Squeezing in a Little Time for ML this Past Summer: John Valen’s Experience

My name is John Valen. Having recently completed my undergraduate degree in statistics and economics here at U of T, and soon moving on to pursue my Master’s in statistics in Europe, the Medical Imaging Volunteer Internship program seemed almost tailored to my goal of getting valuable research experience within a constrained time window. Over the course of only several months this summer, I’ve had the pleasant and enriching experience of contributing ideas and code to the project that summer ROP student Wenda Zhao undertook for the dentistry department at U of T, along with the guidance and contributions of ML lab leader Hershel Stark.

Wenda’s blog post (see here) neatly summarizes the goal of this project, one whose aim is to determine the likelihood that a misdiagnosis may occur, depending on the degree of damage to the dental plate being used for X-rays. Contributions I’ve helped make in particular include:

– Creating sparse matrix representations of the grey scale X-ray images themselves in order to economize on memory and run-time performance
– Hand-engineering features: once the artifacts (damage such as scratches, dents,
blotches, etc) were segmented out via DBSCAN, they were characterized by a variety of different metrics: size (pixel count), average pixel intensity (images are grey scale), location (relative to the center of the plate image), etc. 

– Training a K-Means algorithm to cluster segmented artifacts from the dental plate images based on these hand-engineered features, whereby clustering them in this unsupervised manner gave us insight on their properties;

And much more. If you are not familiar with this machine learning lingo, then do not worry; I was hardly exposed to it myself before I started working in this lab. I went in knowing close to nothing practical and a whole lot theoretical, and came out knowing quite a little more in the way of the first one. Fine, a lot more: or
so I like to think. It may not seem clear how my contributions can be used in the future to help answer the ultimate question. The truth is, nothing is really clear at the moment. The project is still on-going and I intend to keep up with it, making contributions remotely to it while I am away in Belgium pursuing my Master’s degree. This is the greatness of it all, the amount of flexibility we have in answering these questions leaves a lot of room for creativity and contemplation. 

All in all, from my own perspective (which has been greatly expanded over the course of the summer), the volunteer program was a perfect means to experience the sheer amount of work that is enthusiastically undertaken by serious students in answering these important questions. I hope that I too can now consider myself at the very least climbing to their ranks while I move on to other and more numerous serious pursuits in my life. 

Good luck to you all, and do not underestimate yourselves.

John Valen

From YSP to Hanging Out at Stanford: Michelle Cheung

Hello! My name is Michelle Cheung and I am a rising 2nd year student at the University of Toronto. I was one of the Youth Summer Program (YSP) students in Dr. Pascal Tyrrell’s lab in the summer of 2016. During the program, I helped with the Medical Imaging Network Enterprise Project by surveying patients at Sunnybrooks hospital for their perspectives on sharing medical images for research.
Before entering Pascal’s lab in 2016, I took part in YSP the summer before in 2015. It was my two years in the summer program that made me aware of U of T. Being able to live in the dorms, attend classes and labs, and explore the city made me fall in love with the campus, especially the fast-paced metropolitan city life in contrast to the suburban life back home in California. More importantly, through the program, I was exposed to the lab environment. Of course, it was more than the allure of lab coats and micropipettes, but my time in the labs sparked my interest in research, hence am now pursuing genomics and hoping to learn more about hereditary diseases. Thus, when it came down to deciding which college to attend, all these factors placed U of T high up on the list.
Near the beginning of second semester of my first year, I started thinking about what to do over the summer. I couldn’t waste the 4 months and knew I needed the exposure and experience in professional labs if I plan on becoming a genetics researcher, hence started looking for research internships.
I was offered an internship position at the biopharmaceutical company, AbbVie, back in California, and it was quite an interesting experience applying for the position. I thought the first phone interview went decent but I was aware that I didn’t express enough interest in a particular aspect of research associated with the position. A month later, I interviewed a second time. It went really well until the interviewer said, “Let me ask you a challenging question.” I was expecting a deep theoretical question, and it ended up being, “Introduce yourself and your career goals in Cantonese.” In all fairness, my auditory skills are on point and I can understand conversational Cantonese, however, truthfully, my speaking skills had grown too rusty after not speaking it at home anymore. Hence, in my response, I managed to fluently get out my name, age, and school. I tried talking about my hobbies; trying to say “hiking with friends” turned out in me saying “taking walks with friends”, and “baking” turned out to me saying “cooking”. I was stumped when trying to describe my career goals as I blanked on how to say genetics and research and complicated bio words. Least to say, the awkward silence as I tried to come up with the right thing to say was mortifying. Little did I know that the interviewer would become my current manager (great guy), but hey, he hasn’t brought up the mortifying experience and I now have an embarrassing interview story to tell and a lesson learned.
Meanwhile, my parents connected with a family friend who was a scientist at Stanford. She was looking for a student research trainee to help her with her research project studying pulmonary disease, working with mice, and it was a fitting role for me.
I found out I was accepted to the research internship at AbbVie and luckily, the timing works out with my shadowing at Stanford. One internship would give me more practical lab experience while the other would give me a taste of the bio corporate industry. Hence, it’s the best of both worlds this summer – getting to experience both academic and industry research.
All in all, I am here today, about 1.5 months into the research internships, and having a blast. I had a wonderful first year of undergrad, and as I reflect, am very grateful for my time in YSP for bringing me to U of T and exposing me to the medical research world.     
-Michelle Cheung

