Geoffrey Woollard

 
Simulation and inference in cryogenic electron microscopy
 
Why did you decide to pursue a graduate degree?

I became fascinated with cryo-EM in late 2017 with the Nobel Prize in Chemistry, which was awarded jointly to Jacques Dubochet, Joachim Frank, and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution". I am grateful for the opportunity I was given in 2018 to work for a scientific startup, Structural Biotechnology. At that time it was all hands on deck for the release of a full software suite for cryo-EM data processing. During my time there I saw how the co-founder Ali Punjani, a PhD student in computer science and the best boss I've ever had, creatively worked with Professors and company advisors David Fleet and John Rubinstein. The more I looked into the scientific foundations of cryo-EM, the more drawn I felt to pursue this area as a professional calling. It connected so much of my past interests and training. Unfortunately, despite my best efforts, it didn't work out to join the labs of John or David at the University of Toronto. There's steep competition for very few coveted spots in their groups! However, I am grateful for the help and advice I received while interacting with them, and I admire their intelligence, drive, personal warmth, and their intellectual commitment to the truth. I left the University of Toronto to find what I had imagined working with them would have been like.

Why did you decide to study at UBC?

I applied to UBC in 2020, during the pandemic. It was a close call between working with Marcus Brubaker, who co-founded my former employer Structura Biotechnology, before becoming an Assistant Professor at York University, and working with Khanh Dao Duc at UBC. Khanh introduced me to his collaborators at Stanford/SLAC, and there was a lot of common interest in the themes I was trying to explore through some preliminary projects and themes in end-to-end inference of inverse problems. I really wanted to be in a Department of Computer Science, as opposed to my undergraduate training in physics, and Khanh, although his primary appointment is in Mathematics, has an adjoint appointment in CS, and was able to facilitate a co-supervisory arrangement with CS Prof. Michiel van de Panne, who primarily works on human motion. We still haven't quite found a connection between the dynamics of proteins and other biomolecules, and human motion. But there's no shortage of technical common ground in more abstract computational and mathematical spaces.

What is it specifically, that your program offers, that attracted you?

Someone once told me, perhaps Khanh, or one of his applied math colleagues, that it's better to be someone good at math and physics in a computer science department, than the other way around. For whatever reason, computer science communities seem to be THE place to be for tooling up to solve complicated scientific problems. It makes sense when we consider the advances in computing in the past 100 years. Through some recommended reading from colleagues like Boyan Beronov, and perusing the Reading Room, I've come to understand some of these reasons. I highly second Boyan's recommendation of "Turing's Cathedral: The Origins of the Digital Universe" (2012) by George Dyson. The next book I'm reading on the subject is The History of Linear Algebra (SIAM, 2022). My humanities training taught me to understand things in their historical context, and science is no exception. A broader and more popular "The Information: A History, a Theory, a Flood" (2011) by James Gleick, the "biographer of ideas".

What was the best surprise about UBC or life in Vancouver?

I'm no stranger to UBC and have earned two other degrees here. However, before my current studies here I never spent much time in the ICICS/CS building. The best surprise about UBC has been the ICICS/CS Reading Room. Last year I had the opportunity to work with the Coordinator, Nobu Kawaguchi, and help her by suggesting titles to order and planning some in-person events. For instance, we organized a monthly book club, which has delved into truly UNIVERSAL topics surrounding the discipline of computer science. We are at a UNIVERSITY after all! We choose a different title every month, so people can participate even if they have only managed to read a little of the book. My favorites have been "Work Pray Code: When Work Becomes Religion in Silicon Valley" (Princeton University Press, 2022), "Unlocking the Clubhouse: Women in Computing" (The MIT Press, 2022), and "Klara and the Sun" (Knopf, 2021) by Kazuo Ishiguro, who was awarded the 2017 Nobel Prize in Literature.

What aspect of your graduate program do you enjoy the most or are looking forward to with the greatest curiosity?

I most enjoy the synergy between the whiteboard and the code. The ability to brainstorm symbolically, and play with the math, and then code up small examples to build and verify intuition. Frank Wood's probabilistic programming was foundational for this reason. I enjoy time at the whiteboard with my supervisors, Khanh Dao Duc and Michiel van de Panne, and dreaming up the next steps (experiments, figures) with them. Nick Trefethen's memoir "An Applied Mathematician's Apology" (SIAM, 2022) conformed to my intuitions of the centrality of applied mathematics for my work and the human reasons for the estrangement of pure and applied math.

What do you see as your biggest challenge(s) in your future career?

On a technical level: bridging the gap between idealized mathematical treatments, and the messiness and structured noise of empirical data. On a personal level: sitting down and doing the work. Maintaining the focus requires a tremendous amount of discipline in balance with mindfulness (it's not all grid). I'm using all the help I can get and am a big fan of Kevin Majeres's (Harvard) work on the science of focus. He is a medical doctor and psychiatrist and has developed a synthesis with his humanistic training.

How do you feel your program is preparing you for those challenges?

There are some very general approaches to solving inverse problems combining simulation and modeling together with inference: Markov Chain Monte Carlo, differential programming / deep learning, simulation-based inference, and probabilistic programming. I feel that my current academic home in the Dept of Computer Science provides an ideal environment for tooling up. To take things to the next level I have been studying convex optimization, advanced numerical linear algebra and programming languages (compilers, etc), and parallelism. Training in these areas, which is not part of traditional physics education, enables me to understand and leverage existing deep learning, probabilistic programming, and optimization libraries. Engineering fancy things like differentiability in discrete spaces and parallelism with sparse operations draws on many subfields.

