Sophie Wharrie

Sophie Wharrie, Lisa Eick, Lotta Mäkinen et al.

Machine learning strategies like multi-task learning, meta-learning, and transfer learning enable efficient adaptation of machine learning models to specific applications in healthcare, such as prediction of various diseases, by leveraging generalizable knowledge across large datasets and multiple domains. In particular, Bayesian meta-learning methods pool data across related prediction tasks to learn prior distributions for model parameters, which are then used to derive models for specific tasks. However, inter- and intra-task variability due to disease heterogeneity and other patient-level differences pose challenges of negative transfer during shared learning and poor generalizability to new patients. We introduce a novel Bayesian meta-learning approach that aims to address this in two key settings: (1) predictions for new patients (same population as the training set) and (2) adapting to new patient populations. Our main contribution is in modeling similarity between causal mechanisms of the tasks, for (1) mitigating negative transfer during training and (2) fine-tuning that pools information from tasks that are expected to aid generalizability. We propose an algorithm for implementing this approach for Bayesian deep learning, and apply it to a case study for stroke prediction tasks using electronic health record data. Experiments for the UK Biobank dataset as the training population demonstrated significant generalizability improvements compared to standard meta-learning, non-causal task similarity measures, and local baselines (separate models for each task). This was assessed for a variety of tasks that considered both new patients from the training population (UK Biobank) and a new population (FinnGen).

Zachris Björkman, Jorge Loría, Sophie Wharrie et al.

Bayesian causal discovery benefits from prior information elicited from domain experts, and in heterogeneous domains any prior knowledge would be badly needed. However, so far prior elicitation approaches have assumed a single causal graph and hence are not suited to heterogeneous domains. We propose a causal elicitation strategy for heterogeneous settings, based on Bayesian experimental design (BED) principles, and a variational mixture structure learning (VaMSL) method -- extending the earlier differentiable Bayesian structure learning (DiBS) method -- to iteratively infer mixtures of causal Bayesian networks (CBNs). We construct an informative graph prior incorporating elicited expert feedback in the inference of mixtures of CBNs. Our proposed method successfully produces a set of alternative causal models (mixture components or clusters), and achieves an improved structure learning performance on heterogeneous synthetic data when informed by a simulated expert. Finally, we demonstrate that our approach is capable of capturing complex distributions in a breast cancer database.