, I am unable to take on additional students until May 2020.

Personal

For those interested in knowing more about my life outside of work, I also maintain a bare-bones personal webpage.

Last updated June 1, 2019. Please report problems to osgood@cs.usask.ca