Colloquium: Bodies. Deep Learning. – AI and A/I

When and Where

Friday, December 06, 2019 2:00 pm to 4:00 pm
Robert Gill Theatre Lobby
Koffler Student Services Centre
214 College Street, 3rd floor

Speakers

Professors Antje Budde and David Rokeby

Description

Deep learning is a term that WEIRDLY connects the praxis of experiential learning and practices of machine learning while AI, artificial intelligence, and A/I artistic intelligence, are also conceptual aspects of interest for our discussion.

Presenters

Antje Budde, Creative research director, Digital Dramaturgy Lab

David Rokeby, Director of the BMO Lab for Creative Research in the Arts, Performance, Emerging Technologies and AI

The Knowledge Media Design Institute is a co-sponsor for this event. This event is free. No RSVP is necessary.

2019 Schmidt Science Fellow Dr. Ina Anreiter discusses behavioural genetics research

U of T researcher recognized for her work modifying fruit fly foraging behaviours

2019 Schmidt Science Fellow Dr. Ina Anreiter discusses behavioural genetics research

Dr. Ina Anreiter from the University of Toronto was selected as a 2019 Schmidt Science Fellow for her research in behavioural genetics in April in New York.

The Schmidt Science Fellowship is a prestigious program that brings some of the best emerging scientists in the world together, and equips them with new skills to make a positive change in society. Candidates are chosen for their exceptional performance during PhD studies and strong intellectual curiosity to broaden the scope of their future research.

Each fellow, including Anreiter, will complete a year-long postdoctoral placement in a different field than their PhD topic to promote interdisciplinary thinking.

Anreiter’s work as a PhD candidate

Anreiter completed her PhD in the Department of Ecology & Evolutionary Biology at U of T, and was supervised by Dr. Marla Sokolowski. As part of her studies, Anreiter wanted to understand how genetics and environment could influence behaviours. She studied this by looking at the foraging gene of two strains of fruit flies with distinct foraging behaviours: the rovers and the sitters.

The rovers are more active and are usually willing to travel farther for food, while the sitters are less active and tend to travel shorter distances to forage.

“When the food is in the middle of the arena, you have a trade-off of safety versus getting to the food,” explained Anreiter in an interview with The Varsity. “So you can see this difference in rovers and sitters… It’s a circular arena, food is distributed in the middle, and you can see that sitters tend to hug the edges, while rovers are much more exploratory.”

An earlier paper published in 2017 by Anreiter and her colleagues described how they were able to genetically engineer the foraging gene to transform sitters into rovers.

Challenges along the way

Anreiter had to overcome multiple challenges to accomplish what she has. “The way that our publishing system works is very positive-result-oriented. It’s very hard to publish negative results, and there are many arguments to be made,” she remarked.

“We ended up publishing this really nice story about this one epigenetic regulator that regulates individual differences, but that wasn’t the only regulator that we looked at,” she continued. Epigenetic engineering makes modifications to an organism by altering which genes are expressed, rather than directly changing the DNA sequence itself.

However, her research team looked at many other regulators that did not show a positive result. “So there’s a lot of work that goes into this project that is never published because the results are not positive,” she elaborated.

She further acknowledged the challenges that she experienced as a PhD student, but she advised students to not get discouraged when a project seems to come to a dead end.

“It’s not the end of your PhD; it’s not the end of your research. You just change gears a little bit and continue with something new,” she concluded.

Next steps for future research

Anreiter’s work opens up many possibilities for future research in epigenetics. One of the significant findings in this study was that the effect of epigenetic regulators is dependent on the strain of fruit flies. In other words, “You have an interaction where the epigenetic modification is dependent on a genetic difference, and that’s an interaction which… when I started my PhD, [people] weren’t looking at,” she said.

“And that applies not only to fruit flies, not only to feeding behaviour, but applies broadly to animal research.”

Currently, Anreiter has undertaken a project in computer science, where she aims to develop a new computation mechanism to examine epigenetics modifications in RNA as a required component of the Schmidt Science Fellowship.

Offering advice to undergraduates about graduate studies, “Don’t do grad school because you are just not sure what you want to do, because grad school can be really, really tough,” she remarked. “But it is also really rewarding in my experience.”

“If you are excited about research, if you are excited about science, it is a really cool environment where you can really have the freedom of developing you own interests.”

