ABSTRACT
Patient representation learning methods create rich representations of complex data and have potential to further advance the development of computational phenotypes (CP). Currently, these methods are either applied to small predefined concept sets or all available patient data, limiting the potential for novel discovery and reducing the explainability of the resulting representations. We report on an extensive, data-driven characterization of the utility of patient representation learning methods for the purpose of CP development or automatization. We conducted ablation studies to examine the impact of patient representations, built using data from different combinations of data types and sampling windows on rare disease classification. We demonstrated that the data type and sampling window directly impact classification and clustering performance, and these results differ by rare disease group. Our results, although preliminary, exemplify the importance of and need for data-driven characterization in patient representation-based CP development pipelines.