Encoding Domain Knowledge in Multi-view Latent Variable Models: A Bayesian Approach with Structured Sparsity
Abstract
Many real-world systems are described not only by data from a single source but via multiple data views. In genomic medicine, for instance, patients can be characterized by data from different molecular layers. Latent variable models with structured sparsity are a commonly used tool for disentangling variation within and across data views. However, their interpretability is cumbersome since it requires a direct inspection and interpretation of each factor from domain experts. Here, we propose MuVI, a novel multi-view latent variable model based on a modified horseshoe prior for modeling structured sparsity. This facilitates the incorporation of limited and noisy domain knowledge, thereby allowing for an analysis of multi-view data in an inherently explainable manner. We demonstrate that our model (i) outperforms state-of-the-art approaches for modeling structured sparsity in terms of the reconstruction error and the precision/recall, (ii) robustly integrates noisy domain expertise in the form of feature sets, (iii) promotes the identifiability of factors and (iv) infers interpretable and biologically meaningful axes of variation in a real-world multi-view dataset of cancer patients.
BibTeX
@InProceedings{pmlr-v206-qoku23a,
title = {Encoding Domain Knowledge in Multi-view Latent Variable Models: A Bayesian Approach with Structured Sparsity},
author = {Qoku, Arber and Buettner, Florian},
booktitle = {Proceedings of The 26th International Conference on Artificial Intelligence and Statistics},
pages = {11545--11562},
year = {2023},
editor = {Ruiz, Francisco and Dy, Jennifer and van de Meent, Jan-Willem},
volume = {206},
series = {Proceedings of Machine Learning Research},
month = {25--27 Apr},
publisher = {PMLR},
pdf = {https://proceedings.mlr.press/v206/qoku23a/qoku23a.pdf},
url = {https://proceedings.mlr.press/v206/qoku23a.html},
abstract = {Many real-world systems are described not only by data from a single source but via multiple data views. In genomic medicine, for instance, patients can be characterized by data from different molecular layers. Latent variable models with structured sparsity are a commonly used tool for disentangling variation within and across data views. However, their interpretability is cumbersome since it requires a direct inspection and interpretation of each factor from domain experts. Here, we propose MuVI, a novel multi-view latent variable model based on a modified horseshoe prior for modeling structured sparsity. This facilitates the incorporation of limited and noisy domain knowledge, thereby allowing for an analysis of multi-view data in an inherently explainable manner. We demonstrate that our model (i) outperforms state-of-the-art approaches for modeling structured sparsity in terms of the reconstruction error and the precision/recall, (ii) robustly integrates noisy domain expertise in the form of feature sets, (iii) promotes the identifiability of factors and (iv) infers interpretable and biologically meaningful axes of variation in a real-world multi-view dataset of cancer patients.}
}