  Genome-wide association studies (GWAS) are used to identify relationships
between genetic variations and specific traits. When applied to
high-dimensional medical imaging data, a key step is to extract
lower-dimensional, yet informative representations of the data as traits.
Representation learning for imaging genetics is largely under-explored due to
the unique challenges posed by GWAS in comparison to typical visual
representation learning. In this study, we tackle this problem from the mutual
information (MI) perspective by identifying key limitations of existing
methods. We introduce a trans-modal learning framework Genetic InfoMax (GIM),
including a regularized MI estimator and a novel genetics-informed transformer
to address the specific challenges of GWAS. We evaluate GIM on human brain 3D
MRI data and establish standardized evaluation protocols to compare it to
existing approaches. Our results demonstrate the effectiveness of GIM and a
significantly improved performance on GWAS.
