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Research & Technology pages 7 to
U of M lab using AI to advance breast cancer research
Use of AI in diagnosing breast cancer a big step toward precision medicine
RESEARCH & TECHNOLOGY
Emma Rempel, staff Researchers at the Rady faculty of health sciences are innovating breast cancer detection, diagnostics and prognostics. Using artificial intelligence (AI) to analyze medical images and genomic datasets, members of the Hu Lab are making advancements in precision medicine for the fight against breast cancer.
Pingzhao Hu is an associate professor of biochemistry and medical genetics at the University of Manitoba and joint holder of the Manitoba Medical Services Foundation Allen Rouse basic science career development research award. Hu has been working on AI-based approaches to breast cancer diagnostics and prognostics for the past several years.
In medicine, treatments are not generally developed for single individuals, but rather for populations. Increasingly, groups of patients can be identified using genomics, allowing for more specific treatment targeting.
When it comes to breast cancer, diagnosis and treatment programs are undergoing a paradigm shift away from a broad, one-size-fits-all approach to one that’s more personalized. The use of more sophisticated diagnostic techniques, like genomics, allows researchers to better characterize the tumour and results in better patient outcomes.
“I want to look at this question at the DNA level to see whether they have a genetic profile difference,” Hu said.
Hu’s research employs deep learning algorithms, a form of machine learning which trains itself on complex datasets and makes highly accurate predictions. This method requires less manual input than regular machine learning algorithms. The use of deep learning AI in diagnosing breast cancer would potentially result in increased speed and reduced costs, while also delivering precision medicine to the patient.
One of the projects Hu is working on aims to analyze over 20 years of MRI images collected from women in Manitoba. It is recommended that women over the age of 50 undergo mammograms every two years. This screening process has generated a huge quantity of MRI images for both healthy women and women with breast cancer.
Hu is currently in the process of determining whether AI can help radiologists to interpret these images and identify tissue abnormalities earlier.
“[W]e are trying to use this type of AI technology to […] help radiologists to detect the cancer,” said Hu. result in earlier detection of breast cancer by up to two years, which may improve the patient’s prognosis.
Qian Liu is a graduate student currently working on incorporating AI with breast cancer diagnosis. Liu’s PhD program is interdisciplinary, with three contributing departments: biochemistry and medical genetics, computer science and statistics.
Liu’s project combines computer science and statistical testing methods to analyze breast cancer patient outcomes. By applying AI algorithms to MRI images and genomic datasets, Liu can solve clinical questions like whether a reliable indicator for breast cancer can be found in MRI images. Since diagnoses and prognoses for breast cancer are still mainly based on the genetic profile of the patient, an AI approach to MRI would save time and costs.
In addition to breast cancer research, Liu and members of the Hu Lab are working in collaboration with clinicians and researchers to implement their AI algorithms to fight other diseases, including COVID-19.
Liu was recently granted a fellowship to develop a deep learning model and apply it to whole genome sequencing (WGS) data of 10,000 Canadian patients with COVID-19. This would allow researchers to create a scoring system that would predict disease severity for each patient. The funding was provided by the CANSSI Ontario STAGE HostSeq Fellowship, which was created for researchers interested in COVID-19’s genetic factors.
In this area, Liu is analyzing chest CT scans of patients with COVID-19 using AI models to generate risk scores associated with disease severity outcomes.
Due to bottlenecks in rapid PCR testing kits for COVID-19, there have been calls to use CT scans as rapid tests instead. When Liu learned of this, she saw a possibility to implement her research.
“That’s how we decided to transfer or use our knowledge in analysis […] to the COVID-19 images,” said Liu.
Liu’s development of AI algorithms to rapidly analyze these scans would reduce the need for doctors to interpret these images and increase the feasibility of the test.
As an undergraduate student, Liu majored in medical imaging, with no computer science or genetics in her background. She largely credits Hu for creating a supportive environment for learning, and the collaborative nature of the lab for her personal development.
staff Dallin Chicoine / graphic /
—Pingzhao Hu, associate professor
teaching award as well as the Health Sciences Graduate Students’ Association’s Ed Kroeger mentorship award.
Since 2014, students and trainees at the Hu Lab have won 69 international and national awards, collected almost $700,000 in award funds, and have published more than 130 peer-reviewed articles.
To any prospective students interested in such a dynamic area of research, Hu had a few words of advice. A strong background in computer science or statistics and a familiarity with the life sciences will be highly beneficial, and a strong sense of personal initiative will carry you far.
Given the interdisciplinary nature of research in biostatistics, computer science and life sciences, researchers in the Hu Lab come from a variety of backgrounds. Due to the variation in skillsets, it is a highly collaborative space.
“This may include computer science, engineering, statistics and also the life sciences, such as genetics,” said Hu.
