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 https://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 https://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

Lessons Along the Way

https://betakit.com/startupcfo-explains-the-long-windy-road-to-a-closed-funding-round/
 
 
With summer almost here, it’s a good time to reflect on lessons learned from the academic year gone by. Since September, I’ve been working under Dr. Pascal Tyrrell’s supervision on a systematic review (SR) project investigating sample size determination methods (SSDMs) in machine learning (ML) applied to medical imaging. Shout out to the Department of Statistical Sciences where I completed my independent studies course! Here, I share important lessons I learned in the hopes that they may resonate with you.
 
Despite being a stats student (as you know from my previous posts!), I was initially new to ML and confronted with the task of critically reviewing theoretically-dense primary articles. I came to appreciate the first step was to develop a solid background – starting from high-level YouTube videos and lessons on DataCamp, to reading ML blogs and
review articles – all until I was confident enough to evaluate articles on my own. For me, the key to learning a complex subject was to build on foundational concepts and keep things as clear as possible. As Einstein once said: “If you can’t explain it simply, you don’t understand it well enough”.
 
Next, it was time to conduct a systematic search. The University of Toronto library staff were especially helpful at guiding me in use of OVID Medline and Embase, databases with methodical search procedures and a careful search syntax relying on various operators. To be thorough, we also sent a request out to the rest of our research team, who hand-searched through their own stash of literature. Along the way, we garnered support from the university, successfully receiving the Undergraduate Research
Fund grant. The lessons for me here? The importance of seeking expert help where appropriate, and that being resourceful can pay off (literally)! Finally, I valued our strong team culture, without which none of this would have been possible.
 
While working on the SR, I also conducted a subsampling experiment using a medical imaging dataset, testing the effect of class imbalance on a classifier’s performance. Hands-on/practical experiences are critical in developing a more nuanced understanding of subject material – in my case, an understanding that translated to my SR.
 
So now you are probably wondering about the results! The subsampling experiment helped us develop a model for the deleterious effect of class imbalance on classification accuracy and demonstrated that this effect was sensitive to total sample size. Meanwhile in our SR, we observed great variability in SSDMs and model assessment measures, calling for the need to standardize reporting practices.
 
That was a whirlwind recap of the year and I hope some of the lessons I learned resonate with you!
 
See you in the
blogosphere,
 
Indranil Balki
 
A special thanks to Dr. Pascal Tyrrell, as well as Dr.
Afsaneh Amirabadi & Team

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.

All the World’s a Stage

For journalists, authors, bloggers and tweeters, sharing articles has never been easier. Indeed, the public expects to be able to read articles about world events almost in real-time. For example,
the New York Times Twitter account was updated nine minutes ago
, and National Geographic tweeted three minutes ago. This expectation of speediness applies equally to scientific advances as it does to international affairs.
As an avid reader of online news, I would be the last to complain about being able to access such a vast amount of information. But there is something particularly noteworthy about information presented by a visible human. Perhaps that explains the persistence of televised news in the age of Twitter. 

Maybe it also explains the popularity of other media sources like TED talks, which often explain complex ideas in an engaging and understandable format. A personal favourite is “The best stats you’ve ever seen” by Hans Rosling. In his talk, Rosling explains the importance of little-known global public health data that shows the progress (or lack thereof) made by different countries over the past few decades. 

A more recent talk on a similar topic is also informative. One would be hard-pressed to find a paper or article that presents the same information with as much clarity and appeal.

In addition to numerous (maybe too numerous?!) TED talks, I have recently experienced the value of human-to-human information transfer. At the beginning of my ROP project in September, I was lucky to be able to hear about previous students’ research in person. I think it helped address the complexity of the work, but also conveyed its importance and the effort that had gone into it. Thanks Kiersten!
I’m not sure if information is generally more effective this way, but it is almost certainly more memorable. In any case, it has definitely worked for the 3.5 million subscribers to CrashCourse’s YouTube channel, where one can learn about anything from astronomy to macroeconomics.
For me, learning more about how researchers give and receive qualitative information to and from their subjects has allowed for a more well-rounded understanding of information transmission in the digital age.  But I think researchers andthe media have a lot to learn from each other. Communication is key for both, so understanding how others best absorb and respond to information can be instrumental.
That’s all for now, Julia!

Dem Bones Dem Bones Dem Dry Bones

Happy Canadian Thanksgiving!!!

A traditional holiday – originating from the native peoples of the Americas – to celebrate the completion and bounty of the harvest.

This year I am off to Algonquin park for a canoe portage trip with the kids! I will take the time to appreciate some of the successes of our MiVIP program and this blog over the long weekend.

