Dataset Information

Prediction of an outcome using NETwork Clusters (NET-C).

ABSTRACT: Birth weight is a key consequence of environmental exposures and metabolic alterations and can influence lifelong health. While a number of methods have been used to examine associations of trace element (including essential nutrients and toxic metals) concentrations or metabolite concentrations with a health outcome, birth weight, studies evaluating how the coexistence of these factors impacts birth weight are extremely limited. Here, we present a novel algorithm NETwork Clusters (NET-C), to improve the prediction of outcome by considering the interactions of features in the network and then apply this method to predict birth weight by jointly modelling trace element and cord blood metabolite data. Specifically, by using trace element and/or metabolite subnetworks as groups, we apply group lasso to estimate birth weight. We conducted statistical simulation studies to examine how both sample size and correlations between grouped features and the outcome affect prediction performance. We showed that in terms of prediction error, our proposed method outperformed other methods such as (a) group lasso with groups defined by hierarchical clustering, (b) random forest regression and (c) neural networks. We applied our method to data ascertained as part of the New Hampshire Birth Cohort Study on trace elements, metabolites and birth outcomes, adjusting for other covariates such as maternal body mass index (BMI) and enrollment age. Our proposed method can be applied to a variety of similarly structured high-dimensional datasets to predict health outcomes.

SUBMITTER: Lee JW

PROVIDER: S-EPMC7867575 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Prediction of an outcome using NETwork Clusters (NET-C).

Lee Jai Woo JW Zhou Jie J Moen Erika L EL Punshon Tracy T Hoen Anne G AG Romano Megan E ME Karagas Margaret R MR Gui Jiang J

Computational biology and chemistry 20201208

Birth weight is a key consequence of environmental exposures and metabolic alterations and can influence lifelong health. While a number of methods have been used to examine associations of trace element (including essential nutrients and toxic metals) concentrations or metabolite concentrations with a health outcome, birth weight, studies evaluating how the coexistence of these factors impacts birth weight are extremely limited. Here, we present a novel algorithm NETwork Clusters (NET-C), to im ...[more]

PMID: 33360198

Similar Datasets

Project description:BackgroundHigh-dimensional omics data integration has emerged as a prominent avenue within the healthcare industry, presenting substantial potential to improve predictive models. However, the data integration process faces several challenges, including data heterogeneity, priority sequence in which data blocks are prioritized for rendering predictive information contained in multiple blocks, assessing the flow of information from one omics level to the other and multicollinearity.MethodsWe propose the Priority-Elastic net algorithm, a hierarchical regression method extending Priority-Lasso for the binary logistic regression model by incorporating a priority order for blocks of variables while fitting Elastic-net models sequentially for each block. The fitted values from each step are then used as an offset in the subsequent step. Additionally, we considered the adaptive elastic-net penalty within our priority framework to compare the results.ResultsThe Priority-Elastic net and Priority-Adaptive Elastic net algorithms were evaluated on a brain tumor dataset available from The Cancer Genome Atlas (TCGA), accounting for transcriptomics, proteomics, and clinical information measured over two glioma types: Lower-grade glioma (LGG) and glioblastoma (GBM).ConclusionOur findings suggest that the Priority-Elastic net is a highly advantageous choice for a wide range of applications. It offers moderate computational complexity, flexibility in integrating prior knowledge while introducing a hierarchical modeling perspective, and, importantly, improved stability and accuracy in predictions, making it superior to the other methods discussed. This evolution marks a significant step forward in predictive modeling, offering a sophisticated tool for navigating the complexities of multi-omics datasets in pursuit of precision medicine's ultimate goal: personalized treatment optimization based on a comprehensive array of patient-specific data. This framework can be generalized to time-to-event, Cox proportional hazards regression and multicategorical outcomes. A practical implementation of this method is available upon request in R script, complete with an example to facilitate its application.

Project description:Microbiome data are becoming increasingly available in large health cohorts, yet metabolomics data are still scant. While many studies generate microbiome data, they lack matched metabolomics data or have considerable missing proportions of metabolites. Since metabolomics is key to understanding microbial and general biological activities, the possibility of imputing individual metabolites or inferring metabolomics pathways from microbial taxonomy or metagenomics is intriguing. Importantly, current metabolomics profiling methods such as the HMP Unified Metabolic Analysis Network (HUMAnN) have unknown accuracy and are limited in their ability to predict individual metabolites. To address this gap, we developed a novel metabolite prediction method, and we present its application and evaluation in an oral microbiome study. The new method for predicting metabolites using microbiome data (ENVIM) is based on the elastic net model (ENM). ENVIM introduces an extra step to ENM to consider variable importance (VI) scores, and thus, achieves better prediction power. We investigate the metabolite prediction performance of ENVIM using metagenomic and metatranscriptomic data in a supragingival biofilm multi-omics dataset of 289 children ages 3-5 who were participants of a community-based study of early childhood oral health (ZOE 2.0) in North Carolina, United States. We further validate ENVIM in two additional publicly available multi-omics datasets generated from studies of gut health. We select gene family sets based on variable importance scores and modify the existing ENM strategy used in the MelonnPan prediction software to accommodate the unique features of microbiome and metabolome data. We evaluate metagenomic and metatranscriptomic predictors and compare the prediction performance of ENVIM to the standard ENM employed in MelonnPan. The newly developed ENVIM method showed superior metabolite predictive accuracy than MelonnPan when trained with metatranscriptomics data only, metagenomics data only, or both. Better metabolite prediction is achieved in the gut microbiome compared with the oral microbiome setting. We report the best-predictable compounds in all these three datasets from two different body sites. For example, the metabolites trehalose, maltose, stachyose, and ribose are all well predicted by the supragingival microbiome.

Project description:When dealing with a newly emerging disease such as COVID-19, the impact of patient- and disease-specific factors (e.g., body weight or known co-morbidities) on the immediate course of the disease is largely unknown. An accurate prediction of the most likely individual disease progression can improve the planning of limited resources and finding the optimal treatment for patients. In the case of COVID-19, the need for intensive care unit (ICU) admission of pneumonia patients can often only be determined on short notice by acute indicators such as vital signs (e.g., breathing rate, blood oxygen levels), whereas statistical analysis and decision support systems that integrate all of the available data could enable an earlier prognosis. To this end, we propose a holistic, multimodal graph-based approach combining imaging and non-imaging information. Specifically, we introduce a multimodal similarity metric to build a population graph that shows a clustering of patients. For each patient in the graph, we extract radiomic features from a segmentation network that also serves as a latent image feature encoder. Together with clinical patient data like vital signs, demographics, and lab results, these modalities are combined into a multimodal representation of each patient. This feature extraction is trained end-to-end with an image-based Graph Attention Network to process the population graph and predict the COVID-19 patient outcomes: admission to ICU, need for ventilation, and mortality. To combine multiple modalities, radiomic features are extracted from chest CTs using a segmentation neural network. Results on a dataset collected in Klinikum rechts der Isar in Munich, Germany and the publicly available iCTCF dataset show that our approach outperforms single modality and non-graph baselines. Moreover, our clustering and graph attention increases understanding of the patient relationships within the population graph and provides insight into the network's decision-making process.

Dataset Information

Prediction of an outcome using NETwork Clusters (NET-C).

Publications

Prediction of an outcome using NETwork Clusters (NET-C).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets