Cross-References & Citations¶

Topic: LaTeX Lesson: 8 of 16 Prerequisites: Floats and Figures, Tables, Math Typesetting Objective: Master cross-referencing sections, equations, figures, and tables; learn bibliography management with BibTeX and BibLaTeX; create hyperlinks, indexes, and glossaries for professional academic documents.

Introduction¶

Professional documents require extensive cross-referencing: citing figures, tables, equations, sections, and external sources. LaTeX provides a robust system for managing these references automatically, ensuring consistency even when you add, remove, or reorder content. This lesson covers LaTeX's cross-referencing system, bibliography management, and advanced features like hyperlinks, indexes, and glossaries.

Labels and References¶

The Basic System¶

Two commands work together: - \label{key} - marks a location - \ref{key} - inserts the number of the labeled item

Labeling Sections¶

\section{Introduction}
\label{sec:intro}

This is the introduction.

\section{Methods}
\label{sec:methods}

As discussed in Section~\ref{sec:intro}, we propose...

Output: "As discussed in Section 1, we propose..."

Labeling Equations¶

\begin{equation}
  E = mc^2
  \label{eq:einstein}
\end{equation}

Equation~\ref{eq:einstein} shows the mass-energy equivalence.

Important: Place \label inside the equation environment.

Labeling Figures¶

\begin{figure}[htbp]
  \centering
  \includegraphics[width=0.6\textwidth]{plot}
  \caption{Experimental results}
  \label{fig:results}
\end{figure}

Figure~\ref{fig:results} shows the data.

Critical: Place \label after \caption, otherwise the reference will be incorrect.

Labeling Tables¶

\begin{table}[htbp]
  \centering
  \caption{Performance metrics}
  \label{tab:performance}
  \begin{tabular}{lcc}
    \toprule
    Model & Accuracy & Speed \\
    \midrule
    A & 95\% & 12 ms \\
    \bottomrule
  \end{tabular}
\end{table}

Table~\ref{tab:performance} compares the models.

Page References¶

Use \pageref{} to get the page number:

See Figure~\ref{fig:results} on page~\pageref{fig:results}.

Label Naming Conventions¶

Use prefixes to identify reference types:

sec: - sections, subsections, chapters
fig: - figures
tab: - tables
eq: - equations
lst: - code listings
alg: - algorithms
thm: - theorems
lem: - lemmas
def: - definitions

Examples:

\label{sec:introduction}
\label{fig:network_architecture}
\label{tab:results_mnist}
\label{eq:gradient_descent}
\label{thm:convergence}

Why References Matter¶

Bad:

The results are shown in the figure below.

Problem: If you move the figure, "below" becomes wrong.

Good:

The results are shown in Figure~\ref{fig:results}.

This works regardless of where the figure appears.

Smart References with hyperref¶

The hyperref package makes references clickable and adds semantic information:

\usepackage{hyperref}

Basic Features¶

Clickable links: PDF readers can click references to jump to targets
Colored/boxed links: Visual indication of links
Document metadata: PDF title, author, keywords
Automatic "Figure", "Section": With \autoref{}

Configuration¶

\usepackage[
  colorlinks=true,
  linkcolor=blue,
  citecolor=green,
  urlcolor=red,
  bookmarks=true,
  pdfauthor={Your Name},
  pdftitle={Document Title}
]{hyperref}

Options: - colorlinks=true: Colored text instead of boxes - colorlinks=false: Boxes around links - linkcolor: Color for internal links - citecolor: Color for citations - urlcolor: Color for URLs - bookmarks: PDF bookmarks panel

autoref: Automatic Type Detection¶

\autoref{sec:intro}     % → "Section 1"
\autoref{fig:results}   % → "Figure 2"
\autoref{tab:data}      % → "Table 3"
\autoref{eq:einstein}   % → "Equation 4"

No need to type "Figure~\ref{...}", just use \autoref{...}.

nameref: Reference by Name¶

Get the title/caption instead of number:

\section{Introduction}
\label{sec:intro}

% Later:
As discussed in "\nameref{sec:intro}", we...