My Past and Future at U of T: Helena Lan’s Perspective


Hey everyone, it’s been a while since I posted here. In case you don’t remember me – my name is Helena Lan, and I started in Professor Pascal Tyrrell’s group as a ROP299 student. Fast forward to the present, I have finished my specialist program in pharmacology, and will be graduating with an Honours Bachelor of Science degree later this month! But if you think that I am finally leaving U of T – nope, my journey is not over yet. This August, I will be living my dream of many years as I start my MD training at U of T! As I prepare to begin the next chapter of my life, I wanted to share with you how my involvement in Prof. Tyrrell’s group paved the way for me achieving my goal today.

At the end of my first year of undergrad, I connected with Prof. Tyrrell and took on a project investigating how the choice of non-invasive imaging modality for diagnosing carotid stenosis impacts patient care (check out my experience here http://www.tyrrell4innovation.ca/2014/08/helena-lan-summer-2014-rop.html).
Afterwards, I continued on as a research assistant, where I ­explored the need for statistics and research methodology training in the medical imaging department.  My early research endeavours showed me that research was not just pipetting; there is a diversity of research that can drive innovations and improve patient care. 
That being said, I also wanted to experience working in a wet lab setting. So upon completing my second year of undergrad, I ventured to the Karolinska Institute in Sweden to investigate the tumour killing mechanism of Natural Killer cells (find out more about my project here http://www.tyrrell4innovation.ca/2015/02/who-is-going-to-karolinska-institute.html). After a summer in basic science research, I decided to switch gears into translational research, where I worked on strategies to augment the therapeutic utility of stem cells and enhance the drug delivery platforms at Prof. Jeff Karp’s lab at Brigham and Women’s Hospital, Harvard Medical School. After I returned from Boston, my passion for discovering ways to improve existing treatments for diseases led me to my current work at Dr. Albert Wong’s lab at CAMH, where I am assisting with the characterization of a novel animal model for schizophrenia with the ultimate goal of using it as a screening platform for new anti-psychotics.
In my experiences as a researcher, I’ve always been very excited at the prospect that what I am working on right now may be brought into the clinic sometime down the road and offer benefits to patients. Then one day, I thought to myself, “How rewarding would it be if I can get involved in patient care, where I can directly impact the life of the person sitting in front of me?” With this idea planted in my mind, I decided to shadow a physician. As I observed how a doctor applies their scientific knowledge and the findings from medical research to figure out ways to best help their patients, my attraction to medicine gradually evolved. For a long time, my goal in life has been to make a positive impact on other people’s lives. But after that shadowing experience, I realized that I wanted to do so through taking on the role of a clinician.
I am incredibly grateful to the U of T medical school for giving me the opportunity to pursue my dream, as well as the pharmacology department and New College for their recognition of my undergrad academic achievements with the Dr. Walter Roschlau Memorial award and the Tricia L. Carroll Memorial Prize in the Life Sciences. But more importantly, thank you to U of T for the unforgettable undergrad experience. Not only was I able to immerse myself in fascinating science and interesting research, I was also connected with mentors who provided unconditional support to me along my journey. Even though the ROP project I worked on under the supervision of Prof. Pascal Tyrrell and Dr. Eli Lechtman ended years ago, the two of them have provided invaluable mentoring to me even to this day.
University can seem arduous at times, and it is almost inevitable that we run into obstacles here and there. But no matter how difficult the circumstances may be, never, ever, lose sight of your goal. Surround yourself with people who cheer you on, and invest the work that is necessary to reach your ambition. And one day, your dream will come true!  
All the best,
Helena Lan

MiVIP meets AI…

Well, I think it was inevitable. My data science lab has slowly crossed over to the dark side into the world of  Machine Learning and Artificial Intelligence.

