ADD results from the modeling paper
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@ -2265,6 +2265,17 @@ Venn diagram from the venn R package.
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% TODO this section header sucks
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% TODO this section header sucks
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\subsection{AI modeling reveals highly predictive species}
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\subsection{AI modeling reveals highly predictive species}
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Due to the heterogeneity of the multivariate data collected and knowing that no
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single model structure is perfect for all applications, we implemented an
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agnostic modeling approach to better understand these TN+TCM responses. To
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achieve this, a consensus analysis using seven machine learning (ML) techniques,
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Random Forest (RF), Gradient Boosted Machine (GBM), Conditional Inference Forest
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(CIF), Least Absolute Shrinkage and Selection Operator (LASSO), Partial
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Least-Squares Regression (PLSR), Support Vector Machine (SVM), and DataModeler’s
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Symbolic Regression (SR), was implemented to molecularly characterize TN+TCM
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cells and to extract predictive features of quality early on their expansion
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process (Fig.1d-e).
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% TODO this table looks like crap, break it up into smaller tables
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% TODO this table looks like crap, break it up into smaller tables
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\begin{table}[!h] \centering
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\begin{table}[!h] \centering
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\caption{Results for data-driven modeling}
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\caption{Results for data-driven modeling}
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@ -2272,6 +2283,25 @@ Venn diagram from the venn R package.
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\input{../tables/model_results.tex}
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\input{../tables/model_results.tex}
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\end{table}
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\end{table}
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SR models achieved the highest predictive performance (R2>93\%) when using
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multi-omics predictors for all endpoint responses (\cref{tab:mod_results}). SR achieved R2>98\%
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while GBM tree-based ensembles showed leave-one-out cross-validated R2 (LOO-R2)
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>95\% for CD4+ and CD4+/CD8+ TN+TCM responses. Similarly, LASSO, PLSR, and SVM
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methods showed consistent high LOO-R2, 92.9\%, 99.7\%, and 90.5\%, respectively,
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to predict the CD4+/CD8+ TN+TCM. Yet, about 10\% reduction in LOO-R2,
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72.5\%-81.7\%, was observed for CD4+ TN+TCM with these three methods. Lastly, SR
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and PLSR achieved R2>90\% while other ML methods exhibited exceedingly variable
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LOO-R2 (0.3\%,RF-51.5\%,LASSO) for CD8+ TN+TCM cells.
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% FIGURE the CD4/CD8 model results using SR
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The top-performing technique, SR, showed that the median aggregated predictions
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for CD4+ and CD8+ TN+TCM cells increases when IL2 concentration, IL15, and IL2R
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increase while IL17a decreases in conjunction with other features. These
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patterns combined with low values of DMS concentration and GM-CSF uniquely
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characterized maximum CD8+ TN+TCM. Meanwhile, higher glycine but lower IL13 in
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combination with others showed maximum CD4+ TN+TCM predictions (Fig.2).
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\begin{figure*}[ht!]
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\begin{figure*}[ht!]
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\begingroup
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\begingroup
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@ -2291,6 +2321,14 @@ Venn diagram from the venn R package.
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\label{fig:mod_flower}
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\label{fig:mod_flower}
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\end{figure*}
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\end{figure*}
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Selecting CPPs and CQAs candidates consistently for T cell memory is desired.
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Here, \gls{tnfa} was found in consensus across all seven ML methods for predicting
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CD4+/CD8+ TN+TCM when considering features with the highest importance scores
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across models (Fig.3a;Methods). Other features, IL2R, IL4, IL17a, and DMS
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concentration, were commonly selected in >=5 ML methods (Fig.3a,c). Moreover,
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IL13 and IL15 were found predictive in combination with these using SR
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(Supp.Table.S4).
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\section{discussion}
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\section{discussion}
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\chapter{aim 2b}\label{aim2b}
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\chapter{aim 2b}\label{aim2b}
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