HOUSTON, Feb. 16, 2024 Rice University computer science researchers have found bias in widely used machine learning tools used for immunotherapy research.
Ph.D. students Anja Conev, Romanos Fasoulis and Sarah Hall-Swan, working with computer science faculty members Rodrigo Ferreira and Lydia Kavraki, reviewed publicly available peptide-HLA (pHLA) binding prediction data and found it to be skewed toward higher-income communities. Their paper examines the way that biased data input affects the algorithmic recommendations being used in important immunotherapy research.
Peptide-HLA Binding Prediction, Machine Learning and Immunotherapy
HLA is a gene in all humans that encodes proteins working as part of our immune response. Those proteins bind with protein chunks called peptides in our cells and mark our infected cells for the bodys immune system, so it can respond and, ideally, eliminate the threat.
Different people have slightly different variants in genes, called alleles. Current immunotherapy research is exploring ways to identify peptides that can more effectively bind with the HLA alleles of the patient.
The end result, eventually, could be custom and highly effective immunotherapies. That is why one of the most critical steps is to accurately predict which peptides will bind with which alleles. The greater the accuracy, the better the potential efficacy of the therapy.
But calculating how effectively a peptide will bind to the HLA allele takes a lot of work, which is why machine learning tools are being used to predict binding. This is where Rices team found a problem: The data used to train those models appears to geographically favor higher-income communities.
Why is this an issue? Without being able to account for genetic data from lower-income communities, future immunotherapies developed for them may not be as effective.
Each and every one of us has different HLAs that they express, and those HLAs vary between different populations, Fasoulis said. Given that machine learning is used to identify potential peptide candidates for immunotherapies, if you basically have biased machine models, then those therapeutics wont work equally for everyone in every population.
Redefining Pan-Allele Binding Predictors
Regardless of the application, machine learning models are only as good as the data you feed them. A bias in the data, even an unconscious one, can affect the conclusions made by the algorithm.
Machine learning models currently being used for pHLA binding prediction assert that they can extrapolate for allele data not present in the dataset those models were trained on, calling themselves pan-allele or all-allele. The Rice teams findings call that into question.
What we are trying to show here and kind of debunk is the idea of the pan-allele machine learning predictors, Conev said. We wanted to see if they really worked for the data that is not in the datasets, which is the data from lower-income populations.
Fasoulis and Conevs group tested publicly available data on pHLA binding prediction, and their findings supported their hypothesis that a bias in the data was creating an accompanying bias in the algorithm. The team hopes that by bringing this discrepancy to the attention of the research community, a truly pan-allele method of predicting pHLA binding can be developed.
Ferreira, faculty advisor and paper co-author, explained that the problem of bias in machine learning cant be addressed unless researchers think about their data in a social context. From a certain perspective, datasets may appear as simply incomplete, but making connections between what is or what is not represented in the dataset and underlying historical and economic factors affecting the populations from which data was collected is key to identifying bias.
Researchers using machine learning models sometimes innocently assume that these models may appropriately represent a global population, Ferreira said, but our research points to the significance of when this is not the case. He added that even though the databases we studied contain information from people in multiple regions of the world, that does not make them universal. What our research found was a correlation between the socioeconomic standing of certain populations and how well they were represented in the databases or not.
Professor Kavraki echoed this sentiment, emphasizing how important it is that tools used in clinical work be accurate and honest about any shortcomings they may have.
Our study of pHLA binding is in the context of personalized immunotherapies for cancer a project done in collaboration with MD Anderson, Kavraki said. The tools developed eventually make their way to clinical pipelines. We need to understand the biases that may exist in these tools. Our work also aims to alert the research community on the difficulties of obtaining unbiased datasets.
Conev noted that, though biased, the fact that the data was publicly available for her team to review was a good start. The team is hoping its findings will lead new research in a positive direction one that includes and helps people across demographic lines.
Ferreira is an assistant teaching professor of computer science. Kavraki is the Noah Harding Professor of Computer Science, a professor of bioengineering, electrical and computer engineering and director of the Ken Kennedy Institute for Information Technology.
The research was supported by the National Institutes of Health (U01CA258512) and Rice University.
