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The recent advances in the automation of metadata normalization and the invention of a unified schema --- Brick --- alleviate the metadata normalization challenge for deploying portable applications across buildings. Yet, the lack of compatibility between existing metadata normalization methods precludes the possibility of comparing and combining them. While generic machine learning (ML) frameworks, such as MLJAR and OpenML, provide versatile interfaces for standard ML problems, they cannot easily accommodate the metadata normalization tasks for buildings due to the heterogeneity in the inference scope, type of data required as input, evaluation metric, and the building-specific human-in-the-loop learning procedure. We propose Plaster, an open and modular framework that incorporates existing advances in building metadata normalization. It provides unified programming interfaces for various types of learning methods for metadata normalization and defines standardized data models for building metadata and timeseries data. Thus, it enables the integration of different methods via a workflow, benchmarking of different methods via unified interfaces, and rapid prototyping of new algorithms. With Plaster, we 1) show three examples of the workflow integration, delivering better performance than individual algorithms, 2) benchmark/analyze five algorithms over five common buildings, and 3) exemplify the process of developing a new algorithm involving time series features. We believe Plaster will facilitate the development of new algorithms and expedite the adoption of standard metadata schema such as Brick, in order to enable seamless smart building applications in the future.
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Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies
Heterogeneity in different genomic studies compromises the performance of machine learning models in cross-study phenotype predictions. Overcoming heterogeneity when incorporating different studies in terms of phenotype prediction is a challenging and critical step for developing machine learning algorithms with reproducible prediction performance on independent datasets. We investigated the best approaches to integrate different studies of the same type of omics data under a variety of different heterogeneities. We developed a comprehensive workflow to simulate a variety of different types of heterogeneity and evaluate the performances of different integration methods together with batch normalization by using ComBat. We also demonstrated the results through realistic applications on six colorectal cancer (CRC) metagenomic studies and six tuberculosis (TB) gene expression studies, respectively. We showed that heterogeneity in different genomic studies can markedly negatively impact the machine learning classifier’s reproducibility. ComBat normalization improved the prediction performance of machine learning classifier when heterogeneous populations are present, and could successfully remove batch effects within the same population. We also showed that the machine learning classifier’s prediction accuracy can be markedly decreased as the underlying disease model became more different in training and test populations. Comparing different merging and integration methods, we found that merging and integration methods can outperform each other in different scenarios. In the realistic applications, we observed that the prediction accuracy improved when applying ComBat normalization with merging or integration methods in both CRC and TB studies. We illustrated that batch normalization is essential for mitigating both population differences of different studies and batch effects. We also showed that both merging strategy and integration methods can achieve good performances when combined with batch normalization. In addition, we explored the potential of boosting phenotype prediction performance by rank aggregation methods and showed that rank aggregation methods had similar performance as other ensemble learning approaches.
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- Award ID(s):
- 2125142
- PAR ID:
- 10478146
- Editor(s):
- Roy, Sushmita
- Publisher / Repository:
- PLoS
- Date Published:
- Journal Name:
- PLOS Computational Biology
- Volume:
- 19
- Issue:
- 10
- ISSN:
- 1553-7358
- Page Range / eLocation ID:
- e1010608
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1371/journal.pcbi.1010608
