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Abstract MotivationPredictive biological signatures provide utility as biomarkers for disease diagnosis and prognosis, as well as prediction of responses to vaccination or therapy. These signatures are identified from high-throughput profiling assays through a combination of dimensionality reduction and machine learning techniques. The genes, proteins, metabolites, and other biological analytes that compose signatures also generate hypotheses on the underlying mechanisms driving biological responses, thus improving biological understanding. Dimensionality reduction is a critical step in signature discovery to address the large number of analytes in omics datasets, especially for multi-omics profiling studies with tens of thousands of measurements. Latent factor models, which can account for the structural heterogeneity across diverse assays, effectively integrate multi-omics data and reduce dimensionality to a small number of factors that capture correlations and associations among measurements. These factors provide biologically interpretable features for predictive modeling. However, multi-omics integration and predictive modeling are generally performed independently in sequential steps, leading to suboptimal factor construction. Combining these steps can yield better multi-omics signatures that are more predictive while still being biologically meaningful. ResultsWe developed a supervised variational Bayesian factor model that extracts multi-omics signatures from high-throughput profiling datasets that can span multiple data types. Signature-based multiPle-omics intEgration via lAtent factoRs (SPEAR) adaptively determines factor rank, emphasis on factor structure, data relevance and feature sparsity. The method improves the reconstruction of underlying factors in synthetic examples and prediction accuracy of coronavirus disease 2019 severity and breast cancer tumor subtypes. Availability and implementationSPEAR is a publicly available R-package hosted at https://bitbucket.org/kleinstein/SPEAR. 

The Random Forests classifier, a widely utilized off-the-shelf classification tool, assumes training and test samples come from the same distribution as other standard classifiers. However, in safety-critical scenarios like medical diagnosis and network attack detection, discrepancies between the training and test sets, including the potential presence of novel outlier samples not appearing during training, can pose significant challenges. To address this problem, we introduce the Conformalized Semi-Supervised Random Forest (CSForest), which couples the conformalization technique Jackknife+aB with semi-supervised tree ensembles to construct a set-valued prediction 𝐶(𝑥). Instead of optimizing over the training distribution, CSForest employs unlabeled test samples to enhance accuracy and flag unseen outliers by generating an empty set. Theoretically, we establish CSForest to cover true labels for previously observed inlier classes under arbitrarily label-shift in the test data. We compare CSForest with state-of-the-art methods using synthetic examples and various real-world datasets, under different types of distribution changes in the test domain. Our results highlight CSForest’s effective prediction of inliers and its ability to detect outlier samples unique to the test data. In addition, CSForest shows persistently good performance as the sizes of the training and test sets vary. Codes of CSForest are available at https://github.com/yujinhan98/CSForest. 

As immunological and clinical studies become more complex, there is an increasing need to analyze temporal immunophenotypes alongside demographic and clinical covariates, where each subject receives matrix-valued time series observations for potentially high-dimensional longitudinal features, as well as other static characterizations. Researchers aim to find the low-dimensional embedding of subjects using matrix-valued time series observations and investigate relationships between static clinical responses and the embedding. However, constructing these embeddings can be challenging due to high dimensionality, sparsity, and irregularity in sample collection over time. In addition, the incorporation of static auxiliary covariates is frequently desired during such a construction. To address these issues, we propose a smoothed probabilistic PARAFAC model with covariates (SPACO) that utilizes auxiliary covariates of interest. We provide extensive simulations to test different aspects of SPACO and demonstrate its application to an immunological dataset from patients with SARS-CoV-2 infection. Supplemental materials associated with this article are available online. 

Overfitting describes the phenomenon where a highly predictive model on the training data generalizes poorly to future observations. It is a common concern when applying machine learning techniques to contemporary medical applications, such as predicting vaccination response and dis-ease status in infectious disease or cancer studies. This review examines the causes of overfitting and offers strategies to counteract it, focusing on model complexity reduction, reliable model evaluation, and harnessing data diversity. Through discussion of the underlying mathematical models and illustrative examples using both synthetic data and published real datasets, our objective is to equip analysts and bioinformaticians with the knowledge and tools necessary to detect and mitigate overfitting in their research.