Thanks for being a part of it!

Listen to Dem Bones by the famous Delta Rhythm Boys

… and I’ll see you in the blogosphere.

Pascal Tyrrell

MiCUP… Runneth Over?

An interesting quotation from the Hebrew bible. Basically it means that I have sufficient for my needs and I am good with that. So, where am I going with this you ask? Well, let me introduce you to my program MiCUP – Medical imaging Collaborative Undergraduate Program. 


The goal of the program is to bring together students from the faculty of Arts and Sciences and my faculty (Medicine) to learn about medical research in the world of medical imaging. I have a sprinkling of students every term from various programs such as Research Opportunity Program, Independent Studies, Youth Study Program, and MiVIP. It is only a modest number of students BUT provides ample brain power to get some really cool research done. My cup certainly runneth over. 


Have a look below at the timelines from my two recent ROP students.


Great work Kevin and Sylvia!!!




See you in the blogosphere,


Pascal Tyrrell



Kevin Chen ROP F/W 2014

Sylvia Urbanik F/W 2014

Basic Functions and Why You Should Know About Them

No, I did not say “bodily functions”. That is discussed in another blog. We’re talking math today. 


So, my son was doing his homework the other night and yelled out from his room:”Daaaadddyyyy!!! Do you know what a parabola is?” For those of you who do not have teenage children this is code for “can you help me with my homework”. After reliving a few high school memories that came along with the word “parabola” I wondered over to his room to see what the latest homework challenge was going to be…


When helping my kids with their homework, I often think of how important and still relevant some of the basic math is we learnt in high school. I would like to talk a little about basic functions and how they are still used well after you have handed in your last math homework assignment.


Many (most?) scientific laws are expressed as relations between two or more variables – often physical quantities. Next comes the chicken or the egg conundrum. Were the results from an experiment used to formulate “empirical laws” or did we use existing knowledge and math to come up with new theories – that we will invariably later have to test. Welcome to the world of research!


If two variables are related in such a way that one of them (the dependent or response variable) is determined when the other is known (the independent or explanatory variable), then there exists what is termed a functional relationship between the variables.


y = f(x)





For example the relationship of height to weight in humans. In general, the taller we are the heavier we get. This results in what is called a straight-line relationship.













But not all relationships are linear. How about if we were to throw a ball up into the air and measure it’s trajectory? It would look a little like the picture on the left.







Although initially the value of the height of the ball increases with time, there comes a point when the ball stops rising and starts to fall back down to earth. The resulting curve is called – you guessed it – a parabola.




The math functions for the parabola and that of the straight line are actually related. Yes, I am serious! They both belong to the family of math functions called polynomials. In my next posts I will talk a little about how we describe these functions and how we can put them to work for us in the world of medical research.


For now, decompress watching this hilarious movie trailer Biloxi Blues which is all about basic training (you can now relate) and…


… I’ll see you in the blogosphere,




Pascal Tyrrell

MiWord of the Day Is… Xeroradiography!

Who hasn’t done some creative photocopying at some point in their lives? I certainly do NOT condone this type of activity (very naughty) but would you believe me if I were to tell you that for a long while mammography made use of photocopy technology? Yes, I realize this sounds a little funny. Let me explain.


In the 1970s medicine made the association between heavy exposure to radiation for TB and thyroid treatments and the appearance of breast cancer three decades later. A reevaluation of the effects of radiation ensued and a call for ways to minimize exposure to ionizing radiation was made to the industry.


One of the first to answer that call was the radiologist John Wolfe from Detroit Receiving Hospital who in 1966 reported on the advantages of coupling photocopy technology with mammography. Xerox corporation jumped on the idea and developed a commercial unit in 1971 and “xeroradiography” was born! Basically, film from traditional x-ray imaging (yes back then they still used film!) was replaced with a selenium coated aluminum plate that was prepared for the exposure by being electrically charged. The result was that only a short burst of radiation (shorter exposure time means lower dose of radiation) was required to produce a very high quality image.






These xerox mammograms dominated the industry for over 20 years until new technology was developed more recently that provided even finer images with even less radiation. Cool.




Now for the fun part (see the rules here), using Xeroradiography in a sentence by the end of the day:


Serious: Hey Bob, did you know that mammograms produced using xeroradiography were blue? 


Less serious: My friend Jane was scheduled for a mammography. Having heard of xeroradiography reading the MiVIP blog she decided to DIY at her office. Problem was the print kept coming out black and white instead of blue from the Xerox machine…




OK, watch the Copy Cat trailer to decompress (or not?!!!) and I’ll see you in the blogosphere…




Pascal Tyrrell