MiWORD of the Day is… Blur!

Have you ever tried to take a perfect vacation photo in Toronto, only to find your friend’s face is a mysterious smudge and the CN Tower looks like it’s melting? Blur has a way of sneaking into our lives, and it is everywhere. Sometimes it is more fascinating than you might think.

The smudge you see in your photo is blur. Blur has existed since the first camera was invented because film or sensors need time to gather light. If either the subject or the camera moves during this exposure time, the image appears blurred. In our discussion, we will focus on motion blur caused by fast movement, rather than unrelated effects like pixelation or mosaic artifacts. You might have experienced motion blur when taking a shaky phone photo, wearing foggy glasses, or watching a baseball fly past at incredible speed. But blur is not always a flaw.

In the world of art, blur has often been a feature rather than a mistake. Think of Claude Monet’s Water Lilies (link, copyright by The MET — highly recommend seeing it in person and viewing it from different distances): soft edges, blended colors, shapes shimmering in the light. Or consider long-exposure photographs of city traffic, where headlights stretch into glowing ribbons. In these cases, blur captures motion, mood, and mystery, transforming the ordinary into something extraordinary. Even in classic cinema, motion blur helps create a sense of speed or dreamlike atmosphere. In sports, blur can tell an entire story. The fastest recorded baseball pitch reaches 105.8 miles per hour, far too fast for the human eye to follow clearly. To freeze it, cameras must shoot at over 1,000 frames per second. A racecar streaking past the finish line or a sprinter in motion may appear as streaks of color, yet our brains still understand exactly what is happening. Motion blur, in these cases, is not a mistake; it is evidence of speed and energy.

In science, blur can reveal a very different kind of truth. Consider echocardiography, an ultrasound imaging method for the heart. These moving pictures help doctors assess heart function, blood flow, and valve performance. Yet even the tiniest shake of the probe, a restless patient, or the natural motion of the heartbeat can smear crucial details. There is even a trade-off between frame rate and depth of view: a typical knee ultrasound operates at around 20 frames per second, while heart ultrasound often reaches about 50 frames per second. A blurry heart chamber is more than an inconvenience; it can obscure the clues doctors need to make the right decision. Other imaging fields, such as X-ray or MRI, face similar challenges with motion blur. Interestingly, scientists also study the patterns of blur to improve image quality, since sometimes the “smudge” itself contains useful information about movement or structure.

Blur can be playful, expressive, and at times essential. It reminds us that seeing clearly is not always straightforward and that what appears imperfect can still hold meaning. From the sweep of a painter’s brush to the rhythm of a beating heart on a screen, blur reflects a world that is always moving and changing. Sometimes, beauty and truth live within that very imperfection.

Now for the fun part — using blur in a sentence by the end of the day:
Serious: Did you notice the blur in the long-exposure shot of the city at night? The headlights look like flowing rivers of light.
Less serious: While running to catch the bus, I accidentally created a blur of people in my phone photo. What a perfect accidental art piece.

…I’ll see you in the blogosphere.

Qifan Yang

Qifan Yang’s Personal Reflection

My name is Qifan Yang, and I am an incoming third-year student with Statistics Major and Mathematical Applications in Finance and Economics Specialist at the University of Toronto. This past summer, I had the opportunity to work on an ROP299 research project with Professor Tyrrell, and I would like to share my four-month journey in research, a completely new experience for me.

When I started, I was a complete novice in medical imaging and unfamiliar with the full process of scientific research. Before our first meeting, I felt quite nervous. I still remember Professor Tyrrell, during the interview, warning me about the potential challenges ahead. Coming from a statistics and mathematics background, I initially found both machine learning concepts and medical terminology quite intimidating. Although I had completed a few Kaggle courses, I lacked hands-on experience with building models from raw datasets and running end-to-end training and testing.

My research journey began along two paths: first, learning the fundamentals of machine learning and medical imaging, where review papers became my best starting point, and second, exploring rheumatic heart disease (RHD) and its potential for automated diagnosis using transthoracic echocardiography (TTE). The first obstacle I encountered was the lack of publicly available, large-scale datasets for RHD with detailed labels. This led me to pivot toward studying image quality in TTE, since I found a large echocardiography database with quality labels. However, a second challenge soon emerged: I struggled to identify a research question that was both technically meaningful and scientifically impactful.