U of T professor wins grant to study how online psychotherapy can help children with inflammatory bowel disease

Dr. Sara Ahola Kohut is investigating the viability of acceptance and commitment therapy

U of T professor wins grant to study how online psychotherapy can help children with inflammatory bowel disease

Dr. Sara Ahola Kohut, a researcher at the Hospital of Sick Kids and an assistant professor at U of T, received a $50,000 grant from Crohn’s and Colitis Canada to research the promise of online acceptance and commitment therapy (ACT) workshops in supporting children with inflammatory bowel disease (IBD) and their families.

What is inflammatory bowel disease?

IBD is an umbrella term for two conditions characterized by chronic inflammation of the gastro-intestinal tract: ulcerative colitis and Crohn’s disease. Symptoms of these diseases include abdominal cramps and pain, diarrhea, fever, and unintended weight loss.

In an interview with The Varsity, Kohut, who has been researching IBD since 2014, pointed out that the main challenge for patients with IBD and their families is dealing with uncertainty.

“Young people living with IBD don’t know when they may have a flare or be in pain, nor when that pain might end.” She noted that this makes planning day-to-day activities and for the future extremely difficult.

Constantly coping with this state of unpredictability may cause severe anxiety, and research has found that the risk of depression and anxiety disorders is much higher in young people with IBD than the general population, which Kohut hopes to change through her work.

Dealing with uncertainty and stress

ACT is a relatively new form of psychotherapy which encourages patients to accept things and events that are out of their control and commit to making changes that could improve their life.

Unlike most other therapies, ACT does not aim to change unpleasant thoughts, feelings, and sensations. Instead, it employs mindfulness-based strategies to help the patient reduce their feelings of stress and change their relationship with their pain by accepting their struggles as they are, rather than trying to avoid them.

People experiencing chronic pain often exhaust themselves fighting off everything that reminds them of it — not only the obvious unpleasant physical sensations, but also any related thoughts or emotions. However, their attempts to drive off the pain may be futile — this is where ACT comes to the rescue.

The skills one learns through ACT are transferable to a variety of situations, making them especially valuable for dealing with the unpredictability of IBD. Kohut explained that “in moments of [overwhelming] or intense frustration, ACT skills can help you pause and choose to act in ways that are aligned to who you most want to be as a person.”

Benefits of ACT

In Kohut’s clinical experience, ACT has been a popular and successful approach for young people with IBD. This finding led her to develop a new series of online ACT workshops, which focus on helping the participants recognize their values and “develop skills [that] allow them to incorporate their values into their everyday choices and behaviours.”

ACT also helps participants “to respond instead of react to what is happening around [them].” Through this, young patients’ relationships with their families may begin to feel more calm and relaxed, especially during unpleasant moments, such as when receiving injections or taking medication.

Kohut also aims to create a program that is accessible and enjoyable for parents of children with IBD. She moves to teach them to navigate parenting in a way that aligns with their values as a family, which may support them in dealing with the constant challenges of IBD, while also helping them to “model positive adaptation… to IBD so that their kids will be able to emulate that approach.”

There is currently no cure for IBD, yet Kohut’s novel approach may give the 7,000 Canadian children living with IBD and their families hope for a better future.

How to digest plastic and save the world

Toronto team wins gold standard at international synthetic biology event

How to digest plastic and save the world

Hundreds of students, from graduate to high school studies, gathered in Boston to present their research at the International Genetically Engineered Machine (iGEM) Foundation’s Giant Jamboree in early November. Over the past year, they’ve been developing projects in the emerging field of synthetic biology, which uses modern tools and biological building blocks to solve natural problems.

This year, iGEM Toronto, the University of Toronto team, returned with more than just the standard bragging rights. Rather, their project was recognized with a gold standard — the highest evaluation for a project in the iGEM competition — and they were nominated for the best manufacturing project in their competitive category.

What was the team’s project?

Over the past year, the team has conducted cutting-edge research on a possible solution to the world’s plastic waste problem. Three years ago, a team of researchers in Japan discovered a unique strain of bacteria that can break down a common type of plastic, polyethylene terephthalate — commonly called PET plastic — on a molecular level, essentially digesting it.

At the moment, plastics can only be recycled a finite number of times before they start to degrade and have to be disposed of. However, if researchers find a way to break plastics down to their molecular components, they could apply this to make a near-perfect recycling system for plastic.

Recyclers could then recreate the plastics from scratch to be as good as new, with negligible amounts of waste.

Since their conception, the iGEM Toronto team has been designing and testing ways to implement this recycling process in an industrial setting. The recently-discovered bacteria uses a particular protein, called PETase, to break down the plastics that it digests.