Students must support UMFA in its decision Monday
Although a bitter pill to swallow, it is in both parties’ interests to strike
COMMENT
Lucas Edmond, staff A new semester at the University of Manitoba just wouldn’t feel right without a potential strike looming. Now, U of M students can rest assured they’re at home again. It is unsurprising the U of M finds itself at these critical junctures year after year, as the administration has continuously coughed up horrible yearly contracts to put off inevitable discontent among members of the University of Manitoba Faculty Association (UMFA). When students are pointing fingers, direct them at Michael Benarroch and the Progressive Conservatives (PCs) he finds himself beholden to.
The U of M has been pushing appropriate bargaining back since 2016, and the issues that precipitated that strike continue to influence UMFA’s patient deliberation with their squabbling peers at the administration building and the legislature.
In 2016, the U of M offered a meagre 1.5 per cent wage increase to professors after their collective bargaining agreement expired in March. By October, then-president David Barnard was reportedly “summoned” to discuss the negotiations with then-finance minister Cameron Friesen and then-premier Brian Pallister. The administration was instructed to withdraw any discussion of wage increases, effectively strong-arming the negotiations in bad faith. In late November, after significant strike action, UMFA made the decision to accept a one-year deal that included zero per cent wage increases in exchange for improvements to governance and labour relations.
In 2017, the Manitoba Labour Board took exception to the bargaining methods of the U of M and fined it $2.4 million. By complying with the government’s intervention while keeping the disputes a secret, the U of M leapt into a mediation process with little intention of offering the union a deal it desired.
Following the short-term deal, the PCs introduced Bill 28, the Public Services Sustainability Act (PSSA), which attempted to freeze the wages of roughly 120,000 public sector employees for two years. This legislation overlapped with the expired collective agreement that was jammed down UMFA’s throat. As a result, the university and UMFA agreed to reopen contract discussions after the PSSA expired.
However, in June 2020, the PSSA was deemed unconstitutional by the Manitoba Court of Queen’s Bench for violating charter rights and freedoms of association. “The [bill] has made it impossible for the plaintiffs to achieve their collective goals and limits the right to freedom of association,” Justice Joan McKelvey concluded.
After the legislation was voided, a new contract could be discussed. The U of M had ample time to offer a contract prior to the fall semester that year but refused to negotiate in good faith. UMFA demanded fair third-party arbitration, but the university refused to cooperate.
“They’ve just come forward and said they’re not willing or prepared to offer anything in this round of negotiations even though this round was specifically to take into account [the PSSA],” said UMFA member Michael Minor in an interview with the Manitoban last year.
The negotiations that did occur looked unpromising and students were sure a prolonged strike would occur. That year, the PCs intervened in the dispute again and demanded the U of M reject wage increases and cut its labour budget a further 2.5 per cent.
As a result, UMFA reconvened to authorize a strike vote. Of the 85 per cent of union members who showed up to vote, 80 per cent approved of strike action. However, in an attempt to avoid disruption in an already tumultuous year, UMFA moved to ratify a deal offered by the administration that included less-than-ideal terms. The deal passed with less than 55 per cent approval from UMFA members and the strike was called off.
The deal included a small stipend for the horrific working conditions during the pandemic — far from the 1.5 per cent wage increase, better salary grid and more support for professors caring for their children and family during lockdowns that UMFA was expecting.
This deal likely would not have been ratified if not for the unprecedented context of the pandemic. Professors acted in the best interests of the students and sacrificed important wages, benefits and conditions that made navigating the precarity of COVID-19 easier.
Now, with a strike vote being authorized to take place from Oct. 16 to 18, students should work with their peers to show support for the professors who made this sacrifice.
This year, professors are reporting mental exhaustion due to the U of M’s inability to retain employees. According to an internal poll conducted by UMFA, 14 per cent of faculty members are looking for work elsewhere. If these members manage to find work, they will likely leave. Wages have been frozen for five years, resulting in massive salary losses.
In an interview with PressProgress, assistant professor in the department of pharmacology and therapeutics Sachin Katyal noted he found a position at an Ontario university that offered him $40,000 more at the same capacity. “There’s no reason to stick around here because there’s no hope for any growth,” he said.
Like Katyal, almost two hundred other faculty are looking for employment elsewhere. Their departure would take with it crucial grant funding and jobs, and strain the university with a lengthy hiring process. So, the question remains — with millions of dollars hemorrhaging from the university’s budget due to labour flight, how much are they really saving in the long run? It is not hard to imagine that the university’s unsustainable labour relations strategy has cost them more than what they’d spend paying their professors.
With the flight of quality professors, who will the university attract when they leave? Likely nobody that will do a better job. By refusing to pay professors, the administration has taken action to reduce the quality of education that students are paying more than ever for. When professors strike, they are striking for students, too.
The university administration has folded to the PCs’ austerity agenda. This has little to do with the well-being of professors or students. If a strike should be called come Monday, students must support UMFA — not only because they sacrificed key negotiations for us last year, but also because it is in our best interest. As union activist and leader Harry Bridges once said, “The most important word in the language of the working class is ‘solidarity.’” When the time comes, lay down your pens and pick up the pickets.
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