Let me apologize for being MIA for so long. Life has been pretty hectic these past months as I have been building the MiDATA program here in the Department of Medical Imaging at the University of Toronto. The good news is that the MiVIP program will now be inviting students to participate in machine learning and artificial intelligence in medical image research.

This summer will include the launch our our MiStats+ML program where we will have students from the department of statistical sciences, computer sciences, and life sciences all work together on ML/AI projects in the MiDATA lab.

Stay tuned as we ramp up and get back to some our previous threads like MiWORD of the day…

See you in the blogosphere,


The Ram-ifications of Risk

In the final installment of this series, I want to discuss how we can use the Ratios of Risk in a clinical context. To recap, we previously discussed an absolute measure of risk difference (appropriately called the risk difference or RD), as well as a relative measure of risk difference (relative risk or RR). 

To see how we can apply these risks, let’s tweak our original example. Let’s assume that smartphone thumb could potentially lead to loss of thumb function (not really, don’t worry!). Let’s also suppose that surgery is a possible treatment for smartphone thumb, and the following results were obtained after a trial.

No Surgery (control)
thumb function
Lost thumb function

The big question is: how good an option is surgery?
Let’s calculate the RD (note that the “risk” here is of losing thumb function): 4/10 – 3/10= 0.1

In other words, there is a 10% greater risk of loosing thumb function if you did not have the surgery. Based on this information alone (or by calculating the RR and OR), we might be quick to conclude that surgery is a great intervention.

But before we do that, let’s calculate another statistic, which will prove to be very useful: it’s called the number needed to treat (or NNT), and is given by 1/RD. The NNT is the number of patients that must be treated for 1 additional patient to derive some benefit (retain an intact and functioning thumb). In our case, NNT = 1/0.1 = 10. So, in order save 1 patient from loosing his thumb, another 9 will have had to undergo surgery with no apparent benefit. As you can see, the NNT sheds a very humbling light on our intervention. The ideal NNT is equal to 1. Beyond that, we must keep in mind that the additional patients undergoing the treatment have been exposed to all the negative side effects, without the intended benefit.

Throughout this series we discussed the meaning of risk, how it can be used for comparison (the various ratios of risk), and finally its application in a clinical setting (the ramifications of risk). After all these posts, smartphone thumb may have started to seem like a very real threat. But I think you should be fine…. as long as you know the risks!

So what’s up with the Dodge Ram ad (I am actually a F150 guy myself)? Well I just thought it went well with ramifications of risk. Cheesy I know. But who knows maybe it will help you to remember…

See you in the blogosphere,

Indranil Balki and Pascal Tyrrell

A Medical Ethics ROP Journey with Jayun Bae

Jayun Bae – ROP299Y 2016-17
My name is Jayun Bae and I am completing my second year in the Neuroscience and Bioethics majors at the University of Toronto, St. George. I was a 2016-2017 Research Opportunity Program (ROP) student in Dr. Pascal Tyrrell’s lab, working on a study that investigated the ethics of sharing patient data with private organizations (see my timeline above). I am a member of the Hart House Debating Club and an events associate for the Life Science Student Network. 
My ROP project was necessitated by the partnership proposed by the Medical image Networking Enterprise (MiNE) that would establish a data-sharing relationship between public and private sector organizations. The ethical concerns with the partnership involved patient consent, privacy, and financial gain – but there were also issues that I
uncovered throughout the project. It quickly became clear that the answers could not be found through an examination of precedence or legal documents, because many of the research actions that would take place (specifically involving private organizations) fell in the grey area between what was legal and what was ethical. For example, the Personal Information Protection and Electronic Documents Act (PIPEDA) and Personal Health Information Protection Act (PHIPA) are two guidelines for organizations to follow when handling patient data – but neither are able to clearly and positively dictate how this partnership should operate.
Therefore, I developed a study that would seek expert opinions through the administration of a survey. I conducted interviews at Sunnybrook Health Sciences Centre and the University of Toronto and performed qualitative data analysis. My ROP project was presented at the ROP Poster Fair and the Victoria College Research Day events. The ROP was an extremely valuable experience in gaining research skills, and I’m grateful to
Dr. Tyrrell for the guidance and mentorship. The project is not yet completed, so I am looking forward to continuing the study beyond the scope of the ROP.   
Please have a look at my poster from the 2017 ROP Research Day below:

MRI, Statistics, Carotid Arteries, and 1000 Cups of Coffee with George Wang

GeorgeWang – ROP299Y 2016-17
I’m George. I have recently completed my 2nd year undergrad at the University of Toronto studying physiology and physics. In the fall-winter term of 2016-17 I had the privilege to work in Pascal’s group, looking into carotid artery MRI and using the volume of the carotid artery vessel wall as a marker for atherosclerosis. Having an acquired interest in medical imaging and a previous summer position working with PET, I saw this as an excellent opportunity to expand my knowledge of the field while having the chance to be exposed to clinical research methods. Above is my account of how the year went in a nutshell.
Have a look at my poster from the ROP Research Day below…

MiDATA – Enabling Medical Image Research at the University of Toronto

Poster to be presented at the Department of Medical Imaging Resident Achievement Day 2016

Where have a I been you ask? At my desk putting this program together! I apologize for being MIA for the past month or so but I it has been a busy time nurturing this fledgling program of MiNE (pun intended!).

Here is the premise:

Bridging the gap between clinical expertise and the science of managing and analyzing medical imaging data is challenging. To provide direction for data management as well as the analysis and reporting of research findings, we are in the process of introducing a data science unit – MiDATA – offering users an environment geared towards a “soup to nuts” approach to medical imaging research methodology and statistics. The Department of Medical Imaging of the University of Toronto is one of the largest in North America with a clinical faculty of more than 184 faculty, 60 residents and 80 fellows based at nationally and internationally renowned hospitals conducting cutting edge clinical research in the greater Toronto area. The challenge of any successful research and educational program is bridging the “know-do” gap. The goal of MiDATA is to facilitate impactful research through the efficient and creative use of a mentored learning environment.

Shout out to our collaborators the Division of Biostatistics from the Dalla Lana School of Public Health!

Tomorrow is the official unveiling at the 2016 Department of Medical Imaging Resident Achievement Day. I thought I would share with you our poster as a sneak peek…

Once you have digested its contents have a listen to Paper Planes by M.I.A. to decompress and…

… I’ll see you in the blogosphere (or at tomorrow’s event!)

Pascal Tyrrell

U of T Research Opportunity Program – Clare Sheen

Clare Sheen is an undergraduate student at the University of Toronto, in process of completing her Bachelor of Sciences in Genomics and Microbiology/Molecular Genetics. She was a 2015-6 Research Opportunity Program (ROP) student working on designing the Medical Image Network Enterprise (MiNE) interface for Dr. Pascal Tyrrell from U of T’s Department of Medical Imaging. She is currently a social director on the Life Science Student Network exec team and a volunteer at U of T’s Agrawal Lab where she helps with Drosophila experiments. She continues to seasonally work as a student camp teacher in the summer.

At the Research Opportunity Program (ROP) fair on March 3rd, U of T ROP students from different departments came together to share their research. A mock-up of the MiNE interface was presented in PowerPoint with the goal of increasing user engagement and encouraging the development of a medical imaging research community. Some features of the interface are presented below.

Back to Basics… Midpoint Thoughts from an ROP Student

Reaching new heights? (Source: NYT)

Through the ‘Research Opportunity Program‘ (ROP) for second year students at U of T, I have been working on a project about physicians’ willingness to use MRI as the front-line diagnostic imaging technology for carotid stenosis patients. For a description see here.

After a recent discussion with Dr. Tyrrell (my supervisor), and as I approach the midpoint of my ROP project, I thought it would be a good idea to review some of my background knowledge of carotid stenosis from my work in the Fall term. Having a certain amount of independence while working on this project has been a great experience, but it also means I am responsible for keeping track of my own learning.

So, during the first week of January, I took out my notes, my Physiology textbook, and several articles in order to compile what I have learned so far and highlight areas that need further review.

Review in process!

Begrudgingly, I’ll admit that this ‘self-directed’ review process has shed new light on the usefulness of midterms in other courses. However, I still prefer this project-based review format. It has allowed me to review necessary information to make sure that it is fresh in my mind. Now I feel more prepared to begin the second half of the project. I’m looking forward to a major meeting this month and all the other exciting parts of the project to come.

Julia Robson