How the team collaborated to win gold

The team’s computational lab created the necessary tools to redesign the protein so that it could process plastics quicker, while keeping them sturdy enough to survive in an industrial setting. Building on the work of researchers like Dr. Jennifer Listgarten and David Brookes, several team members trained a neural network to search for more efficient versions of the protein.

Others used protein-modelling software to redesign PETases, giving them more useful chemical properties. Together, they modelled five alternate versions of the protein, hoping that some would be more efficient at digesting plastics than naturally-occurring PETases.

In the final analysis, all versions of the protein were successful.

The team’s biology lab then produced millions of copies of these proteins in order to test their practical efficiency. Other members of the team interviewed experts to get a better understanding of the current recycling industry, and developed preliminary models for a PETase ‘bioreactor’ that could be used in a recycling plant.

The impact of iGEM’s success

The research team considers the victory to be a huge validation. “I was able to lead a team of people who never knew each other at first, and now could come up with something that’s now on a world stage, and is worth it,” said Amy Yeung, the outgoing president of iGEM Toronto, in an interview with The Varsity.

“That sense of feeling of accomplishment, from when I’ve started to now, is the best thing I think I’ve picked up.”

What’s more, the iGEM program at U of T has the potential to set a precedent for undergraduate research. “A lot of undergrads get stuck just doing somebody’s side jobs in a lab,” said Daniel Kiss, who took over as the club’s co-president this year, to The Varsity.

iGEM Toronto’s research model is different. Although their projects are designed and run by members from a wide variety of programs — from computational biology to ethics — they’re almost entirely undergraduates.

“It’s like Lord of the Flies, but [with a] happy ending,” joked Kiss. “Let’s put all these undergrads in a room and see what happens.”

U of T-student founded campaign launches Queering STEM Scholarship

Two awards of $2,000 are available for LGBTQ+ students entering university

U of T-student founded campaign launches Queering STEM Scholarship

Toronto-based LGBTQ+ advocacy group LoveisLoveisLove has launched the Queering STEM Scholarship program for LGBTQ+ youth in Ontario who are entering a STEM undergraduate program in Ontario for the 2020–2021 academic year. There are two awards of $2,000 available.

Academic excellence, personal charisma, and civic engagement are the three major factors that the scholarship selection committee is looking for in an applicant. In addition to the personal essay and application form, every applicant is also asked to submit a short video detailing “the importance of LGBTQ+ inclusion in STEM.”

“We want people who can be leaders, who can be visible and instigate change in their own way when they mature in their careers,” said Adam Zivo, who is the founder of LoveisLoveisLove, as well as a graduate student at U of T’s Munk School of Global Affairs and Public Policy.

According to Zivo, “people working in STEM tend to be underrepresented in LGBTQ+ issues and activism,” especially when compared to their counterparts in arts and culture. The scholarship is meant to support future LGBTQ+ leaders in STEM and support their acceptance across a number of fields of study.

Students can email their application, which can be found on the company’s website by January 1, 2020. The committee will make their decisions by late January, and finalists will be contacted by the end of February.

LoveisLoveisLove partnered with Mongrel Media to raise the money through a charitable film premiere, and ScholarTree for the administration processes relating to the scholarship.

The launch of LoveisLoveisLove

Zivo founded LoveisLoveisLove in 2016. Its first project was a photo booth about “celebrating queer relationships and giving positive messages in a time of trauma,” as part of an LGBTQ+ street festival in Toronto.

After the Orlando Pulse shooting that year, some of Zivo’s friends posted images of themselves with friends and romantic partners on social media in response, as a “symbolic resistance against homophobia and violence.”

Having noticed that phenomenon, Zivo rebranded the project to adapt to the trauma that the community was feeling. Later, the LoveisLoveisLove team collected photos from the participants to be published it on their Facebook page and website.

In 2017, the project was scaled up so that the participants with the most-liked photos received a prize. “In mass cultural depictions of LGBT folks, it has to be one of two on a spectrum. You have either a hypersexualized image, or an image that strips LGBT people of their sexuality and romance entirely,” Zivo said.

The campaign hoped to address this by showing the “sentimental and candid side” of queer interpersonal relationships.

Enduring outreach to the community

Later in 2018, Zivo decided to do something in a physical space that would have lasting impacts and reach beyond the social media bubbles of LGBTQ+ culture. His team produced a large-scale banner installation at Toronto City Hall in collaboration with Meridian Credit Union. This was one of the largest installations ever presented there, and he later created similar banners for the Ottawa City Hall and the Scarborough Civic Centre.