Output: 'As discussed in "Introduction", we...'

Customizing autoref Names¶

\renewcommand{\figureautorefname}{Fig.}
\renewcommand{\tableautorefname}{Tab.}
\renewcommand{\sectionautorefname}{Sec.}

Now \autoref{fig:test} produces "Fig. 1" instead of "Figure 1".

The cleveref Package¶

Even smarter than hyperref:

\usepackage{cleveref}

Load after hyperref:

\usepackage{hyperref}
\usepackage{cleveref}

Basic Usage¶

\cref{fig:plot}         % → "figure 1"
\Cref{fig:plot}         % → "Figure 1" (capitalized)
\cref{eq:main}          % → "equation 2"
\Cref{eq:main}          % → "Equation 2"

Multiple References¶

\cref{fig:a,fig:b,fig:c}        % → "figures 1, 2, and 3"
\cref{eq:first,eq:second}       % → "equations 4 and 5"
\cref{sec:intro,sec:methods}    % → "sections 1 and 2"

Cleveref automatically handles ranges:

\cref{fig:a,fig:b,fig:c,fig:d}  % → "figures 1 to 4"

Cross-Type References¶

\cref{fig:plot,tab:results,eq:main}
% → "figure 1, table 2, and equation 3"

Customization¶

% Abbreviate
\crefname{figure}{fig.}{figs.}
\crefname{equation}{eq.}{eqs.}

% Capitalized versions
\Crefname{figure}{Figure}{Figures}
\Crefname{equation}{Equation}{Equations}

Example: Complete Document¶

\documentclass{article}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{hyperref}
\usepackage{cleveref}

\begin{document}

\section{Introduction}
\label{sec:intro}

We present a new method.

\section{Theory}
\label{sec:theory}

The governing equation is:
\begin{equation}
  \frac{\partial u}{\partial t} = \nabla^2 u
  \label{eq:heat}
\end{equation}

As shown in \cref{eq:heat}, heat diffuses over time.

\section{Results}

\Cref{fig:temp} shows the temperature distribution.

\begin{figure}[htbp]
  \centering
  \includegraphics[width=0.6\textwidth]{temperature}
  \caption{Temperature evolution over time}
  \label{fig:temp}
\end{figure}

Comparing \cref{sec:intro,sec:theory}, we see that...

\end{document}

Bibliography Management with BibTeX¶

The BibTeX Workflow¶

Create a .bib file with bibliographic entries
Cite references in your document with \cite{}
Specify bibliography style
Run: pdflatex → bibtex → pdflatex → pdflatex

Creating a .bib File¶

File: references.bib

@article{einstein1905,
  author  = {Einstein, Albert},
  title   = {On the Electrodynamics of Moving Bodies},
  journal = {Annalen der Physik},
  year    = {1905},
  volume  = {17},
  pages   = {891--921},
  doi     = {10.1002/andp.19053221004}
}

@book{knuth1984,
  author    = {Knuth, Donald E.},
  title     = {The {\TeX}book},
  publisher = {Addison-Wesley},
  year      = {1984},
  address   = {Reading, MA}
}

@inproceedings{lecun1998,
  author    = {LeCun, Yann and Bottou, L{\'e}on and Bengio, Yoshua and Haffner, Patrick},
  title     = {Gradient-based learning applied to document recognition},
  booktitle = {Proceedings of the IEEE},
  year      = {1998},
  volume    = {86},
  number    = {11},
  pages     = {2278--2324}
}

@misc{vaswani2017,
  author = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and others},
  title  = {Attention is All You Need},
  year   = {2017},
  eprint = {1706.03762},
  archivePrefix = {arXiv},
  primaryClass  = {cs.CL}
}

BibTeX Entry Types¶

Common types: - @article - journal articles - @book - books - @inproceedings - conference papers - @phdthesis - PhD dissertations - @mastersthesis - Master's theses - @techreport - technical reports - @misc - miscellaneous (arXiv, web pages, etc.) - @incollection - book chapters - @manual - manuals

Required Fields¶

@article: - author, title, journal, year

@book: - author/editor, title, publisher, year

@inproceedings: - author, title, booktitle, year

Optional Fields¶

volume, number, pages - volume/issue information
doi - Digital Object Identifier
url - web address
isbn - ISBN number
address - publisher location
month - publication month
note - additional information

Using Citations¶

In your LaTeX document:

\documentclass{article}

\begin{document}

Einstein's theory \cite{einstein1905} revolutionized physics.