Source: John Bogna, Rice University
See the rest here:
Rice University Researchers Uncover Bias in Machine Learning Tools for Immunotherapy - Datanami
- University of California expands list of courses that meet math requirement for admission - EdSource [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Bombshell Betty Race car to be Reengineered and Restored By UVU Students to honor the Legacy of its Owner - GlobeNewswire [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Phyllis Coleman Mouton to receive Trailblazer Award at Women Who Mean Business ceremony - The Advocate [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Fairfield University Partners with Pulse Secure on New Cybersecurity Lab to Prepare the Next Generation of Information Security Professionals -... [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Global Cloud Identity and Access Management(IAM) Market Segmentation By Top Key Players- IBM Microsoft Oracle Computer Science CA Okta NetIQ Sailpoint... [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Stanford supports alliance of universities in diversifying STEM postdocs - The Stanford Daily [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- N.C. A&T Welcomes New and Newly-Appointed Administrators and Faculty - Yes! Weekly [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Calvin Students Place In Top 10% Of Worldwide Programming Competition - News - Calvin News [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Multiple tenure-track positions in Computer Science & Engineering job with University of Minnesota-Twin Cities Computer Science & Engineering... [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- New smartwatch app alerts deaf and hard-of-hearing users to common home-related sounds - National Science Foundation [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- MTRAC Innovation Hub for Advanced Computing awards $270000 to Wayne State University artificial intelligence projects - The South End [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- New study outlines steps higher education should take to prepare a new quantum workforce | College of Science | RIT - RIT University News Services [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Carleton Hosts Herzberg Lecture on Increasing Diversity in Computer Science with Maria Klawe - Carleton Newsroom [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- Baylor University Invites Application for McCollum Endowed Chair of Data Science - Analytics Insight [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- CHEN | Put Computer Science in the Common Core - Cornell University The Cornell Daily Sun [Last Updated On: November 11th, 2020] [Originally Added On: November 11th, 2020]
- GCVI's Tremain running to the NCAA on scholarship - GuelphToday [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Faculty, alumni, other members of U of T community named to Order of Canada - News@UofT [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Why 4-year colleges are tapping Amazon to help deliver cloud computing degrees - Education Dive [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Army Teams With Howard University on AI Center MeriTalk - MeriTalk [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- McGrath one of 10 women to earn STEM scholarship - The Riverdale Press [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- This learning platform is proving adults can benefit greatly from learning math and science - iMore [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Artificial Intelligence Is Now Smart Enough to Know When It Can't Be Trusted - ScienceAlert [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Students and schools in the news - Blue Springs Examiner [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Missouri S&T News and Events Missouri S&T faculty honored for outstanding teaching - Missouri S&T News and Research [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- HCCC Offers Opportunities for Adjunct Faculty and Instructors at Virtual Job Fair - The Hudson Reporter [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- 4-H ignites a passion for science and technology in Minnesota youth - Southernminn.com [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- MIT's New Center to Advance Predictive Simulation Research Will Focus on Exascale Simulation of Materials in Hypersonic Flow Environments -... [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Computer scientist James Allen named AAAS fellow - University of Rochester [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Center to advance predictive simulation research established at MIT Schwarzman College of Computing - MIT News [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Setting the pace in computer science education | Opinion - Paragould Daily Press [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Mohammed VI University in Benguerir Launches School of Computer Science - Morocco World News [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Asa Hutchinson: Setting the pace in computer science education - Searcy Daily Citizen [Last Updated On: November 28th, 2020] [Originally Added On: November 28th, 2020]
- Former FX tech person points out the racist trajectory of skin and hair CGI - Boing Boing [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- AI is not yet perfect, but it's on the rise and getting better with computer vision - TechRepublic [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- Philosophy Threatened at University of Evansville - Daily Nous [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- Two Maryland Teachers Receive National Honors in Math, Science Education - maryland.gov [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- Special Scientist Research, Department of Computer Science job with UNIVERSITY OF CYPRUS | 238208 - Times Higher Education (THE) [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- Computer science jobs pay well and are growing fast. Why are they out of reach for so many of America's students? - The Conversation US [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- Computer science grad finds success and a new academic family in cybersecurity - ASU Now [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- What is Computer Science? in the US - International Student [Last Updated On: December 11th, 2020] [Originally Added On: December 11th, 2020]