They also collaborated with the non-profit organization, Scarborough Arts, to create a Scarborough city name sign that was similar to the multi-coloured tourist attraction in Nathan Phillips Square, except it was covered with a vinyl wrap of photos taken by Zivo for LoveisLoveisLove.

It was one of the efforts aimed to resolve geographic discrepancy in LGBTQ+ acceptance through suburban engagement.

Zivo went on to explain how LoveisLoveisLove came to their signature initiative in 2019: Toronto’s Big Gay Bus, a TTC bus that the team transformed into a mobile resource which educates non-LGBTQ+ people with educational materials and by “answering simple questions about LGBTQ+ issues that [people] might not be aware of,” according to Zivo. As an example, he provided the question: “What is the difference between a drag queen and a trans person?” So far, the bus has reached hundreds of thousands of people.

Beyond that, LoveisLoveisLove’s latest project was a 20-foot “Marvellous Mobile Mural” at Ottawa City Hall. LoveisLovisLove expects to make more murals this year and bring them through smaller communities.

“Many LGBT activists are downtown-centric and kind of on the radical side,” Zivo said, “We can’t just give up on the inner suburbs and suburban communities because that’s giving up on the vast majority of Canadians. We also have to recognize that not everyone is going to be receptive to the most progressive and aggressive forms of LGBT activism.”

Zivo’s team aims to extend the campaign to more suburban areas, and maintain “friendly, non-aggressive” language, hoping to make LGBTQ+ rights “better understood by audiences who are unfamiliar [with them].”

“We’re like, ‘hey, you don’t know these things. That’s cool. Here’s the answer,’” Zivo said.

Building a career out of a chemical engineering degree

U of T chapter of Canadian Society for Chemical Engineering hosts alumni career panel

Building a career out of a chemical engineering degree

The perennial question of what to do with one’s degree was answered in part for chemical engineering students at an alumni career panel last week. Alumni from U of T’s Department of Chemical Engineering & Applied Chemistry, who now work in fields ranging from biotechnology to environmental engineering, shared advice on how to apply their skills to business and building unique skill sets.

The Canadian Society for Chemical Engineering — University of Toronto Student Chapter hosted the event at the Haultain Building on November 27.

From graduate school to business development

Dr. Darren Rodenhizer, the Business Development and Partnerships Lead at the biotechnology startup AmacaThera, spoke about the value of earning a PhD in science.

He explained that his education has enabled him to develop a technical expertise with the firm’s products, which lets him speak “down in the weeds” with scientists about his firm’s offerings.

Beyond technical expertise, Rodenhizer also noted that his graduate studies taught him the skills to work in business without specifically studying the field.

“You’re going to learn how to tell data-driven stories, which are what many companies hiring today are looking for,” he said. “You’ll be able to collect and analyze data; it’s going to open up a whole new realm of job opportunities.”

However, Rodenhizer did note drawbacks of pursuing a PhD. For example, he said that graduate students could feel a lack of recognition for their work. “You’re going to extend your student living… for another five years. You’re not going to make very much money,” he added.

“And there’s a lot of publications coming out now [about] the mental health side effects of going to grad school,” he said. He recalled a study that found that graduate students in the US are at least three times more likely to experience mental health issues than the average American. This study was conducted on economics PhD students.

Making the leap to a career in industry

According to Cathy Grant, a Principal Consultant at C&S Grant Environmental Consulting, “Once you graduate, the hard part’s over.”

“You did all the hard slogging; you did all the technical stuff. And really what you walk away with is the ability to teach yourself what you need to know,” she said.

She noted that learning on the spot is a strong advantage, as there is a great deal of information that employees who start out in their respective fields need to learn that may not be taught in a traditional engineering degree program.

Grant also shared interview advice, noting that if you get nervous, it is helpful to reflect on the top three bits of information that you wish to convey.

“Always go into a situation thinking, ‘What do I want to say?’” she said. She also recommended preparing for general questions, such as why you think you’re qualified for the job.

Getting the most out of your undergraduate years

Firas Ghazali, a consultant at Deloitte, advised undergraduate students to make the most of their degrees.

Ghazali, while noting that his experiences might not be valid for everyone, recommended that students find time to build relationships with their colleagues during their studies. He also recommended that they schedule time to disconnect from their work and unwind.

