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SickKids

Anna Goldenberg

Title: Senior Scientist, Genetics and Genome Biology
Designations: PhD
Email: anna.goldenberg@sickkids.ca
Alternate Contact Name: Freda Lai
Alternate Phone: 416-813-7654 ext. 309588
Alternate Email: freda.lai@sickkids.ca

Research Positions

Co-chair of the AI in Medicine Initiative

Chair Positions

Varma Family Chair in Biomedical Informatics and Artificial Intelligence
CIFAR AI Chair

Biography

Dr. Anna Goldenberg is a Senior Scientist in Genetics and Genome Biology program at the SickKids Research Institute, and is also the first Varma Family Chair in Biomedical Informatics and Artificial Intelligence. She is an Associate Professor in the Department of Computer Science at the University of Toronto, faculty member and an Associate Research Director, Health at Vector Institute and a fellow at the Canadian Institute for Advanced Research (CIFAR), Child and Brain Development group.

Goldenberg trained in machine learning at Carnegie Mellon University, with a post-doctoral focus in computational biology and medicine. The current focus of her lab is on developing machine learning methods that capture heterogeneity and identify disease mechanisms in complex human diseases as well as developing risk prediction and early warning clinical systems. Goldenberg is a recipient of the Early Researcher Award from the Ministry of Research and Innovation. She is strongly committed to creating responsible AI to benefit patients across a variety of conditions.

Research

The great promise of AI in healthcare is taking time to materialize. Besides difficulties with access to the data and unrealistic expectations of the AI due to the hype fueled by the media, there are many fundamental machine learning advances that need to be made to achieve the widespread use of AI in healthcare.

Some of the current shortcomings include, but are not limited to:

  • high error rates in predicting rare critical events (such as cardiac arrest)
  • lack of the model explainability that makes it hard for clinicians to act upon predictions that diverge from their intuition
  • the effects of adopting imperfect machine learning models in practice and the feedback loop of error such adoption creates.

Goldenberg’s lab is working on addressing these fundamental issues to build the foundation for responsible AI and healthcare, ensuring realization of the AI potential in healthcare.

Education and experience

  • 2011–2017: Scientist, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON
  • 2012–2018: Assistant Professor, Department of Computer Science, U of T, Toronto, ON
  • 2017–present: Faculty Member and Associate Research Director Health, Vector Institute, Toronto, ON
  • 2017–present: Co-chair of AI in Medicine Initiative, The Hospital for Sick Children, Toronto, ON
  • 2018–present: Associate Professor, Department of Computer Science, University of Toronto, Toronto, ON
  • 2018–present: Senior Scientist, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON
  • 2018–present: Associate Research Director, Health, Vector Institute, Toronto, ON
  • 2018–present: Varma Family Chair in Biomedical Informatics and Artificial Intelligence, The Hospital for Sick Children, Toronto, ON

Achievements

  • 2016: Award for exceptional mentoring and outstanding commitment to graduate student recruitment, University of Toronto, Computer Science
  • 2016: Early Researcher Award, Ministry of Research and Innovation
  • 2016: Child and Brain Development Research Support, CIFAR
  • 2016: Fellow of the Candian Institute for Advanced Research in Child & Brain Development program, CIFAR
  • 2017: Program committee, ISMB
  • 2017: Co-chair, Analytical Framework Working Group, UCAN CAN-DU committee
  • 2017: Organizer of the PI Prep School, The Hospital for Sick Children
  • 2017: Faculty Member, F1000prime, Bioinformatics, Biomedical Informatics & Computational Biology Faculty
  • 2017: Canadian Research Chair in Computational Medicine Tier II, Government of Canada
  • 2018: Education Program Committee Member, 2018 AACR Annual Meeting
  • 2018: Area Chair, ISMB
  • 2019: Member of the AI Task Force at the Royal College of Physicians and Surgeons
  • 2019: AI task force for Healthcare (AI4H) organized by CIFAR
  • 2019: International Advisory Board, The Lancet Digital Health
  • 2019: AI Chair, CIFAR

Publications

  1. GA Adam, L Rampášek, Z Safikhani, P Smirnov, B Haibe-KainsA Goldenberg. (2020) Machine Learning Approaches to Drug Response Prediction: Challenges and Recent Progress. Nature Precision Oncology 4 (9).
  2. J Wiens, S Saria, M Sendak, M Ghassemi, VX Liu, F Doshi-Velez, K Jung, K Heller, D Kale, M Saeed, PN Ossorio, S Thadaney-IsraniA Goldenberg (2019). Do no harm: a roadmap for responsible machine learning for health care. Nature Medicinedoi: 10.1038/s41591-019-0548-6 free version: https://rdcu.be/bO6ed
  3. W Nelson, M Zitnik, B Wang, J Leskovec, A Goldenberg*, R Sharan*. (2019) To embed or not: network embedding as a paradigm in computational biology. Frontiers in Genetics, section Systems Biology. 1;10:381
  4. Rampasek, D.Hidru, P. Smirnov, B. Haibe-KainsA. Goldenberg. (2019). Dr. VAE: Improving drug response prediction via modeling of drug perturbation effects. Bioinformatics. Oxford University Press. btz158, https://doi.org/10.1093/bioinformatics/btz158
  5. Aristizabal, IAnreiter, T Halldorsdottir, CL. Odgers, TW. McDade, A Goldenberg, S Mostafavi, MS. Kobor, EB. Binder, MB. Sokolowski, KJ. O’Donnell (2019). Biological Embedding of Experience: a primer on epigenetics, PNAS. https://doi.org/10.1073/pnas.1820838116 