This is where Professor Tyrrell’s mentorship made all the difference. In one group meeting, he mentioned severe motion blur he had observed in knee ultrasound images. That sparked the idea for my project: detecting and correcting non-uniform motion blur in echocardiography using deep learning. This was the turning point when the project truly began to take shape.

The real research work involved splitting and labeling datasets, designing a neural network model, training and testing on GPUs, and visualizing and evaluating results. Each of these steps was entirely new to me, requiring both technical learning and persistent problem-solving. I am deeply grateful for the guidance of Professor Tyrrell, as well as the support from Giuseppe, Noushin, and other members of the lab, including previous students whose work provided valuable reference points.

By the end of the summer, I had taken full charge of the project, running it from start to end. This responsibility taught me far more than technical skills. I developed a stronger sense of self-motivation, learned to manage my time effectively, and built the resilience needed to handle research setbacks. I realized that research is not just about repetitive lab work; it is about thinking critically, asking meaningful questions, and telling a compelling story through data and results.

The experience was more than an introduction to the research world; it taught me to think boldly and work carefully. I learned not to let ideas live only in conversation or in my head, but to translate them into small, testable experiments that turn speculation into evidence. Each modest prototype, whether a quick data split, a minimal model, or a rough visualization, sharpened my questions, exposed constraints, and informed the next step. Gradually, those incremental wins compounded into a coherent pipeline and credible results. The discipline I gained is simple but powerful: think wild, start small, measure honestly, and move steadily. This balance of wild curiosity with careful craftsmanship now guides how I approach complex, unfamiliar problems, and it’s the mindset I’ll carry into future research and professional work.

Winnie Ye in STA299

This was my first course related to research, and also my first time working with medical imaging. When I heard that we would be doing independent research, I immediately realized that this course would undoubtedly be a great challenge for me. Independent research meant there was no clear “standard answer”; instead, I had to explore and persist on my own.

At the beginning of my ROP project, I was actually the first student in the class to finalize a research direction. I quickly chose skin tone bias in melanoma detection as my topic and decided to work with the ISIC dataset. At that time, I felt well prepared: even though I noticed that dark-skin samples were rare, I believed the number would be “enough.” I even imagined finishing the project in less than two months.

But soon, reality hit me. Out of more than 30,000 ISIC images, there were almost no dark-skin cases. After that, I kept switching datasets: PAD, Fitzpatrick17k, MSKCC. However, each of them had serious problems: some had almost no melanoma cases, some had almost no dark-skin samples, some images contained a lot of background noise rather than just lesions, and some lacked skin tone labels altogether. Even when I combined them, the total number of dark-skin melanoma images was barely more than one hundred. During that period, I felt like I was constantly “starting over,” and every time I thought I had found a breakthrough, it quickly fell apart.

In this struggle, I tried almost everything I could think of. I trained my own U-Net, experimented with CLIP, SVM, EfficientNet, and ResNet; I tested light-skin-trained models directly on dark-skin data; I even used YOLO to crop lesions in order to reduce background noise. My research focus also shifted again and again: from melanoma, to pigmented lesions, and finally to red scaly diseases; and my tasks shifted from classification to segmentation and back again. Altogether, I must have attempted more than a dozen different approaches, yet none of them produced satisfactory results.

As the deadline drew closer, my anxiety grew stronger. By the last month, despite all the models, tasks, and research objects I had tried, I still had no meaningful results to show. At times I felt completely lost, unsure of what else I could even do. In desperation, I wrote Dr. Tyrrell a very long email, confessing that I might not be able to continue and even considered abandoning the project altogether. I told him that if I could start over, I would never choose to study bias so hastily, but would first spend more time carefully understanding the limitations of the datasets.

That month was probably the hardest part of the entire ROP. I stayed up late almost every day, exhausted and anxious, sometimes even afraid to run my code because I expected yet another failure. Dr. Tyrrell was sometimes worried and even a bit frustrated, which made me feel sad, but I was also deeply grateful that he cared so much. In the final weeks, Giuseppe also began to support me more closely, and I truly appreciated his help. During that time, even the smallest result—no matter how unrepresentative—felt important enough for me to immediately share with Dr. Tyrrell and Giuseppe for feedback.

Finally, near the very end, something changed. About ten days before the deadline, I obtained a result that was still imperfect, but at least demonstrated a sign of bias. It was not a breakthrough, but it was enough to build a conclusion. In the last week, I focused on writing the report, experimenting with bias-mitigation methods, and managed to finish everything just in time.

