From ad0b0531fc20b82403d5a6843b2b9c01445d6ca2 Mon Sep 17 00:00:00 2001 From: will king Date: Fri, 6 Oct 2023 10:29:37 -0700 Subject: [PATCH] Saving updates, added new causal graph --- Latex/Presentation/presentation.tex | 186 +++++++++++++-------- Latex/assets/tikzit/CausalGraph_joint.tikz | 37 ++++ 2 files changed, 152 insertions(+), 71 deletions(-) create mode 100644 Latex/assets/tikzit/CausalGraph_joint.tikz diff --git a/Latex/Presentation/presentation.tex b/Latex/Presentation/presentation.tex index eefeeb5..67339c8 100644 --- a/Latex/Presentation/presentation.tex +++ b/Latex/Presentation/presentation.tex @@ -65,7 +65,7 @@ Washington State University \\ % Your institution for the title page \vspace{12pt} - This research investigates the ways by which market conditions + My research investigates the ways by which competing compounds affect clinical trial completion. \end{frame} %-------------------------------- @@ -140,7 +140,7 @@ Washington State University \\ % Your institution for the title page \frametitle{This research, in context} In contrast to previous work looking at multiple phases of trials, - I seek to figure out what causes individual trials to fail. + I seek to figure out what causes individual (phase 3) trials to fail. % \vspace{12pt} % @@ -199,7 +199,7 @@ Washington State University \\ % Your institution for the title page \end{enumerate} \end{column} \begin{column}{0.5\textwidth} - What does an \textbf{Terminated} trial look like? + What does a \textbf{Terminated} trial look like? \begin{enumerate} \item Study sponsor comes up with design \item Apply for NCT ID from ClinicalTrials.gov @@ -381,8 +381,7 @@ Washington State University \\ % Your institution for the title page \begin{enumerate} \item Population Effects \item Fundamental Safety and Efficacy of compound/dosage/route - \item How long the trial is taking - \item the total effects + \item How long the trial is taking. \end{enumerate} \end{frame} %------------------------------- @@ -426,6 +425,20 @@ Washington State University \\ % Your institution for the title page \cite{pearl_causality_2000} \end{frame} %------------------------------- +\begin{frame} + \frametitle{Complete graph - Joint} + %introduce backdoor criterion + + \begin{figure} + \scalebox{0.6}{ + \tikzfig{../assets/tikzit/CausalGraph_joint} + } + \label{FIG:CausalGraphJoint} + \caption{Causal Graph with Joint RV} + \end{figure} + +\end{frame} +%------------------------------- \begin{frame} \frametitle{Sufficent Adjustment Set} %introduce backdoor criterion @@ -438,7 +451,6 @@ Washington State University \\ % Your institution for the title page \item Condition \item Population \end{itemize} - Discuss Regime Switching For the direct effect these are controls for: \begin{itemize} @@ -447,32 +459,30 @@ Washington State University \\ % Your institution for the title page \item Population (optional) \item Enrollment \end{itemize} - Not causally identified due to Regime Switching - \end{frame} %------------------------------- -\begin{frame} - \frametitle{Other testable hypotheses} - One advantage of this approach is that there are tools that can automatically - \begin{itemize} - \item verify causal identification - \item generate hypotheses to verify model - \end{itemize} - - In this case, the following are testable hyptheses - \begin{itemize} - \item Decision to continue Phase III $\perp$ Elapsed Duration - \item Decision to continue Phase III $\perp$ Market Conditions $\Vert$ Condition - \item Decision to continue Phase III $\perp$ Population $\Vert$ Condition - \item Elapsed Duration $\perp$ Market Conditions - \item Elapsed Duration $\perp$ Condition - \item Elapsed Duration $\perp$ Population - \item Population $\perp$ Terminated $\Vert$ Condition, Decision to continue Phase III, Elapsed Duration, Enrollment Status, Market Conditions - \end{itemize} - - \href{http://dagitty.net/mLyFuc5}{Dagitty.net model} -\end{frame} +%\begin{frame} +% \frametitle{Other testable hypotheses} +% One advantage of this approach is that there are tools that can automatically +% \begin{itemize} +% \item verify causal identification +% \item generate hypotheses to verify model +% \end{itemize} +% +% In this case, the following are testable hyptheses +% \begin{itemize} +% \item Decision to continue Phase III $\perp$ Elapsed Duration +% \item Decision to continue Phase III $\perp$ Market Conditions $\Vert$ Condition +% \item Decision to continue Phase III $\perp$ Population $\Vert$ Condition +% \item Elapsed Duration $\perp$ Market Conditions +% \item Elapsed Duration $\perp$ Condition +% \item Elapsed Duration $\perp$ Population +% \item Population $\perp$ Terminated $\Vert$ Condition, Decision to continue Phase III, Elapsed Duration, Enrollment Status, Market Conditions +% \end{itemize} +% +% \href{http://dagitty.net/mLyFuc5}{Dagitty.net model} +%\end{frame} %------------------------------- \begin{frame} \frametitle{Questions?} @@ -524,7 +534,8 @@ Washington State University \\ % Your institution for the title page \begin{itemize} \item USP Drug Classification (2023) \begin{itemize} - \item Used to measure which drugs + \item A list of drugs that have certain effects. + \item Required manual matching between trials and categories. \end{itemize} \item NSDE Files (New drug code Structured product labels Data Element) \begin{itemize} @@ -532,9 +543,8 @@ Washington State University \\ % Your institution for the title page \end{itemize} \item RxNorm \begin{itemize} - \item Links pharmaceuticals between MeSH standardized terms and - NSDE files. - \item Used to find brand names that share active ingredients with those from trial. + \item Links pharmaceuticals between MeSH standardized terms, + NSDE files, and USP Files. \end{itemize} \end{itemize} \end{frame} @@ -545,7 +555,6 @@ Washington State University \\ % Your institution for the title page \item Global Disease Burden Survey (2019) \begin{itemize} \item Estimates of DALYs for categories of disease - \item Links of Categories to ICD-10 Codes \end{itemize} \item ICD-10 (2019) \begin{itemize} @@ -556,14 +565,13 @@ Washington State University \\ % Your institution for the title page \item Unified Medical Language System Thesaurus \begin{itemize} \item Used to link MeSH standardized terms and ICD-10 conditions - \item Manual matching process \end{itemize} \end{itemize} \end{frame} %------------------------------- \begin{frame} \frametitle{Linking data} - % + The following linking process was used: \begin{enumerate} \item AACT trials to snapshots (internal ID) @@ -627,7 +635,7 @@ Washington State University \\ % Your institution for the title page Note the implicit conditioning on trials treating diseases with IHME data\footnote{ IHME does not track data for W61.62XD: Struck by duck, subsequent encounter - }. + } or easily matched to codes and categories. \end{frame} %------------------------------- @@ -712,17 +720,26 @@ Washington State University \\ % Your institution for the title page \item Allows for transfer of probability between groups \end{itemize} \end{itemize} + + \begin{align} + y_i &\sim \text{Bernoulli}(p_i) \\ + p_i &= \text{logistic}(X_i \vec\beta_{c(i)}) \\ + \vec\beta_{c(i)} &\sim \text{MvNormal}(\vec\mu,\vec\sigma I)\\ + \mu_c &\sim \text{Normal}(0, 0.05) \\ + \sigma_c &\sim \text{Gamma}(4,20) + \end{align} + Gamma is using the shape and rate parameterization \end{frame} %------------------------------- \begin{frame} \frametitle{Total Effects Model} - \begin{align} - y_i &\sim \text{Bernoulli}(p_i) \\ - p_i &= \text{logistic}(X_i \vec\beta_{c(i)}) \\ - \vec\beta_{c(i)} &\sim \text{MvNormal}(\vec\mu,\vec\sigma I) - \end{align} + %TODO: describe X\beta +\end{frame} +%------------------------------- +\begin{frame} + \frametitle{Direct Effects Model} %TODO: describe X\beta \end{frame} @@ -748,6 +765,33 @@ Washington State University \\ % Your institution for the title page %%%%%%%%%%%%%%%%%%%% Results \subsection{Results} %-------------------------------- +%------------------------------- +\begin{frame} + \frametitle{Priors - Mu} + \begin{figure} +% \includegraphics[height=0.8\textheight]{../assets/img/Images/} + \label{FIG:Prior:Mu} + \caption{Prior - Mu} + \end{figure} +\end{frame} +%------------------------------- +\begin{frame} + \frametitle{Priors - Sigma} + \begin{figure} +% \includegraphics[height=0.8\textheight]{../assets/img/Images/} + \label{FIG:Prior:Sigma} + \caption{Prior - Sigma} + \end{figure} +\end{frame} +%------------------------------- +\begin{frame} + \frametitle{Priors - $p$} + \begin{figure} +% \includegraphics[height=0.8\textheight]{../assets/img/Images/} + \label{FIG:Prior:p} + \caption{Prior - $p$} + \end{figure} +\end{frame} %-------------------------------- \subsubsection{Total Effect} % - Review Parameter Values @@ -781,35 +825,35 @@ Washington State University \\ % Your institution for the title page \frametitle{Questions?