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Optimal Sparse Linear Prediction for Block-missing Multi-modality Data without Imputation.

ABSTRACT: In modern scientific research, data are often collected from multiple modalities. Since different modalities could provide complementary information, statistical prediction methods using multi-modality data could deliver better prediction performance than using single modality data. However, one special challenge for using multi-modality data is related to block-missing data. In practice, due to dropouts or the high cost of measures, the observations of a certain modality can be missing completely for some subjects. In this paper, we propose a new DIrect Sparse regression procedure using COvariance from Multi-modality data (DISCOM). Our proposed DISCOM method includes two steps to find the optimal linear prediction of a continuous response variable using block-missing multi-modality predictors. In the first step, rather than deleting or imputing missing data, we make use of all available information to estimate the covariance matrix of the predictors and the cross-covariance vector between the predictors and the response variable. The proposed new estimate of the covariance matrix is a linear combination of the identity matrix, the estimates of the intra-modality covariance matrix and the cross-modality covariance matrix. Flexible estimates for both the sub-Gaussian and heavy-tailed cases are considered. In the second step, based on the estimated covariance matrix and the estimated cross-covariance vector, an extended Lasso-type estimator is used to deliver a sparse estimate of the coefficients in the optimal linear prediction. The number of samples that are effectively used by DISCOM is the minimum number of samples with available observations from two modalities, which can be much larger than the number of samples with complete observations from all modalities. The effectiveness of the proposed method is demonstrated by theoretical studies, simulated examples, and a real application from the Alzheimer's Disease Neuroimaging Initiative. The comparison between DISCOM and some existing methods also indicates the advantages of our proposed method.

SUBMITTER: Yu G

PROVIDER: S-EPMC8612700 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundEpistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. An effective method for imputing interactions would therefore increase the types of possible analysis, as well as increase the potential to identify novel functional interactions between gene pairs. Several methods have been developed to handle missing values in microarray data, but it is unclear how applicable these methods are to E-MAP data because of their pairwise nature and the significantly larger number of missing values. Here we evaluate four alternative imputation strategies, three local (Nearest neighbor-based) and one global (PCA-based), that have been modified to work with symmetric pairwise data.ResultsWe identify different categories for the missing data based on their underlying cause, and show that values from the largest category can be imputed effectively. We compare local and global imputation approaches across a variety of distinct E-MAP datasets, showing that both are competitive and preferable to filling in with zeros. In addition we show that these methods are effective in an E-MAP from a different species, suggesting that pairwise imputation techniques will be increasingly useful as analogous epistasis mapping techniques are developed in different species. We show that strongly alleviating interactions are significantly more difficult to predict than strongly aggravating interactions. Finally we show that imputed interactions, generated using nearest neighbor methods, are enriched for annotations in the same manner as measured interactions. Therefore our method potentially expands the number of mapped epistatic interactions. In addition we make implementations of our algorithms available for use by other researchers.ConclusionsWe address the problem of missing value imputation for E-MAPs, and suggest the use of symmetric nearest neighbor based approaches as they offer consistently accurate imputations across multiple datasets in a tractable manner.

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Optimal Sparse Linear Prediction for Block-missing Multi-modality Data without Imputation.

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