From d5dc986d580c7e75c6459e00f800661994de1059 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Mon, 16 Nov 2020 17:42:26 +0100 Subject: [PATCH 1/5] Fix multiple definitions of the label sec:tools --- Manuscript/QUEST_WIREs.tex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 1db57c5..4a8d338 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -745,7 +745,7 @@ The project containing two parts \subsubsection{Website} %------------------------------------------------ This is the main part of the project. All the calculation are made locally on the dataset page. -Firstly the website proposes to the user to import new data \ref{sec:tools}. +Firstly the website proposes to the user to import new data \ref{sec:gentools}. these data are added to the current session (and removed after lost the page). There are four multi selection list. Each list depends on the previous ones. These lists allow to select information about the selected sets \ref{fig:scheme}. @@ -779,7 +779,7 @@ On the website the statistics are forwarded in a table and in a box plot graph. %------------------------------------------------ \subsubsection{Data generation tools} -\label{sec:tools} +\label{sec:genTools} %------------------------------------------------ There are currently two main tools to generate data \texttt{datafileBuilder} and \texttt{ADC25generator} \paragraph{datafileBuilder} From 2893edc82c2f35396df352255a2e0b3bb5b7cc4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Wed, 18 Nov 2020 09:28:41 +0100 Subject: [PATCH 2/5] Add scenar and intro to tools --- .gitignore | 1 + Manuscript/QUEST_WIREs.tex | 26 +++++++++++++++++++++++++- 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index b014bce..9ab9f30 100644 --- a/.gitignore +++ b/.gitignore @@ -22,6 +22,7 @@ *latexmk *.run.xml *-blx.bib +*.thm # pdf output QUEST_WIREs.pdf diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 2544013..f679919 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -15,7 +15,7 @@ % \documentclass[blind,alpha-refs]{wiley-article} % Add additional packages here if required -\usepackage{graphicx,dcolumn,bm,xcolor,microtype,multirow,amscd,amsmath,amssymb,amsfonts,physics,longtable,mhchem,siunitx,rotating} +\usepackage{graphicx,dcolumn,bm,xcolor,microtype,multirow,amscd,amsmath,amssymb,amsfonts,physics,longtable,mhchem,siunitx,rotating,ntheorem} \usepackage[ colorlinks=true, @@ -736,6 +736,28 @@ The website specification are the following \item Display a box plot graph to easily show the methods accuracy \end{itemize} This solve the issues described at \ref{sec:websiteIntro} +%======================= +\subsection{Usage} +%======================= +We built the website to meet mainly two useage. +\theoremstyle{break} +\theorembodyfont{\normalfont} +\newtheorem{scenar}{Scenario}{} +\begin{scenar} + \label{scenar:choose} + The user wants to choose a method for his calculation or a series of calculations. + In this case he wants to compare the accuracy of each method with a subset of excitations data corresponding to his target. + He can optimise the filter to correspond to his target (Molecular size, molecule or excitation type). + If it's possible he can only select the target molecule when this molecule is available in the QUEST data. +\end{scenar} +\begin{scenar} + \label{scenar:new} + The user has created a new method and want to compare it with the methods of the QUEST project. + Fistly the user must create an input file for the Python tools \ref{sec:gentools} by formating the calculated results as a {\LaTeX} \texttt{tabular}. + After the data generation using the same python tools we are used to import the QUEST data, the user must to import the new absorption and the fluorescence data files using the button on the website. + So the new data are used in the same way than the references data to generate statistics and he can use the website to compute the statistics to compare the methods. +\end{scenar} + %======================= \subsection{Project} %======================= @@ -781,6 +803,8 @@ On the website the statistics are forwarded in a table and in a box plot graph. \subsubsection{Data generation tools} \label{sec:gentools} %------------------------------------------------ +There are multiple that we used to generate the data. +These tools can also be used by the user (see scenario \ref{scenar:new}) There are currently two main tools to generate data \texttt{datafileBuilder} and \texttt{ADC25generator} \paragraph{datafileBuilder} The \texttt{datafileBuilder} tool is used to build datafile from {\LaTeX} \texttt{tabular}. From 796f197e7f0d5be9bbd2f160a3feaf0b2131aaec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Wed, 18 Nov 2020 11:33:23 +0100 Subject: [PATCH 3/5] Use lowercase e for error vector --- Manuscript/QUEST_WIREs.