} \end{frame} -%%------------------------------- -%%-------------------------------- -%%\subsubsection{Direct Effects} -%%% - Review Parameter Values -%%% - hyperparameters -%%% - Table of MLE -%%% - Distributions -%%% - betas -%%% - Table of MLE -%%% - Distributions -%%% - Review Posterior Prediction for interventions -%%%-------------------------------- -%%%------------------------------- -%%\begin{frame} -%% \frametitle{Convergence} -%% Sampling details -%% %TODO: UPDATE -%% \begin{itemize} -%% \item 6 chains -%% \item 2,500 warm-up, 2,500 sampling runs -%% \item seed = 11021585 -%% \end{itemize} -%%\end{frame} -%%%------------------------------- -%%\begin{frame} -%% \frametitle{Questions?} -%% -%%\end{frame} -%%------------------------------- +%------------------------------- +%-------------------------------- +\subsubsection{Direct Effects} +% - Review Parameter Values +% - hyperparameters +% - Table of MLE +% - Distributions +% - betas +% - Table of MLE +% - Distributions +% - Review Posterior Prediction for interventions +%-------------------------------- +%------------------------------- +\begin{frame} + \frametitle{Convergence} + Sampling details + %TODO: UPDATE + \begin{itemize} + \item 6 chains + \item 2,500 warm-up, 2,500 sampling runs + \item seed = 11021585 + \end{itemize} +\end{frame} +%------------------------------- +\begin{frame} + \frametitle{Questions?} + +\end{frame} +%------------------------------- %------------------------------------------------------------------------------------- %%%%%%%%%%%%%%%%%%%% Conclusion %%%%%%%%%%%%%%%%%%%%%%%% \section{Conclusion} diff --git a/Latex/assets/tikzit/CausalGraph_joint.tikz b/Latex/assets/tikzit/CausalGraph_joint.tikz new file mode 100644 index 0000000..29ab787 --- /dev/null +++ b/Latex/assets/tikzit/CausalGraph_joint.tikz @@ -0,0 +1,37 @@ +\begin{tikzpicture} + \begin{pgfonlayer}{nodelayer} + \node [style=Red Box] (0) at (4, -1.5) {Will Terminate?}; + \node [style=Red Box] (1) at (-4.25, -1.5) {Market Measures}; + \node [style=emptyBox] (4) at (-6, -7.5) {Unobserved}; + \node [style=Red Box] (5) at (2.5, 2) {Enrollment Status - Elapsed Duration}; + \node [style=Red Box] (8) at (-5.75, -6) {Relationships of interest}; + \node [style=emptyBox] (9) at (12.25, 6.25) {Fundamental Efficacy/Safety}; + \node [style=emptyBox] (10) at (-0.25, 8) {Previously Observed Efficacy/Safety}; + \node [style=emptyBox] (12) at (14, 0.25) {Currently Observed Efficacy/Safety}; + \node [style=Gray Box] (13) at (7, -6) {Observed}; + \node [style=Gray Box] (18) at (-6.5, 1.5) {Population}; + \node [style=Gray Box] (20) at (-0.25, 5) {Decision to procced with Phase III}; + \node [style=Gray Box] (21) at (0, -3.5) {Condition}; + \end{pgfonlayer} + \begin{pgfonlayer}{edgelayer} + \draw [style=RightArrow] (18) to (5); + \draw [style=RightArrow] (18) to (1); + \draw [style=RightArrow] (9) to (10); + \draw [style=RightArrow] (10) to (20); + \draw [style=RightArrow] (9) to (12); + \draw [style=RightArrow] (12) to (0); + \draw [style=Light Arrow] (21) to (1); + \draw [style=Light Arrow] (21) to (0); + \draw [style=Light Arrow, in=-120, out=165, looseness=2.00] (21) to (18); + \draw [style=Light Arrow, in=180, out=180, looseness=2.75] (21) to (20); + \draw [style=Light Arrow, bend right=60, looseness=1.75] (21) to (9); + \draw [style=Light Arrow] (21) to (5); + \draw [style=RightArrow, in=-180, out=165, looseness=2.00] (1) to (20); + \draw [style=RightArrow] (20) to (5); + \draw [style=RightArrow, bend left] (20) to (0); + \draw [style=PurpleArrow] (1) to (0); + \draw [style=PurpleArrow] (1) to (5); + \draw [style=PurpleArrow] (5) to (0); + \draw [style=PurpleArrow, in=135, out=45, loop] (8) to (); + \end{pgfonlayer} +\end{tikzpicture}