In system analysis and design optimization, multiple computational models are typically available to represent a given physical system. These models can be broadly classified as high-fidelity models, which provide highly accurate predictions but require significant computational resources, and low-fidelity models, which are computationally efficient but less accurate. Multi-fidelity methods integrate high- and low-fidelity models to balance computational cost and predictive accuracy. This perspective paper provides an in-depth overview of the emerging field of machine learning-based multi-fidelity methods, with a particular emphasis on uncertainty quantification and optimization. For uncertainty quantification, a particular focus is on multi-fidelity graph neural networks, compared with multi-fidelity polynomial chaos expansion. For optimization, our emphasis is on multi-fidelity Bayesian optimization, offering a unified perspective on multi-fidelity priors and proposing an application strategy when the objective function is an integral or a weighted sum. We highlight the current state of the art, identify critical gaps in the literature, and outline key research opportunities in this evolving field.