- Accurate Neural Network Computer Vision Without The 'Black Box' - Duke Today [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Crick Named Mathematical Sciences Distinguished Alumnus Of The Year - The Chattanoogan [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Nadya's Hot Chocolate Bombs: yummy for the tummy - theday.com [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Trouble hearing in a crowded room? New 'cone of silence' could help - Science Magazine [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- James Fujimoto wins the Visionary Prize from the Greenberg Prize to End Blindness - MIT News [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- To the brain, reading computer code is not the same as reading language - MIT News [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- U of Texas will stop using controversial algorithm to evaluate Ph.D. applicants - Inside Higher Ed [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Gift from Ann S. Bowers '59 creates new college of computing and information science | Cornell Chronicle - Cornell Chronicle [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- NYS Board of Regents adopts first-ever learning standards for computer science and digital fluency - RochesterFirst [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Computer science prof Townsend recognized for educational contributions - DePauw University [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Missouri S&T News and Events New faculty in computer science - Missouri S&T News and Research [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- Retired UW computer science professor embroiled in Twitter spat over AI ethics and cancel culture - GeekWire [Last Updated On: December 19th, 2020] [Originally Added On: December 19th, 2020]
- How UC fought COVID-19 in 2020 - University of California [Last Updated On: December 23rd, 2020] [Originally Added On: December 23rd, 2020]
- Search committee appointed for dean of Princeton's School of Public and International Affairs - Princeton University [Last Updated On: December 23rd, 2020] [Originally Added On: December 23rd, 2020]
- How Yale economists are informing India's COVID-19 response - Yale News [Last Updated On: December 23rd, 2020] [Originally Added On: December 23rd, 2020]
- Top MIT research stories of 2020 - MIT News [Last Updated On: December 23rd, 2020] [Originally Added On: December 23rd, 2020]
- St. Albans City School kids were 'on the case' for Computer Science Week. What mystery did they solve? - St. Albans Messenger [Last Updated On: December 23rd, 2020] [Originally Added On: December 23rd, 2020]
- Cobb Schools receives grant for computer science teacher training - The Catoosa County News [Last Updated On: December 23rd, 2020] [Originally Added On: December 23rd, 2020]
- Scholarship honors the legacy of Terry Arthur's dedication to students - Augusta Free Press [Last Updated On: December 24th, 2020] [Originally Added On: December 24th, 2020]
- This tool helps predict which COVID patients will need hospitalization and which can be sent home - Press-Enterprise [Last Updated On: December 24th, 2020] [Originally Added On: December 24th, 2020]
- Students express concerns over teaching appointment of Jason Mars - The Michigan Daily [Last Updated On: December 24th, 2020] [Originally Added On: December 24th, 2020]
- Prince Mohammad Bin Fahd University hosted the International Conference on Computing, Mobility, and Manufacturing (CMM 2020) - PRNewswire [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- These Are the College Majors That Pay Off the Most - 24/7 Wall St. [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- He Was Going to Close the Family Diner. Then He Got a Sign. - The New York Times [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- Members of Several Well-Known Hate Groups Identified at Capitol Riot - FRONTLINE [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- Carver Community Center to offer free pampers to mothers, free coding classes for youth - Marshall News Messenger [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- MIT's College of Computing building takes shape as Alexandria and BioMed make moves in Boston - Cambridge Day [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- Bylaws of the Department of Computer Science and Engineering - Nevada Today [Last Updated On: January 10th, 2021] [Originally Added On: January 10th, 2021]
- Student-run HPAIR conference goes virtual this year - Harvard Gazette [Last Updated On: January 16th, 2021] [Originally Added On: January 16th, 2021]
- JUST IN: Computer scientists in breakthrough - The Herald [Last Updated On: January 16th, 2021] [Originally Added On: January 16th, 2021]
- Optimizing Traffic Signals To Reduce Intersection Wait Times - Texas A&M University Today [Last Updated On: January 16th, 2021] [Originally Added On: January 16th, 2021]
- STEM Majors: Interested in a 1-Credit Course About Teaching Math, Science or Computer Science? - University of Arkansas Newswire [Last Updated On: January 16th, 2021] [Originally Added On: January 16th, 2021]
- Stanford AI scholar Fei-Fei Li writes about humility in tech - Fast Company [Last Updated On: January 16th, 2021] [Originally Added On: January 16th, 2021]
- Professor in Computer Science - The Voice Online [Last Updated On: January 16th, 2021] [Originally Added On: January 16th, 2021]
- Expansion project to grow computer science learning, research at Algoma University - Northern Ontario Business [Last Updated On: January 31st, 2021] [Originally Added On: January 31st, 2021]
- Teacher of Year finalist expanding Walden Grove computer science program - KGUN [Last Updated On: January 31st, 2021] [Originally Added On: January 31st, 2021]
- Here's why you should get a master's in computer science - Study International News [Last Updated On: January 31st, 2021] [Originally Added On: January 31st, 2021]
- Two UWF teams place in top 5 in national artificial intelligence competition - University of West Florida Newsroom - UWF Newsroom [Last Updated On: February 5th, 2021] [Originally Added On: February 5th, 2021]
- WNMU Board of Regents Virtually Sits Down With Legislators, Governor - WNMU News [Last Updated On: February 5th, 2021] [Originally Added On: February 5th, 2021]
- Department name change signals broad impact on computer and information technologies - Princeton University [Last Updated On: February 5th, 2021] [Originally Added On: February 5th, 2021]