Wednesday, April 21, 2021

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• Federal government launches national quantum strategy
• Using machine learning to develop personalized cancer treatment
• New Community of Practice for continuous improvement and change management
• Participate in GreenHouse's first Health Challenges Forum
• Wednesday's notes

Federal government launches national quantum strategy

This article originally appeared on the Institute for Quantum Computing website.

The University of Waterloo’s Institute for Quantum Computing welcomes the federal budget commitment to investing in a national quantum strategy.

Alongside industry partners and other Canadian universities, the University of Waterloo has been advocating for a national quantum strategy to maintain Canada’s competitive edge as we develop and commercialize tomorrow’s technological breakthroughs, and train the workforce needed to bring these discoveries to market.

The government has shown its willingness to invest in innovative areas where Canada plays a leadership role. Canada was one of the first to prioritize quantum research, which has positioned us well to lead in this emergent technology.

“We are grateful for the federal government’s ongoing support and commitment toward this important strategy,” said Charmaine Dean, vice-president, research & international at the University of Waterloo.

“Canada was an early leader in foundational quantum science and technology development, and while collectively this country continues to punch above its weight ranking behind only the United States and China in quantum computing IP, this strategy will help retain Canada’s first-mover advantage in the field.” 

IQC was established nearly 20 years ago to bring together scientists, mathematicians, and engineers to advance fundamental and applied research on quantum technologies. Through the development of quantum communications, computing, materials and sensor applications, the work done at IQC is instrumental in transforming some of the world’s largest industries and driving future economies.

The many companies that have spun out of IQC include Quantum Benchmark, an error-correcting software for quantum-computing hardware, and QEYnet, which is developing satellite-based quantum key distribution.

To learn more about how the research at the University of Waterloo harnesses the quantum laws of nature to develop powerful new technologies and drive future economies, visit the IQC website.

Using machine learning to develop personalized cancer treatment

Ming Li (L) is a University Professor at the Cheriton School of Computer Science and the Canada Research Chair in Bioinformatics. Hieu Tran (R) is an Adjunct Assistant Professor at the Cheriton School of Computer Science and Senior Research Scientist at Bioinformatics Solutions, a Waterloo-based company that uses machine learning to sequence and identify proteins.

Researchers at the Cheriton School of Computer Science have applied machine learning to identify tumour-specific antigens, which could help make personalized cancer vaccines practically feasible and more accurate.

In cancer, when a missense mutation occurs in a cell’s DNA, a single nucleotide substitution in the DNA results in a different amino acid in the peptide the cell produces, explains Hieu Tran, an Adjunct Assistant Professor at the Cheriton School of Computer Science. “The peptide that has the changed amino acid is recognized by our immune system as foreign, even though it is synthesized by cancer cells from our own body.”

This mutated peptide is known as a neoantigen — an antigen that’s present only on the surface of cancer cells, Hieu Tran explained. “If we can figure out what the neoantigens are on cancer cells, they can be used to develop a cancer vaccine — a vaccine that’s personalized to the cancer patient and which uses the patient’s own immune system to attack the tumour.”

“When a cell becomes cancerous the human leukocyte antigen or HLA system knows about it,” adds Ming Li, a University Professor at the Cheriton School of Computer Science, who also holds the Canada Research Chair in Bioinformatics. “The HLA system presents peptides on the surface of cells. If the HLA system presents a normal peptide on a cell’s surface, the T cells of our immune system know that it is a self-peptide and they don’t attack it. The T cells attack only the cells with mutated peptides, the ones with neoantigens on their surface.”

The trick, however, is finding these tumour-specific neoantigens — essentially a needle in a large haystack. Not surprisingly, it is a bewilderingly difficult task to do using conventional methods, but it is crucially important when developing a personalized cancer vaccine.

Amino acids are the building blocks of peptides and ultimately protein molecules. By convention, amino acids are labelled using a one-letter code. For example, the amino acid alanine is labelled A, arginine is labelled R, asparagine is labelled N, and so on. A peptide’s amino acid sequence can be considered as a word of composed of these letters.

“If you are familiar with natural language processing, you’ve likely seen your mobile phone guess the next word you might have typed as you compose a message. You write ‘how’ and it suggests ‘are’ and if you type ‘are’ it suggests ‘you’,” Hieu Tran said.

“We applied a similar machine-learning model to determine the amino acid sequence of neoantigens based on this one-letter amino acid code. If I know your immunopeptidome — the thousands of short 8 to 12 amino acid peptide antigens displayed on the cell surface — and I know that a neoantigen is different from your existing peptides by just one mutation, I can train a machine learning model using your normal peptides to predict the mutated peptides. We used a recurrent neural network — a machine learning model we call DeepNovo — to predict the amino acid sequence of neoantigens.”