Looking back on these four months, I went through so many emotions: the early excitement of being “ahead,” the anxiety of being overtaken, the regret and despair of repeated failures, and the relief of a small last-minute success. If you ask me what kept me going, I honestly don’t know, perhaps the support from Dr. Tyrrell and Giuseppe, perhaps the stubborn voice in my head saying “try one more time,” or perhaps just a little bit of luck.

Through this course, I developed a new understanding of medical imaging and machine learning: they are not only technical problems but also involve fairness, data limitations, and persistence throughout the research process. I realized that the true value of research is not in quickly achieving a perfect result, but in continuously experimenting, reflecting, and learning from failures. In the future, I hope to further explore fairness in medical imaging, especially to investigate why my findings differed from previous studies and how I can avoid or better explain such discrepancies. I believe this will not only help me improve my research methods but also allow me to move forward more confidently on my academic path.

IMPACT-MED 2024: Innovations in Medical Precision, Accessibility and Collaborative Technology

The IMPACT-MED 2024 Conference is a one-day online event scheduled for Wednesday, October 30th, 2024. It aims to advance global health innovation and entrepreneurship. The conference is supported by the University of Toronto’s Global Classrooms initiative and the Institute of Medical Science’s (IMS) two specialized courses: MSC1114H: Artificial Intelligence in Medicine and MSC1122H: Startups in the Medical Sciences. The conference will be hosted on the Zoom platform, offering interactive and engaging experiences for participants. Key activities include expert lectures, practical workshops, and breakout sessions, covering topics such as AI applications in healthcare, medical startup ecosystems, and global healthcare system comparisons. This event fosters international collaboration and provides students with valuable insights into both AI and entrepreneurship within medical sciences.

The conference is free to attend.

You can register online here, via the Zoom registration page.

Yan Qing Lee’s ROP299 Journey

Hi! I’m Yan Qing Lee, an incoming 3rd-year Computer Science and Psychology double major undergraduate student. This past summer, I was given the opportunity to embark on my first research project in the field of artificial intelligence, and I’m excited to share my experience.

My research topic investigated if individuals who receive a false-positive mammogram result by an AI model have a higher risk of receiving a breast cancer diagnosis later on. Past studies have found that receiving a false-positive mammogram result from radiologists is associated with a higher risk of future breast cancer, but no studies have yet investigated if this holds true for AI breast cancer detection models. In this project, I used a longitudinal dataset of breast cancer mammograms, and ran a trained AI breast cancer classifier, made of an ensemble of 4 Convnext-small models, to obtain false-positive and true-negative results. Cox proportional hazards models were then used to investigate the hazard ratio of receiving a false-positive result, from both the AI model, and from radiologists.

As a student who entered the Computer Science major out-of-stream, I started the ROP feeling really out of place. Although I’ve known I wanted to pursue AI, I had no real experience in neither AI nor medical imaging, and I wondered if I was too under-qualified for this experience. Still, I was determined to put in as many hours as I needed to succeed. 

I first began by familiarizing myself with ML terms, and choosing an area of interest (breast cancer mammography) to formulate a research question upon. As I’m sure other ROP students would agree, this process was extremely challenging; as weeks passed by, I found that my research questions were always either over-ambitious or not feasible. Over time, however, I realized that my difficulty with creating a research question stemmed from my lack of knowledge in exactly how ML models work, and the existing literature and gaps within the field of breast cancer mammography. As I dug deeper into existing literature, the one interesting finding regarding radiologists’ false-positives caught my eye, and this finally led me to my research question. 

Once I began working on my project, the many challenges of research revealed themselves to me. This included difficulties of downloading and parsing through a large dataset, of installing packages and working around incompatible versions of libraries to set up a working environment, and, worst of all, of finding out an AI breast cancer detection model you originally centered your project around is not as replicable as you assumed it would be. Despite that I made sure to set up my research question to be relatively simple, the process of setting up, debugging preprocessing code, training and running an AI breast cancer classification model and obtaining undesirable training results was nothing short of complicated. Still, with the weekly lab meetings keeping me on track, and the support of Dr. Tyrrell, Mauro and the other students in the lab, I slowly but surely overcame every obstacle, and learned immense amounts every week to successfully complete my project. Even though I had to find a new AI model to use near the end, and redo my experimentation, I found that with my experience with the previous AI model, I was now able to independently set up and run the new model much more efficiently than before. It was proof of how much I’d learned, and I’m glad to now be able to look back and be proud of how much I’ve accomplished in the span of a few months.