“You need to disconnect so that you can restart that following week and keep going. This is not an easy program.”

“I would say [too much stress] is not worth it,” he said. “So try to balance your personal health and mental health… because it really is not that bad at U of T.”

Building a valuable skill set

Mark Angelo, the CEO of LMC Healthcare, spoke about his unconventional career path that took him from U of T as an undergraduate, to Harvard Business School, and finally to industry.

He also presented a list of takeaways for students interested in starting their careers.

“Try to keep your options open for as long as possible. Don’t close any doors until you’re forced to close them,” he said.

He also recommended having a “focused breadth.” To Angelo, that means having breadth in your skills, but also finding ways to take these divergent interests and synthesize them into a unique skill set.

Angelo, for example, studied engineering, health care, and social enterprise, and uses all three fields in his career.

“I think that gives you a competitive advantage. It allows you to be unique in what you do, because anyone can do maybe one of those three things, but there [are few] people who have maybe done all of those three things and combined them.”

He recommends that students reflect on three or four passions and build a unique skill set from them.

To embark on a career path, Angelo endorsed pursuing what makes you happy. “Trust your gut. Get feedback and input from others; it’s your life, and it’s your happiness.”

“Go out there and do what makes you come alive,” he said. “Because what the world needs is people who have come alive.”

How augmented reality could impact the future of surgical training

Study demonstrates how smart glasses could be used to train surgeons

How augmented reality could impact the future of surgical training

Augmented reality could hold promise for improving surgical training, using the Osterhout Design Group (ODG) R-7 Smartglasses, according to a recent study conducted with the University of British Columbia (UBC).

A research team, which included Dr. Neil Chadha, a former fellow at The Hospital for Sick Children in Toronto, recruited staff surgeons and resident trainees to participate in the study at Vancouver General Hospital. Resident trainees used the ODG R-7 Smartglasses to perform a synthetic surgery for educational purposes in the temporal bone cadaver drilling laboratory .

Applying the use of Osterhout Design Group R-7 Smartglasses

One main aspect of the study involved the use of a device to create an augmented reality. For the research team, the decision to use the ODG R-7 Smartglasses was simple.

“The [ODG] already had partners doing research with the R-7 Smartglasses,” said Dr. Michael Yong, a resident physician at UBC’s Faculty of Medicine, and a co-author of the study, in an interview with The Varsity.

In terms of set-up, the research team further believed that the smart glasses would be suitable to the operating room due to their battery life and wear-ability. However, Yong noted that while the maximum two-hour battery life is not currently a concern, it could pose a challenge in the future during clinical situations.

The study’s design and results

The study was completed at Vancouver General Hospital with two supervisors and five resident trainees using the temporal bone cadaver drilling laboratory.

“The temporal bone-drilling lab is… something that every residency program in [otolaryngology, which concerns the ear, nose, and throat] has access to, and so it was an easy place for us to start,” said Yong. 

After the trials, the researchers collected comments and a completed survey from the supervisors and residents participating in the study. Many comments recognized the promise of augmented reality in advancing surgical training. However, they also noted areas of improvement with the techniques.

The strongest advantage of the smart glasses was their potential to communicate remotely and exchange editable images with other practitioners. Other reviews of smart-glasses technology have noted applications, including monitoring patient vitals remotely and review patient charts on the go.

Some of the suggested improvements of the teaching experience included better lighting with the glasses, reduced time for images to be processed, and the reduction of connectivity issues. One of the more notable suggestions was to avoid the temporal cadaver bone lab for such, due to drawbacks caused by drilling.

“When you’re drilling the skull, bone dust comes up into the air,” said Yong. “Usually we wear masks and protective goggles, but the R-7 glasses are not designed to be an industrial-grade protective goggles, and so, there’s openings on the sides of it and little spaces here and there, that allow for bone dust to come in.”

Further research is needed to make the use of this technology widespread. However, Yong remarked, “It’s just a matter of getting more institutions to do these kinds of feasibility studies, to do these kinds of tests and get some feedback as to how best we can adapt this rapidly-growing industry technology to surgery… in a useful and efficient matter.”

UTSG: BRITE x BGSA Game Night

Black Researchers Initiative to Empower (BRITE) in Collaboration with the Black Graduate Students Association (BGSA) are hosting our second annual games night on November 28th! Come and join us for a fun evening of games, food and prizes. 
When? November 28th at 6:00 PM 
Where? OISE Room 2286, 252 Bloor Street W
https://www.facebook.com/events/1191612181033714/