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Title: Cooperative learning for multiview analysis
We propose a method for supervised learning with multiple sets of features (“views”). The multiview problem is especially important in biology and medicine, where “-omics” data, such as genomics, proteomics, and radiomics, are measured on a common set of samples. “Cooperative learning” combines the usual squared-error loss of predictions with an “agreement” penalty to encourage the predictions from different data views to agree. By varying the weight of the agreement penalty, we get a continuum of solutions that include the well-known early and late fusion approaches. Cooperative learning chooses the degree of agreement (or fusion) in an adaptive manner, using a validation set or cross-validation to estimate test set prediction error. One version of our fitting procedure is modular, where one can choose different fitting mechanisms (e.g., lasso, random forests, boosting, or neural networks) appropriate for different data views. In the setting of cooperative regularized linear regression, the method combines the lasso penalty with the agreement penalty, yielding feature sparsity. The method can be especially powerful when the different data views share some underlying relationship in their signals that can be exploited to boost the signals. We show that cooperative learning achieves higher predictive accuracy on simulated data and real multiomics examples of labor-onset prediction. By leveraging aligned signals and allowing flexible fitting mechanisms for different modalities, cooperative learning offers a powerful approach to multiomics data fusion.  more » « less
Award ID(s):
2113389
NSF-PAR ID:
10355842
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Proceedings of the National Academy of Sciences
Volume:
119
Issue:
38
ISSN:
0027-8424
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the official views of any of these organizations. REFERENCES [1] I. Obeid and J. Picone, “The Temple University Hospital EEG Data Corpus,” in Augmentation of Brain Function: Facts, Fiction and Controversy. Volume I: Brain-Machine Interfaces, 1st ed., vol. 10, M. A. Lebedev, Ed. Lausanne, Switzerland: Frontiers Media S.A., 2016, pp. 394 398. https://doi.org/10.3389/fnins.2016.00196. [2] V. Shah et al., “The Temple University Hospital Seizure Detection Corpus,” Frontiers in Neuroinformatics, vol. 12, pp. 1–6, 2018. https://doi.org/10.3389/fninf.2018.00083. [3] A. Hamid et, al., “The Temple University Artifact Corpus: An Annotated Corpus of EEG Artifacts.” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2020, pp. 1-3. https://ieeexplore.ieee.org/document/9353647. [4] Y. Roy, R. Iskander, and J. Picone, “The NeurekaTM 2020 Epilepsy Challenge,” NeuroTechX, 2020. [Online]. Available: https://neureka-challenge.com/. [Accessed: 01-Dec-2021]. [5] S. Rahman, A. Hamid, D. Ochal, I. Obeid, and J. Picone, “Improving the Quality of the TUSZ Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2020, pp. 1–5. https://ieeexplore.ieee.org/document/9353635. [6] V. Shah, E. von Weltin, T. Ahsan, I. Obeid, and J. Picone, “On the Use of Non-Experts for Generation of High-Quality Annotations of Seizure Events,” Available: https://www.isip.picone press.com/publications/unpublished/journals/2019/elsevier_cn/ira. [Accessed: 01-Dec-2021]. [7] D. Ochal, S. Rahman, S. Ferrell, T. Elseify, I. Obeid, and J. Picone, “The Temple University Hospital EEG Corpus: Annotation Guidelines,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/tuh_eeg/annotations/. [8] D. 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