Quantifying Uncertainty in Ensemble Deep Learning

Neural networks are an emerging topic in the data science industry due to their high versatility and efficiency with large data sets. The purpose of this modern machine learning technique is to recognize relationships and patterns in vast amounts of data that would not be explored otherwise. Past research has utilized machine learning on experimental data in the material sciences and chemistry field to predict properties of metal oxides. Neural networks can determine underlying optical properties in complex images of metal oxides and capture essential features which are unrecognizable by observation. However, neural networks are often referred to as a “black box algorithm” due to the underlying process during the training of the model. The explanation for a prediction is unable to be traced, therefore poses a concern on how robust and reliable the prediction model actually is. Building ensemble neural networks allows for the analysis of the error bars of the prediction model. The project’s objective is to determine the comparative differences between the predictive ability of each individual convolutional neural network versus the ensemble neural network. Additionally, the paper explores how to use the ensemble model as a method of uncertainty quantification. Overall, ensemble neural networks outperform singular networks and demonstrate areas of uncertainty and robustness in the model

Ensemble Deep Learning

Machine learning has become a common tool within the tech industry due to its high versatility and efficiency with large datasets. Partnering with the Nevada National Security Site, our goal is to improve accuracy of machine predictions by utilizing deep learning, which will enable the power and accuracy of a prediction to grow from the model. To build a deep learning model, multiple neural network architectures were developed and combined to create an ensemble neural network. The project’s objective is to determine the comparative differences between the efficiency of the ensemble neural network versus each individual neural network. The data set used to test, validate, and train the networks is 1D regressive. After testing architecture and determining accuracy of certain networks, the model will be updated and tested again to compare accuracies. Accuracy is the number of correct predictions over the total number of predictions. As model precision is a key aspect of machine learning, emphasis is placed on the efficiency of ensemble neural networks

Developing Predictive Algorithm for Possible Fuel Stops for Private Aviation

Machine learning algorithms\u27 capacity to improve over time is one of their main advantages. When more and more data is handled, machine learning technology often becomes more effective and accurate. Machine learning can be used to address problems in industry. OneSky Flight is an aviation company under an umbrella of companies offering technology services for other private jet companies. One problem they face as a business is predicting when a flight will need a fuel stop upon a booking request. Given a data set of approximately 230,000 flights from OneSky, dating back to 2019, a prediction model will be made in order to achieve the overall objective of the project: a fuel stop predictor. Therefore, the customer is aware and can upgrade the aircraft or plan for the necessary fuel stop, saving the customer money and time

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

Academi

Dynamic landscape and regulation of RNA editing in mammals

Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules1. Although many editing sites have recently been discovered2,3,4,5,6,7, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood8,9,10. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.Y

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.11Nsciescopu