scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex

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+% Nature Journal Article Template
+% For submission to Nature family journals
+% Last updated: 2024
+
+\documentclass[12pt]{article}
+
+% Packages
+\usepackage[margin=2.5cm]{geometry}
+\usepackage{times}
+\usepackage{graphicx}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{hyperref}
+\usepackage{lineno}  % Line numbers for review
+\usepackage[super]{natbib}  % Superscript citations
+
+% Line numbering (required for submission)
+\linenumbers
+
+% Title and Authors
+\title{Insert Your Title Here: Concise and Descriptive}
+
+\author{
+First Author\textsuperscript{1}, Second Author\textsuperscript{1,2}, Third Author\textsuperscript{2,*}
+}
+
+\date{}
+
+\begin{document}
+
+\maketitle
+
+% Affiliations
+\noindent
+\textsuperscript{1}Department Name, Institution Name, City, State/Province, Postal Code, Country \\
+\textsuperscript{2}Second Department/Institution \\
+\textsuperscript{*}Correspondence: [email protected]
+
+% Abstract
+\begin{abstract}
+\noindent
+Write a concise abstract of 150-200 words summarizing the main findings, significance, and conclusions of your work. The abstract should be self-contained and understandable without reading the full paper. Focus on what you did, what you found, and why it matters. Avoid jargon and abbreviations where possible.
+\end{abstract}
+
+% Main Text
+\section*{Introduction}
+% 2-3 paragraphs setting the context
+Provide background on the research area, establish the importance of the problem, and identify the knowledge gap your work addresses. Nature papers should emphasize broad significance beyond a narrow specialty.
+
+State your main research question or objective clearly.
+
+Briefly preview your approach and key findings.
+
+\section*{Results}
+% Primary results section
+% Organize by finding, not by experiment
+% Reference figures/tables as you describe results
+
+\subsection*{First major finding}
+Describe your first key result. Reference Figure~\ref{fig:example} to support your findings.
+
+\begin{figure}[ht]
+\centering
+% Include your figure here
+% \includegraphics[width=0.7\textwidth]{figure1.pdf}
+\caption{{\bf Figure title in bold.} Detailed figure caption explaining what is shown, experimental conditions, sample sizes (n), statistical tests, and significance levels. Panels should be labeled (a), (b), etc. if multiple panels are present.}
+\label{fig:example}
+\end{figure}
+
+\subsection*{Second major finding}
+Describe your second key result objectively, without interpretation.
+
+\subsection*{Third major finding}
+Describe additional results as needed.
+
+\section*{Discussion}
+% Interpret results, compare to literature, acknowledge limitations
+
+\subsection*{Main findings and interpretation}
+Summarize your key findings and explain their significance. How do they advance our understanding?
+
+\subsection*{Comparison to previous work}
+Compare and contrast your results with existing literature\cite{example2023}.
+
+\subsection*{Implications}
+Discuss the broader implications of your work for the field and beyond.
+
+\subsection*{Limitations and future directions}
+Honestly acknowledge limitations and suggest future research directions.
+
+\section*{Conclusions}
+Provide a concise conclusion summarizing the main take-home messages of your work.
+
+\section*{Methods}
+% Detailed methods allowing reproducibility
+% Can be placed after main text in Nature
+
+\subsection*{Experimental design}
+Describe overall experimental design, including controls.
+
+\subsection*{Sample preparation}
+Detail procedures for sample collection, preparation, and handling.
+
+\subsection*{Data collection}
+Describe instrumentation, measurement procedures, and data collection protocols.
+
+\subsection*{Data analysis}
+Explain analytical methods, statistical tests, and software used. State sample sizes, replication, and significance thresholds.
+
+\subsection*{Ethical approval}
+Include relevant ethical approval statements (human subjects, animal use, biosafety).
+
+\section*{Data availability}
+State where data supporting the findings can be accessed (repository, supplementary files, available on request).
+
+\section*{Code availability}
+If applicable, provide information on code availability (GitHub, Zenodo, etc.).
+
+\section*{Acknowledgements}
+Acknowledge funding sources, technical assistance, and other contributions. List grant numbers.
+
+\section*{Author contributions}
+Describe contributions of each author using CRediT taxonomy or similar (conceptualization, methodology, investigation, writing, etc.).
+
+\section*{Competing interests}
+Declare any financial or non-financial competing interests. If none, state "The authors declare no competing interests."
+
+% References
+\bibliographystyle{naturemag}  % Nature bibliography style
+\bibliography{references}  % Your .bib file
+
+% Alternatively, manually format references:
+\begin{thebibliography}{99}
+
+\bibitem{example2023}
+Smith, J. D., Jones, M. L. \& Williams, K. R. Groundbreaking discovery in the field. \textit{Nature} \textbf{600}, 123--130 (2023).
+
+\bibitem{author2022}
+Author, A. A. \& Coauthor, B. B. Another important paper. \textit{Nat. Methods} \textbf{19}, 456--
+
+460 (2022).
+
+% Add more references as needed
+
+\end{thebibliography}
+
+% Figure Legends (if not included with figures)
+\section*{Figure Legends}
+
+\textbf{Figure 1 | Figure title.} Comprehensive figure legend describing all panels, experimental conditions, sample sizes, and statistical analyses.
+
+\textbf{Figure 2 | Second figure title.} Another detailed legend.
+
+% Extended Data Figures (optional - supplementary figures)
+\section*{Extended Data}
+
+\textbf{Extended Data Figure 1 | Supplementary data title.} Description of supplementary figure supporting main findings.
+
+\end{document}
+
+% Notes for Authors:
+% 1. Nature articles are typically ~3,000 words excluding Methods, References, Figure Legends
+% 2. Use superscript numbered citations (1, 2, 3)
+% 3. Figures should be high resolution (300+ dpi for photos, 1000 dpi for line art)
+% 4. Submit figures as separate files (TIFF, EPS, or PDF)
+% 5. Double-space the manuscript for review
+% 6. Include line numbers using \linenumbers
+% 7. Follow Nature's specific author guidelines for your target journal
+% 8. Methods section can be quite detailed and placed after main text
+% 9. Check word limits and specific requirements for your Nature family journal
+

scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex

@@ -0,0 +1,283 @@
+% NeurIPS Conference Paper Template
+% For submission to Neural Information Processing Systems (NeurIPS)
+% Last updated: 2024
+% Note: Use the official neurips_2024.sty file from the conference website
+
+\documentclass{article}
+
+% Required packages (neurips_2024.sty provides most formatting)
+\usepackage{neurips_2024}  % Official NeurIPS style file (download from conference site)
+
+% Recommended packages
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{amsthm}
+\usepackage{graphicx}
+\usepackage{algorithm}
+\usepackage{algorithmic}
+\usepackage{hyperref}
+\usepackage{url}
+\usepackage{booktabs}  % For better tables
+\usepackage{multirow}
+\usepackage{microtype}  % Improved typography
+
+% Theorems, lemmas, etc.
+\newtheorem{theorem}{Theorem}
+\newtheorem{lemma}{Lemma}
+\newtheorem{proposition}{Proposition}
+\newtheorem{corollary}{Corollary}
+\newtheorem{definition}{Definition}
+
+% Title and Authors
+\title{Your Paper Title: Concise and Descriptive \\ (Maximum Two Lines)}
+
+% Authors - ANONYMIZED for initial submission
+% For initial submission (double-blind review):
+\author{
+  Anonymous Authors \\
+  Anonymous Institution(s) \\
+}
+
+% For camera-ready version (after acceptance):
+% \author{
+%   First Author \\
+%   Department of Computer Science \\
+%   University Name \\
+%   City, State, Postal Code \\
+%   \texttt{first.author@university.edu} \\
+%   \And
+%   Second Author \\
+%   Company/Institution Name \\
+%   Address \\
+%   \texttt{second.author@company.com} \\
+%   \And
+%   Third Author \\
+%   Institution \\
+%   \texttt{third.author@institution.edu}
+% }
+
+\begin{document}
+
+\maketitle
+
+\begin{abstract}
+Write a concise abstract (150-250 words) summarizing your contributions. The abstract should clearly state: (1) the problem you address, (2) your approach/method, (3) key results/findings, and (4) significance/implications. Make it accessible to a broad machine learning audience.
+\end{abstract}
+
+\section{Introduction}
+\label{sec:introduction}
+
+Introduce the problem you're addressing and its significance in machine learning or AI. Motivate why this problem is important and challenging.
+
+\subsection{Background and Motivation}
+Provide necessary background for understanding your work. Explain the gap in current methods or knowledge.
+
+\subsection{Contributions}
+Clearly state your main contributions as a bulleted list:
+\begin{itemize}
+    \item First contribution: e.g., "We propose a novel architecture for..."
+    \item Second contribution: e.g., "We provide theoretical analysis showing..."
+    \item Third contribution: e.g., "We demonstrate state-of-the-art performance on..."
+\end{itemize}
+
+\subsection{Paper Organization}
+Briefly describe the structure of the remainder of the paper.
+
+\section{Related Work}
+\label{sec:related}
+
+Discuss relevant prior work and how your work differs. Organize by themes or approaches rather than chronologically. Be fair and accurate in describing others' work.
+
+Cite key papers \cite{lecun2015deep, vaswani2017attention, devlin2019bert} and explain how your work builds upon or differs from them.
+
+\section{Problem Formulation}
+\label{sec:problem}
+
+Formally define the problem you're solving. Include mathematical notation and definitions.
+
+\subsection{Notation}
+Define your notation clearly. For example:
+\begin{itemize}
+    \item $\mathcal{X}$: input space
+    \item $\mathcal{Y}$: output space
+    \item $f: \mathcal{X} \rightarrow \mathcal{Y}$: function to learn
+    \item $\mathcal{D} = \{(x_i, y_i)\}_{i=1}^n$: training dataset
+\end{itemize}
+
+\subsection{Objective}
+State your learning objective formally, e.g.:
+\begin{equation}
+\min_{\theta} \mathbb{E}_{(x,y) \sim \mathcal{D}} \left[ \mathcal{L}(f_\theta(x), y) \right]
+\end{equation}
+where $\mathcal{L}$ is the loss function and $\theta$ are model parameters.
+
+\section{Method}
+\label{sec:method}
+
+Describe your proposed method in detail. This is the core technical contribution of your paper.
+
+\subsection{Model Architecture}
+Describe the architecture of your model with sufficient detail for reproduction. Include figures if helpful.
+
+\begin{figure}[t]
+\centering
+% \includegraphics[width=0.8\textwidth]{architecture.pdf}
+\caption{Model architecture diagram. Describe the key components and data flow. Use colorblind-safe colors.}
+\label{fig:architecture}
+\end{figure}
+
+\subsection{Training Procedure}
+Explain how you train the model, including:
+\begin{algorithm}[t]
+\caption{Training Algorithm}
+\label{alg:training}
+\begin{algorithmic}[1]
+\STATE \textbf{Input:} Training data $\mathcal{D}$, learning rate $\alpha$
+\STATE \textbf{Output:} Trained parameters $\theta$
+\STATE Initialize $\theta$ randomly
+\FOR{epoch $= 1$ to $T$}
+    \FOR{batch $(x, y)$ in $\mathcal{D}$}
+        \STATE Compute loss: $\mathcal{L} = \mathcal{L}(f_\theta(x), y)$
+        \STATE Update: $\theta \leftarrow \theta - \alpha \nabla_\theta \mathcal{L}$
+    \ENDFOR
+\ENDFOR
+\RETURN $\theta$
+\end{algorithmic}
+\end{algorithm}
+
+\subsection{Key Components}
+Describe key technical innovations or components in detail.
+
+\section{Theoretical Analysis}
+\label{sec:theory}
+
+If applicable, provide theoretical analysis of your method.
+
+\begin{theorem}
+\label{thm:main}
+State your main theoretical result here.
+\end{theorem}
+
+\begin{proof}
+Provide proof or sketch of proof. Full proofs can go in the appendix.
+\end{proof}
+
+\section{Experiments}
+\label{sec:experiments}
+
+Describe your experimental setup and results.
+
+\subsection{Experimental Setup}
+\textbf{Datasets:} Describe datasets used (e.g., ImageNet, CIFAR-10, etc.).
+
+\textbf{Baselines:} List baseline methods for comparison.
+
+\textbf{Implementation Details:} Provide implementation details including hyperparameters, hardware, training time.
+
+\textbf{Evaluation Metrics:} Define metrics used (accuracy, F1, AUC, etc.).
+
+\subsection{Main Results}
+Present your main experimental results.
+
+\begin{table}[t]
+\centering
+\caption{Performance comparison on benchmark datasets. Bold indicates best performance. Results reported as mean ± std over 3 runs.}
+\label{tab:main_results}
+\begin{tabular}{lcccc}
+\toprule
+Method & Dataset 1 & Dataset 2 & Dataset 3 & Average \\
+\midrule
+Baseline 1 & 85.3 ± 0.5 & 72.1 ± 0.8 & 90.2 ± 0.3 & 82.5 \\
+Baseline 2 & 87.2 ± 0.4 & 74.5 ± 0.6 & 91.1 ± 0.5 & 84.3 \\
+\textbf{Our Method} & \textbf{91.7 ± 0.3} & \textbf{79.8 ± 0.5} & \textbf{94.3 ± 0.2} & \textbf{88.6} \\
+\bottomrule
+\end{tabular}
+\end{table}
+
+\subsection{Ablation Studies}
+Conduct ablation studies to understand which components contribute to performance.
+
+\subsection{Analysis}
+Provide deeper analysis of results, failure cases, limitations, etc.
+
+\section{Discussion}
+\label{sec:discussion}
+
+Discuss your findings, limitations, and broader implications.
+
+\subsection{Limitations}
+Honestly acknowledge limitations of your work.
+
+\subsection{Broader Impacts}
+Discuss potential positive and negative societal impacts (required by NeurIPS).
+
+\section{Conclusion}
+\label{sec:conclusion}
+
+Summarize your main contributions and findings. Suggest future research directions.
+
+% Acknowledgments (add after acceptance, not in submission version)
+\section*{Acknowledgments}
+Thank collaborators, funding sources (with grant numbers), and compute resources. Not included in double-blind submission.
+
+% References
+\bibliographystyle{plainnat}  % or other NeurIPS-compatible style
+\bibliography{references}  % Your .bib file
+
+% Appendix (optional, unlimited pages)
+\appendix
+
+\section{Additional Proofs}
+\label{app:proofs}
+
+Provide full proofs of theorems here.
+
+\section{Additional Experimental Results}
+\label{app:experiments}
+
+Include additional experiments, more ablations, qualitative results, etc.
+
+\section{Hyperparameters}
+\label{app:hyperparameters}
+
+List all hyperparameters used in experiments for reproducibility.
+
+\begin{table}[h]
+\centering
+\caption{Hyperparameters used in all experiments}
+\begin{tabular}{ll}
+\toprule
+Hyperparameter & Value \\
+\midrule
+Learning rate & 0.001 \\
+Batch size & 64 \\
+Optimizer & Adam \\
+Weight decay & 0.0001 \\
+Epochs & 100 \\
+\bottomrule
+\end{tabular}
+\end{table}
+
+\section{Code and Data}
+\label{app:code}
+
+Provide links to code repository (anonymized for review, e.g., anonymous GitHub):
+\begin{itemize}
+    \item Code: \url{https://anonymous.4open.science/r/project-XXXX}
+    \item Data: Available upon request / at [repository]
+\end{itemize}
+
+\end{document}
+
+% Notes for Authors:
+% 1. Main paper: 8 pages maximum (excluding references and appendix)
+% 2. References: unlimited pages
+% 3. Appendix: unlimited pages (reviewed at discretion of reviewers)
+% 4. Use double-blind anonymization for initial submission
+% 5. Include broader impact statement
+% 6. Code submission strongly encouraged (anonymous for review)
+% 7. Use official neurips_2024.sty file (download from NeurIPS website)
+% 8. Font: Times, 10pt (enforced by style file)
+% 9. Figures should be colorblind-friendly
+% 10. Ensure reproducibility: report seeds, hyperparameters, dataset splits
+