At the end of it all, I have to thank Dr. Tyrrell for fostering my passion towards AI and its applications in fields as impactful and important as breast cancer mammography. This experience only made me more excited to delve into the applications of AI in other fields in the future, and I can’t thank the MiData lab enough for this experience.

MiWord of the Day is… Region of Interest!

Look! You’ve finally made it to Canada! You gloriously take in the view of Lake Ontario when your friend beside you exclaims, “Look, they have beaver tails!” You excitedly scan the lake, asking, “Where?” 

“There!”

“Where?”

“There!”

You see no movement from the lake. It isn’t until your friend pulls you to the front of a storefront says “BeaverTails” with a picture of delicious pastries that you realize they didn’t mean actual beavers’ tails. It turns out you were looking at the wrong place the whole time!

Often times, it’s easy for us to quickly identify objects because we know the context of where things should be. These are the kinds of things we take for granted, until it’s time to hand the same tasks over to machines. 

In medical imaging, experts label what are called Regions of Interests (ROIs), which are specific areas of a medical image that contain pathology, such as the specific area of a lesion. Having labelled ROIs are important, as it can help prevent extra time from being wasted on analyzing non-relevant areas of an image, especially since medical images contain complex structures that take time to interpret. But in the area of machine learning (ML) in medical imaging, having labelled ROIs is also useful because it can help with training ML models that classify whether a medical image contains a pathology or not; with ROIs identified, cropping can be done during the preprocessing of images so that only relevant areas of images are compared for the model to learn differences between positive and negative images faster.

In fact, having ROIs is so important, there is an entire field in artificial intelligence dedicated to it: Computer Vision. The field of computer vision focuses on automating the extraction of ROIs in images or videos, which plays a critical role in the mechanization of tasks like object detection and tracking for things like self-driving cars. In object detection, for example, things like ROI Pooling can be utilized; this is where multiple ROIs are used to obtain input feature maps, from which maximum values are used to detect the presence of features, giving rise to the ability to identify many objects at once – this is extremely useful, especially once you’re on the road and there are 10 other cars around you!

Now, the fun part: using Region of Interest in a sentence!

Serious: The coordinates of ROIs are given for the positive mammogram images in the dataset I’m using. Maybe I could use Grad-CAM to see if the ML breast cancer classification model I’m using uses the same regions of the image to arrive at its classification decision; this way, I can see if its decision making aligns with the decision making of radiologists.

Less serious: I forced my friend to watch my favorite movie with me, but I can’t lie – I think the attractive male lead was her only region of interest!

See you in the blogosphere,

Yan Qing Lee

Yuxi Zhu’s ROP Journey

Hi, I am Yuxi Zhu, a Bioinformatics and Computational Biology specialist and Molecular Genetics Major who just finished my second year. Like most people, this is my first formal research experience. Professor Tyrrell warned me from the start that I would need to be independent in this lab, but my genuine interest in ML and its applications gave me the confidence to take on the challenge. Overall, this summer’s ROP journey in the MiDATA lab was filled with both excitement and challenges.

The first challenge was finding a research question. I’m incredibly grateful to Daniel, a volunteer and former ROP student, who introduced me to the concept of “adversarial examples” and helped me formulate my research question from the start. During the first two months of the literature review, I often found myself diving too deeply into theoretical aspects that were less applicable to Medical Imaging, or exploring questions that, while feasible, didn’t capture my interest. Luckily, I was able to settle down with understanding the differential effects between random perturbations (like random noise and loss of resolution) and non-random adversarial perturbations on the model. 

As the project progressed, I encountered a series of obstacles and bugs that required constant problem-solving and debugging. For example, my initial findings showed very low performance, all under 50%. Professor Tyrrell pointed out that the accuracy of a binary classifier should never drop below 50%, as that would mean it’s performing worse than a random model. I quickly realized there were bugs in my code and implementation. Additionally, after obtaining results, I thought interpreting them would be straightforward. However, when Professor Tyrrell asked me why adversarial perturbations led to accuracies below 50% while the others didn’t, I found myself at a loss for words. In the end, with Professor Tyrrell’s guidance, I was able to interpret the results correctly and articulate them in my report.