What aspects of your life or career before now have best prepared you for your UBC graduate program?

My mother and father both started teaching and fostered a great love for learning and I think a great capacity to learn. They've accompanied me along my life journey, offering tireless encouragement. I've felt quite free around them because I trust they want what is good for me. My teacher in the first three years of elementary, Mrs. Elliot, fostered curiosity, a sense of play, embodied intuition, and the joy of sharing knowledge and discoveries with others. I'm very thankful for her "Montessori style", along with all the involvement of everyone's mom and dad that she fostered. I met up with her recently in my hometown of Winnipeg, and she told me the whole school eventually changed to this "alternative" style. As an adolescent, I was captivated by skateboarding and spent many hot summer days (and cold winter nights in parking garages) imagining my body performing a new trick, with just the right flick of the ankle and tension in the back, and weight distribution. UBC must be one of the only campuses that has its own skatepark! I've thought for some time that there's a deep connection between the embodied creativity in skateboarding and in scientific creativity. It particularly came to the fore when I was doing experimental work at the University of Toronto. Especially the interplay between the internal mental world of imagination and the external reality of communication with an audience. I've talked to some other skateboarders about this, including ones who have gotten into creative writing and the fine arts. Although skateboarding is in a new era as an Olympic sport, many of my favorite skaters described their craft as an art form. My undergraduate education at UBC overlapped with the Carl Wieman Education in Science Initiative (CWESI; 2007-2017). What best prepared me was the tutorials and office hours with Prof. Mona Berciu (I took Lagrangian Mechanics and Statistical Mechanics with her), and other symbolic heavy physics courses were great training. Some favorites were Modern Physics (QM and special relativity) with Mark van Raamsdonk, Biological Physics with Carl Hanson, Thermal Physics with Domingo Louis-Martinez, Electricity and Magnetism with Ariel Zhitnitsky, Quantum Mechanics with Kirk Madison. Although there were definitely other life science and chemistry courses that helped along the way, the physics department was unmatched in the quality of undergraduate instruction. My Master's supervisor, Jörg Gsponer, modeled scientific integrity and gave me and others a lot of freedom to use the tools that were working for us. I remember asking for advice if I should code in Python or Pearl! Now I suppose it would be Python or Julia, and we'll look back and laugh... but about which one? My time at two Toronto scientific startups developing a codebase as a team and working with large coding bases was precious preparation for my current work. Looking back I should have seriously tried to stay at Structura and do a part-time Master's...

What do you like to do for fun or relaxation?

Spend time in contemplative prayer in the Nitobe Memorial Garden. Do laps down in Pacific Spirit: my favourite route these days is down Canyon Trail down to Spanish Banks, and sprinting back up the Spanish Trail to Chancellor Boulevard. Tennis at the outdoor Thurderbird courts. Soccer with colleagues in the mini field next to the baseball diamond. Nature poetry to wind down at night. The family-friendly films of Studio Ghibli.

What advice do you have for new graduate students?

The best advice I can give is going to be for people with a similar biography and goals. So my advice is for ambitious domain experts who want to tool up in computer science and solve challenging scientific problems. I would advise them to take very challenging courses that stretch their capacities and strike up collaborations with senior PhD students. Set up regular in-person work sessions (not a one hour meeting!) with your collaborators where you project your screen and do pair programming. Invest in an orderly development workflow (IDE like VS Code, a modern debugger, tunneling remotely onto a cluster with good resources like UBC's Sockeye, and organized software engineering practices). Learn by doing. Make sure there's enough silence in your day to maintain focus and do deep work. Graduate school is a privileged time to lay the foundations for your life's work as a contribution to humanity.

Outside of your academic work, what are the ways that you engage with your local or global community? Are there projects in particular that you are proud of?

After my Master's in 2014, I decided to work in youth development for Westbrook Education Fund and dedicate myself to studying philosophy, languages, and theology. During this time I had the chance to engage in partnerships with Musqueam (through the Dept. of Fisheries, especially Terry Fisher and Willard (Woody) Sparrow), and with other community partners in Portugal, Spain, Nicaragua and in remote Manitoban communities around Lake Winnipeg. I learned a lot about governance and long-term sustainable development from collaborating with Musqueam. The projects with them involved ecological work around Musqueam Stream and Musqueam Park. These had started before 2010 and I returned to the same locations for week long annual projects for more than half a decade and studied our impact. Some years later Woody told me how he continued this work and pushed into Pacific Spirit with help from Metro Vancouver (including their extra hands and equipment). Besides what I learned through interacting in person with community members, I attended some anthropology guest speakers hosted by the community, and studied books on their history, anthropology, and mythology. Reflecting on all of this, it's given me a grander perspective on truth and reconciliation, especially through the lens of technology and our relationship with the cosmos. I continue to think about the wisdom I've witnessed, and what this means for areas in physics and computer science. I have followed some indigenous themed initiatives on computer science education and language revitalization. While still at UBC I would like to build some bridges between the Computer Science Department and community partners that could outlast me. I recently wrote a paper about some of my thoughts for a local conference, extending the thought of Robin Wall Kimmerer (Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants, 2013) to the scientific areas I'm focusing on.

 
 
 

Explore our wide range of course-based and research-based program options!