Locally Sparse Neural Networks for Tabular Biomedical Data

Junchen Yang, Ofir Lindenbaum, Yuval Kluger
Proceedings of the 39th International Conference on Machine Learning, PMLR 162:25123-25153, 2022.

Abstract

Tabular datasets with low-sample-size or many variables are prevalent in biomedicine. Practitioners in this domain prefer linear or tree-based models over neural networks since the latter are harder to interpret and tend to overfit when applied to tabular datasets. To address these neural networks’ shortcomings, we propose an intrinsically interpretable network for heterogeneous biomedical data. We design a locally sparse neural network where the local sparsity is learned to identify the subset of most relevant features for each sample. This sample-specific sparsity is predicted via a gating network, which is trained in tandem with the prediction network. By forcing the model to select a subset of the most informative features for each sample, we reduce model overfitting in low-sample-size data and obtain an interpretable model. We demonstrate that our method outperforms state-of-the-art models when applied to synthetic or real-world biomedical datasets using extensive experiments. Furthermore, the proposed framework dramatically outperforms existing schemes when evaluating its interpretability capabilities. Finally, we demonstrate the applicability of our model to two important biomedical tasks: survival analysis and marker gene identification.

Cite this Paper

BibTeX
@InProceedings{pmlr-v162-yang22i, title = {Locally Sparse Neural Networks for Tabular Biomedical Data}, author = {Yang, Junchen and Lindenbaum, Ofir and Kluger, Yuval}, booktitle = {Proceedings of the 39th International Conference on Machine Learning}, pages = {25123--25153}, year = {2022}, editor = {Chaudhuri, Kamalika and Jegelka, Stefanie and Song, Le and Szepesvari, Csaba and Niu, Gang and Sabato, Sivan}, volume = {162}, series = {Proceedings of Machine Learning Research}, month = {17--23 Jul}, publisher = {PMLR}, pdf = {https://proceedings.mlr.press/v162/yang22i/yang22i.pdf}, url = {https://proceedings.mlr.press/v162/yang22i.html}, abstract = {Tabular datasets with low-sample-size or many variables are prevalent in biomedicine. Practitioners in this domain prefer linear or tree-based models over neural networks since the latter are harder to interpret and tend to overfit when applied to tabular datasets. To address these neural networks’ shortcomings, we propose an intrinsically interpretable network for heterogeneous biomedical data. We design a locally sparse neural network where the local sparsity is learned to identify the subset of most relevant features for each sample. This sample-specific sparsity is predicted via a gating network, which is trained in tandem with the prediction network. By forcing the model to select a subset of the most informative features for each sample, we reduce model overfitting in low-sample-size data and obtain an interpretable model. We demonstrate that our method outperforms state-of-the-art models when applied to synthetic or real-world biomedical datasets using extensive experiments. Furthermore, the proposed framework dramatically outperforms existing schemes when evaluating its interpretability capabilities. Finally, we demonstrate the applicability of our model to two important biomedical tasks: survival analysis and marker gene identification.} }
Endnote
%0 Conference Paper %T Locally Sparse Neural Networks for Tabular Biomedical Data %A Junchen Yang %A Ofir Lindenbaum %A Yuval Kluger %B Proceedings of the 39th International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2022 %E Kamalika Chaudhuri %E Stefanie Jegelka %E Le Song %E Csaba Szepesvari %E Gang Niu %E Sivan Sabato %F pmlr-v162-yang22i %I PMLR %P 25123--25153 %U https://proceedings.mlr.press/v162/yang22i.html %V 162 %X Tabular datasets with low-sample-size or many variables are prevalent in biomedicine. Practitioners in this domain prefer linear or tree-based models over neural networks since the latter are harder to interpret and tend to overfit when applied to tabular datasets. To address these neural networks’ shortcomings, we propose an intrinsically interpretable network for heterogeneous biomedical data. We design a locally sparse neural network where the local sparsity is learned to identify the subset of most relevant features for each sample. This sample-specific sparsity is predicted via a gating network, which is trained in tandem with the prediction network. By forcing the model to select a subset of the most informative features for each sample, we reduce model overfitting in low-sample-size data and obtain an interpretable model. We demonstrate that our method outperforms state-of-the-art models when applied to synthetic or real-world biomedical datasets using extensive experiments. Furthermore, the proposed framework dramatically outperforms existing schemes when evaluating its interpretability capabilities. Finally, we demonstrate the applicability of our model to two important biomedical tasks: survival analysis and marker gene identification.
APA
Yang, J., Lindenbaum, O. & Kluger, Y.. (2022). Locally Sparse Neural Networks for Tabular Biomedical Data. Proceedings of the 39th International Conference on Machine Learning, in Proceedings of Machine Learning Research 162:25123-25153 Available from https://proceedings.mlr.press/v162/yang22i.html.

Related Material