Despite the stress I felt before presenting my findings at our weekly meetings, these sessions became invaluable learning experiences. Professor Tyrrell would scrutinize my work with questions and critiques, pushing me to think more deeply and critically about every aspect of my research. The other lab members also provided very helpful insights and shared their work. These meetings not only allowed me to understand what others were working on but also gave me the chance to get involved in or observe lively discussions that often took place. 

Looking back on the last few months, this experience has been invaluable. I am deeply thankful to Professor Tyrrell who offered me this wonderful opportunity in ML and guided me through my research project. I especially appreciate how we weren’t just taught to implement a given research project or conduct a specific experiment; we were taught how to find gaps and how to conduct research. I also want to express my gratitude to Daniel for his support and insights when I was in doubt, and to Atsuhiro for his helpful suggestions. Completing my first-ever research project was challenging yet rewarding, and I am grateful for all the guidance and help I received. I’m confident that what I have learned will stay with me in my future research and career.

Today’s MiWORD of the day is… Adversarial Example!

According to the dictionary, the term “adversarial” refers to a situation where two parties or sides oppose each other. But what about the “adversarial example”? Does it imply an example of two opposing sides? In a way, yes.

In machine learning, an example is one instance of the dataset. Adversarial examples are examples with calculated and imperceptible perturbation that tricks the model into the wrong prediction but look the same to humans. So “adversarial”, in this case, indicates opposition between something (or human) and the model. The adversarial examples are intentionally crafted to trick the model by exploiting its vulnerabilities.

How it works? There are many ways to find weak spots and generate adversarial examples, but FGSM is one classic way, and the goal is to make small changes to a picture such that it outputs the wrong prediction. First, we input the model with the picture. Assume the model outputs the correct prediction, so the loss function, which represents the difference between the prediction and the true label, will be low. Second, we compute the gradient of the loss function to tell us whether we should add or subtract a certain value epsilon to each pixel to make the loss bigger. Epsilon is typically very small, resulting in a tiny change to the value. Now, we have a picture that looks the same as the original but will trick the model into the opposite prediction!

One exciting property of adversarial examples is their transferability. It is known that adversarial examples created for one model can also trick other unknown models. This might be due to inherent flaws in the pattern recognition mechanisms of all models and, sometimes, model similarities, allowing these adversarial examples to exploit common vulnerabilities and lead to incorrect predictions.

Now, use “adversarial example” in a sentence by the end of the day: 

Kinda Serious: “Oh I can’t believe my eyes. I am seeing a dog right here and the model says it’s a cupcake…So you’re saying it might be an adversarial image? What even is that? The model is just dumb.”

Less Serious: Apparently, the movie star has an adversarial relationship with the media, but which stars have a good relationship with the media nowadays?

See you in the blogosphere,

Yuxi Zhu

MiWord of the Day is… Learned Perceptual Image Patch Similarity (LPIPS)!

Imagine you’re trying to compare two images—not just any images, but complex medical images like MRIs or X-rays. You want to know how similar they are, but traditional methods like simply comparing pixel values don’t always capture the whole picture. This is where Learned Perceptual Image Patch Similarity, or LPIPS, comes into play.

Learned Perceptual Image Patch Similarity (LPIPS) is a cutting-edge metric for evaluating perceptual similarity between images. Unlike traditional methods like Structural Similarity Index (SSIM) or Peak Signal-to-Noise Ratio (PSNR), which rely on pixel-level analysis, LPIPS utilizes deep learning. It compares images by passing them through a pre-trained convolutional neural network (CNN) and analyzing the features extracted from various layers. This approach allows LPIPS to capture complex visual differences more closely aligned with human perception. It is especially useful in applications such as evaluating generative models, image restoration, and other tasks where perceptual accuracy is critical.

Why is this important? In medical imaging, where subtle differences can be crucial for diagnosis, LPIPS provides a more accurate assessment of image quality, especially when images have undergone various types of degradation, such as noise, blurring, or compression.

Now, let’s use LPIPS in sentences!

Serious: When evaluating the effectiveness of a new medical imaging technique, LPIPS was used to compare the generated images to the original scans, showing that it was more sensitive to perceptual differences than traditional metrics.

Less Serious: I used LPIPS to compare my childhood photos with recent ones. According to the metric, I’ve definitely “degraded” over time!

See you in the blogosphere!

Jingwen (Lisa) Zhong