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index f679919..1786992 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -713,7 +713,7 @@ MAE & & 0.22 & 0.16 & 0.22 & 0.11 & 0.12 & 0.05 & 0.04 & 0.02 & 0.20 & 0.22 { \newcommand{\meth}{\text{meth}} -\newcommand{\err}{\mathcal{E}} +\newcommand{\err}{e} \newcommand{\nEx}{X} \newcommand{\nExnn}{\mathcal{X}} %======================= From d0f860572ab55541334dbe05cce21b0663e3dd1e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Thu, 19 Nov 2020 14:40:15 +0100 Subject: [PATCH 4/5] Some fixes and improvement of the website part --- Manuscript/QUEST_WIREs.tex | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 1786992..994c2b8 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -746,16 +746,17 @@ We built the website to meet mainly two useage. \begin{scenar} \label{scenar:choose} The user wants to choose a method for his calculation or a series of calculations. + Of course he search a compromise between the accuracy and the cost of the method. In this case he wants to compare the accuracy of each method with a subset of excitations data corresponding to his target. He can optimise the filter to correspond to his target (Molecular size, molecule or excitation type). - If it's possible he can only select the target molecule when this molecule is available in the QUEST data. + If it is possible he can only select the target molecule when this molecule is available in the QUEST data. \end{scenar} \begin{scenar} \label{scenar:new} - The user has created a new method and want to compare it with the methods of the QUEST project. - Fistly the user must create an input file for the Python tools \ref{sec:gentools} by formating the calculated results as a {\LaTeX} \texttt{tabular}. - After the data generation using the same python tools we are used to import the QUEST data, the user must to import the new absorption and the fluorescence data files using the button on the website. - So the new data are used in the same way than the references data to generate statistics and he can use the website to compute the statistics to compare the methods. + The user has created a new method and wants to compare its accuracy with the methods of the QUEST project. + Fistly he has to create an input file for the Python tools (see Sec.~\ref{sec:gentools}) by formating the calculated results as a {\LaTeX} \texttt{tabular}. + After the data generation using the same python tools we are used to import the QUEST data, he must to import the new absorption and the fluorescence data files using the button on the website. + So the new data are used in the same way than the references data to generate statistics and he can use the website to compute the statistics in order to compare the methods. \end{scenar} %======================= @@ -767,11 +768,11 @@ The project containing two parts \subsubsection{Website} %------------------------------------------------ This is the main part of the project. All the calculation are made locally on the dataset page. -Firstly the website proposes to the user to import new data \ref{sec:gentools}. +Firstly the website proposes to the user to import new data (see Sec.~\ref{sec:gentools}). these data are added to the current session (and removed after lost the page). There are four multi selection list. Each list depends on the previous ones. These lists allow to select information about the selected sets \ref{fig:scheme}. -Molecules \ref{fig:molecules} methods and basis \ref{sec:methods}. +Molecules \ref{fig:molecules} methods and basis (see Sec.~\ref{sec:methods}). After there are many filters to choose the properties of included excitations. We provide also the ability to filter by molecule size or the active character percentage. After that we need to define a reference method to compare with (TBE by default). @@ -793,10 +794,13 @@ So with $\nExnn$ the size of the vector $\vec{\err^x_\meth}$ \begin{gather} MSE_\meth = \overline{{\vec{\err_\meth}}} = \frac{1}{\nExnn}\sum_{x=1}^\nExnn\err_\meth^x \\ MAE_\meth = \overline{\abs{\vec{\err_\meth}}} \\ - RMSE_\meth = \sqrt{\overline{\vec{\err_\meth}^2}} \\ - SDE_\meth = \sqrt{\frac{1}{\nExnn}\sum_{x=1}^\nExnn\err_x^2-MAE^2} \end{gather} -These statistics allow user to determine the accuracy of each couple methods/basis. +These statistics data inform about the accuracy of the methods compared to the reference. +\begin{gather} + RMSE_\meth = \sqrt{\overline{\vec{\err_\meth}^2}} \\ + SDE_\meth = \sqrt{\frac{1}{\nExnn}\sum_{x=1}^\nExnn(\err_x-MAE)^2} +\end{gather} +These statistics data inform about the precision of the methods compared to the reference. On the website the statistics are forwarded in a table and in a box plot graph. %------------------------------------------------ From 50e1d0025e35640659f84e9e94114ff7138d48bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Thu, 19 Nov 2020 15:04:04 +0100 Subject: [PATCH 5/5] Fix RMSE indicate the accuracy not the precision --- Manuscript/QUEST_WIREs.tex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 994c2b8..6eef08f 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -794,13 +794,13 @@ So with $\nExnn$ the size of the vector $\vec{\err^x_\meth}$ \begin{gather} MSE_\meth = \overline{{\vec{\err_\meth}}} = \frac{1}{\nExnn}\sum_{x=1}^\nExnn\err_\meth^x \\ MAE_\meth = \overline{\abs{\vec{\err_\meth}}} \\ + RMSE_\meth = \sqrt{\overline{\vec{\err_\meth}^2}} \\ \end{gather} These statistics data inform about the accuracy of the methods compared to the reference. \begin{gather} - RMSE_\meth = \sqrt{\overline{\vec{\err_\meth}^2}} \\ SDE_\meth = \sqrt{\frac{1}{\nExnn}\sum_{x=1}^\nExnn(\err_x-MAE)^2} \end{gather} -These statistics data inform about the precision of the methods compared to the reference. +This statistics data inform about the precision of the methods compared to the reference. On the website the statistics are forwarded in a table and in a box plot graph. %------------------------------------------------