To do this the researchers downloaded the immunopeptidome datasets of five patients with melanoma, a type of skin cancer, which they then used to train, validate and test their machine learning model.

“Our machine-learning model expanded the predicted immunopeptidomes of those patients by 5 to 15 percent,” Hieu Tran said. “We also discovered neoantigens, including those with validated T-cell responses that had not been reported in previous studies.”

Even more impressively, the machine learning model is able to personalize the results — that is, it identifies specific neoantigens for each individual patient.

“Cancer immunotherapy is quickly becoming a fourth modality of cancer treatment, alongside surgery, chemotherapy and radiotherapy,” adds University Professor Li. “Every patient is different and every cancer is different, so cancer treatment shouldn’t be the same for all. Treatment should be tailored to the patient, and that’s what our personalized machine learning model allows us to do.”

New Community of Practice for continuous improvement and change management

A message from Human Resources.

The Office of the Associate Provost, Human Resources is excited to announce the successful launch of a University wide Continuous Improvement (CI) and Change Management (CM) Community of Practice. To further develop institutional CI/CM expertise, the CoP aims to provide a supportive space for those seeking to learn more about CI and CM or, those who are already working on similar initiatives. 

Hosted on March 31, 2021, the inaugural session was attended by 60 members and focused on the principles of CI and CM and showcased the benefits of an integrated model. Improving the communities learning roadmap, our members also helped to identify suitable topics for future meetings and knowledge-sharing networks.

“The CoP is an awesome opportunity to learn from talented people across the campus community. I am really looking forward to learning more about continuous improvement and change management tools and resources. Hearing stories from others across campus is really thought provoking and provides inspiration for new ways of tackling big challenges in my own work,” writes Amanda Annarilli, manager, operations, Student Success Office.

Get involved, become a CI&CM CoP member today. We invite members of our University community to join the growing CoP. Together we can expand our institutional expertise and shape the future of CI and CM at Waterloo.

Questions? Please contact Raghda Sabry, HR project manager, or Samantha Murray, change management advisor.

Participate in GreenHouse's first Health Challenges Forum

The GreenHouse social impact incubator at St. Paul’s University College in collaboration with Concept at the University of Waterloo will be hosting its first Health Challenges Forum on Tuesday, May 18, 2021 from 2:00 to 4:30 p.m.

This free virtual event will explore the most pressing challenges faced by healthcare professionals at local acute care, long term care, and home care medical organizations.

Interested in joining the forum? We’re looking for students and researchers to join the discussion with speakers from Grand River Hospital, Schlegel Villages, and the Local Health Integration Network. The goal is to discuss problems of various themes under all three sectors to gain a better understanding of why these challenges exist, who is impacted and how. 

Register by May 9, 2021 to learn more about the issues that exist within healthcare, create new research collaborations and begin developing solutions.

Wednesday's notes

"Due to a recent Workday update, employees registering for Organizational and Human Development’s current workshops may notice Workday lists the delivery mode as in-person even though they have been set-up as instructor-led webinars," says a note from Organizational and Human Development (OHD). "A few employees have contacted us with questions about the matter. Rest assured that our workshops continue to be held online using Microsoft Teams and not in-person. It appears this error is occurring with scheduled workshops that require a specific date/time unlike self-led webinars which have open access with no date or time limitations."  

"The wording error has been brought to Workday’s attention so hopefully the next update will reflect the actual method of delivery. If you have any questions about our current spring workshop offerings, please contact ohd@uwaterloo.ca for clarification and assistance."

Yesterday, former Minneapolis Police officer Derek Chauvin was found guilty of murder and manslaughter in the May 2020 death of George Floyd. Though justice was done in this instance, the University recognizes that elements brought out in the trial, and the ongoing issue of anti-Black racism, may have an effect on members of our University community.

If you or anyone you know are in need of support, below are resources, including mental health supports, available to members of the University:

• Mental Health Resources
  • Students: If you feel overwhelmed or anxious and need to talk to somebody, please contact the University’s Campus Wellness services. Gillian Wells was recently hired as Counsellor for Black Student Support in Campus Wellness.
  • Employees: Our Employee and Family Assistance Program is available 24/7 for counselling, coaching and support. Call 1-800-663-1142 or visit Homeweb.ca.
  • These community supports are also available:
    • Here 24/7 - 1-844-437-3247
    • Good2Talk - 1-866-925-5454
    • Crisis Services Canada - 1-833-456-4566 or by text 45645  
    • K-W Counselling
• Accommodations for racial trauma: understand your options for academic accommodations related to traumatic experience based on race
• The Human Rights, Equity and Inclusion team has compiled alist ofAnti-Racism resources.
• Information about the University’s anti-racism initiatives.
• If the news cycle is overwhelming, the Library has published a resource guide on how to avoid information overload.