Knowledge-Informed Machine Learning for Cancer Diagnosis and Prognosis:
  A review
Lingchao Mao Hairong Wang Leland S. Hu Nhan L Tran Peter D Canoll Kristin R Swanson Jing Li
Cancer remains one of the most challenging diseases to treat in the medical
field. Machine learning has enabled in-depth analysis of rich multi-omics
profiles and medical imaging for cancer diagnosis and prognosis. Despite these
advancements, machine learning models face challenges stemming from limited
labeled sample sizes, the intricate interplay of high-dimensionality data
types, the inherent heterogeneity observed among patients and within tumors,
and concerns about interpretability and consistency with existing biomedical
knowledge. One approach to surmount these challenges is to integrate biomedical
knowledge into data-driven models, which has proven potential to improve the
accuracy, robustness, and interpretability of model results. Here, we review
the state-of-the-art machine learning studies that adopted the fusion of
biomedical knowledge and data, termed knowledge-informed machine learning, for
cancer diagnosis and prognosis. Emphasizing the properties inherent in four
primary data types including clinical, imaging, molecular, and treatment data,
we highlight modeling considerations relevant to these contexts. We provide an
overview of diverse forms of knowledge representation and current strategies of
knowledge integration into machine learning pipelines with concrete examples.
We conclude the review article by discussing future directions to advance
cancer research through knowledge-informed machine learning.