View more of Anna Goldenberg's publications:

PubMed  Google Scholar

2016-2021: Early Researcher Award from the Ministry of Research and Innovation
Title: Improving personalized medicine - integrating multiple biological data sources to study variation in disease
PI: Anna Goldenberg  

2016-2020: CIHR - Project Grant
Title: Identifying integrative biomarkers of risk and resilience to childhood psychopathology
PI: Anna Goldenberg 

2016-2021: CIHR - Personalized Medicine in Inflammation Network
Title: UCAN CAN-DU: Canada-Netherlands Personalized Medicine Network in Childhood Arthritis and Rheumatic Disease
PI: Rae Yeung, Co-applicant: Anna Goldenberg 

2017-2019: Tel Aviv University – University of Toronto  Joint Research Projects in Big Data in Health and Biomedical Research.
Title: A Network Propagation Approach to Drug Repurposing
PI: Anna Goldenberg, Roded Sharan 

2020-2025: NSERC, Discovery Grant Program
Title: Robust machine learning for healthcare
PI: Anna Goldenberg  

2017 – 2020: Baxter-Shire
Title: Radiogenomics: Personalized Imaging of Arthropathy in Boys with Hemophilia in China.
PI: Andrea Doria, Co-investigator: Anna Goldenberg  

2017 – 2022: Genome Canada - Genomics Technology Platforms Operations Support & Technology Development Funds.
Title: Canadian Centre for ComputationalGenomics (C3G)
PI: Michael Brudno, Co-Applicant, Anna Goldenberg  

2018-2021: TRCHR - Innovative Strategic Grant
Novel clinical, molecular, and -omics approaches to prediction of heart failure Baxt(HF) readmission
PI: Douglas Lee, Heather Ross, Slava Epelman, Patrick Lawler, Anthony Gramolini, Co-investigator: Anna Goldenberg 

2018-2022: Genome Canada - Large-Scale Applied Research Project (LSARP)
Childhood asthma and the microbiome – precision health for life: The Canadian Healthy Infant Longitudinal Development (CHILD) study
PI: Stuart Turvey, Michael Kobor, Brett Finlay, Padmaja Subbarao. Collaborator: Anna Goldenberg

2018-2022: Genome Canada - Large-Scale Applied Research Project (LSARP)
Title: UCAN CURE: Precision decisions for childhood arthritis
PI: Rae S. M. Yeung. Co-PI: Susanne Benseler. Co-investigator: Anna Goldenberg 

2020-2021: CIHR Catalyst Grant: Understanding   Disease Prevention and Risk Factor Modification
Title: Personalized Medicine for Children: The Early Childhood Obesity (EChO) Clinical Prediction Tool
Maguire JL (NPA).  Aglipay M, Alton G, Birken CS, Goldenberg A, Juni P, Mamdani M, Persaud N, Ray J, Thorpe K. 

2018-2022: NIMH
Title: Social Processes Initiative in Neurobiology of Autism-spectrum and Schizophrenia spectrum, Grant, Operating
PI: Stephanie Aimes Co-investigator: Anna Goldenberg   

2018-2023: The Terry Fox Foundation
Title: The​ ​Terry​ ​Fox​ ​New​ ​Frontiers​ ​Program​ ​Project​ ​Grant​ ​in​ ​the​ ​Early​ ​Detection​ ​and Prevention​ ​of​ ​Cancer​ ​in​ ​Li-Fraumeni​ ​Syndrome
PI: David Malkin. Co-PI: Anna Goldenberg    

2019-2021: Helmsley Foundation
Title: Leveraging wearables to measure stress and forecast symptom transitions in Chron's Disease
PI: Stephen Friend Co-PI: Anna Goldenberg   

2019-2022: CHRP-CIHR 
Title: Utilizing high resolution physiological data and artificial intelligence to develop a pediatric cardiac arrest prediction tool for integration into bedside clinical practice
PI: Anna Goldenberg Co-PI: Mjaye Mazwi  

2020-2021: CIHR  
Title: Modeling Cognitive Impairment in Patients with Systemic Lupus Erythematosus: Clinical Phenotyping, Predictive Trajectory and Associated Risk Factors
PI: Zahi Touma Co-PI: Robin Green, Dorcas Beaton, Lesley Ruttan, Carmela Tartaglia, Kathleen Bingham, Joan Wither, Anna Goldenberg  

2019-2020: Mark Foundation for Cancer Research 
Title: Federated Machine Learning to Automate Early Cancer Detection  
PI: Anna Goldenberg Co-PI: Andrea Doria, Lisa States  

2020-2023: University of Toronto, Department of Psychiatry
Title: Using smartphone technology for the early detection of bipolar episodes in youth
PI: Jacob Vorstman Co-PI: Stefan Kloiber, John Strauss, Anna Goldenberg, Marco Battaglia, M.J.H. Kas, Raj Jagesar, Niels Jong, M.C. Roozen  

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