The TeX typesetting system \cite{knuth1984} is still widely used.

Convolutional neural networks \cite{lecun1998} and transformers \cite{vaswani2017}
are foundational in deep learning.

\bibliographystyle{plain}
\bibliography{references}

\end{document}

Citation Styles¶

Specify with \bibliographystyle{}:

plain: - [1] A. Einstein. "On the Electrodynamics..." - Numeric, sorted alphabetically

unsrt: - [1] A. Einstein... - Numeric, sorted by citation order

alpha: - [Ein05] A. Einstein... - Alphabetic labels based on author/year

abbrv: - [1] A. Einstein. "On the Electrodyn..." - Abbreviated first names and months

apalike: - Einstein, 1905 - Author-year style

Citation Commands (natbib)¶

Load the natbib package for more citation options:

\usepackage{natbib}

Commands:

\cite{key}        % Standard: [1] or (Einstein, 1905)
\citet{key}       % Textual: Einstein (1905)
\citep{key}       % Parenthetical: (Einstein, 1905)
\citeauthor{key}  % Author only: Einstein
\citeyear{key}    % Year only: 1905

Multiple citations:

\citep{einstein1905,knuth1984}  % (Einstein, 1905; Knuth, 1984)

With notes:

\citep[see][p. 10]{einstein1905}  % (see Einstein, 1905, p. 10)

Compilation Process¶

pdflatex document.tex    # First pass
bibtex document          # Process bibliography
pdflatex document.tex    # Second pass (resolve citations)
pdflatex document.tex    # Third pass (resolve references)

Why multiple passes? 1. First pdflatex: Writes .aux file with \cite{} keys 2. bibtex: Reads .aux, generates .bbl bibliography 3. Second pdflatex: Includes bibliography, writes citation numbers 4. Third pdflatex: Resolves all cross-references

BibLaTeX + Biber (Modern Alternative)¶

BibLaTeX is a modern replacement for BibTeX with more features and better Unicode support.

Basic Setup¶

\usepackage[style=apa,backend=biber]{biblatex}
\addbibresource{references.bib}

\begin{document}

Text with citation \parencite{einstein1905}.

\printbibliography

\end{document}

Compilation¶

pdflatex document.tex
biber document          # Use biber instead of bibtex
pdflatex document.tex
pdflatex document.tex

Citation Styles¶

BibLaTeX has many built-in styles:

% Numeric
\usepackage[style=numeric]{biblatex}

% Alphabetic
\usepackage[style=alphabetic]{biblatex}

% Author-year
\usepackage[style=authoryear]{biblatex}

% APA (requires biblatex-apa package)
\usepackage[style=apa]{biblatex}

% IEEE
\usepackage[style=ieee]{biblatex}

% Nature
\usepackage[style=nature]{biblatex}

BibLaTeX Citation Commands¶

\cite{key}          % Basic citation
\parencite{key}     % Parenthetical (Author, Year)
\textcite{key}      % Textual: Author (Year)
\footcite{key}      % Footnote citation
\autocite{key}      % Automatic (adapts to style)
\citeauthor{key}    % Author only
\citeyear{key}      % Year only
\citetitle{key}     % Title only

Filtering Bibliography¶

Show only cited works:

\printbibliography[heading=bibintoc]

By type:

\printbibliography[type=book,title={Books only}]
\printbibliography[type=article,title={Journal articles}]

By keyword:

\printbibliography[keyword=machine-learning,title={ML papers}]

BibLaTeX Advantages¶

Unicode support: Non-ASCII characters work better
Customization: Easier to modify styles
Features: More entry types, fields, and citation commands
Localization: Better support for non-English languages
Sorting: More flexible sorting options

Bibliography Management Tools¶

JabRef¶

Open-source, cross-platform
BibTeX/BibLaTeX editor
Search, organize, import citations
https://www.jabref.org/

Zotero¶

Free, open-source reference manager
Browser integration
Export to BibTeX
https://www.zotero.org/

Mendeley¶

Reference manager + PDF organizer
Elsevier-owned
Export to BibTeX
https://www.mendeley.com/

Google Scholar¶

Export citations directly: 1. Search for paper 2. Click "Cite" 3. Click "BibTeX" 4. Copy into .bib file

Hyperlinks¶

The hyperref package provides hyperlink commands:

URL Links¶

\url{https://www.latex-project.org/}

Output: https://www.latex-project.org/ (clickable)

Hyperlinked Text¶

\href{https://www.latex-project.org/}{LaTeX Project}

Output: LaTeX Project (clickable, hides URL)

Email Links¶

\href{mailto:user@example.com}{Email me}

Internal Links¶

% Jump to label
\hyperref[sec:intro]{Click here} to read the introduction.

% Jump to page
\hyperlink{page.5}{Go to page 5}

Configuration¶

\hypersetup{
  colorlinks=true,
  linkcolor=blue,
  urlcolor=cyan,
  citecolor=green,
  pdfauthor={Your Name},
  pdftitle={Document Title},
  pdfsubject={Subject},
  pdfkeywords={keyword1, keyword2}
}

Index¶

Create an alphabetical index of terms:

Setup¶

\usepackage{makeidx}
\makeindex

\begin{document}
% content
\printindex
\end{document}

Marking Index Entries¶

LaTeX\index{LaTeX} is a typesetting system.

The \texttt{article}\index{document classes!article} class is common.

Einstein's equation\index{Einstein, Albert}\index{relativity} is famous.

Subentries¶

\index{neural networks}
\index{neural networks!convolutional}
\index{neural networks!recurrent}

Produces:

neural networks, 10
    convolutional, 12
    recurrent, 15

Formatting Index Entries¶

\index{important|textbf}      % Bold page number
\index{definition|textit}      % Italic page number
\index{see also|see{related}}  % Cross-reference

Compilation¶

pdflatex document.tex
makeindex document.idx    # Process index
pdflatex document.tex

Glossaries¶

For terminology definitions:

Setup¶

\usepackage{glossaries}
\makeglossaries

% Define terms
\newglossaryentry{latex}{
  name=LaTeX,
  description={A document preparation system}
}

\newglossaryentry{cpu}{
  name=CPU,
  description={Central Processing Unit},
  first={Central Processing Unit (CPU)}
}

\begin{document}
% content
\printglossaries
\end{document}

Using Glossary Terms¶

\gls{latex}      % "LaTeX" (lowercase)
\Gls{latex}      % "LaTeX" (uppercase)
\glspl{cpu}      % "CPUs" (plural)
\Glspl{cpu}      % "CPUs" (capitalized plural)

Acronyms¶

\newacronym{ml}{ML}{Machine Learning}
\newacronym{ai}{AI}{Artificial Intelligence}

% First use: Machine Learning (ML)
% Subsequent: ML
\gls{ml}

Compilation¶

pdflatex document.tex
makeglossaries document     # Process glossary
pdflatex document.tex

Complete Example: Academic Paper¶

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage[backend=biber,style=ieee]{biblatex}
\usepackage{hyperref}
\usepackage{cleveref}

\addbibresource{references.bib}

\title{Deep Learning for Image Classification}
\author{Author Name}
\date{\today}

\begin{document}

\maketitle

\begin{abstract}
We present a novel deep learning approach for image classification.
\end{abstract}

\tableofcontents
\listoffigures
\listoftables

\section{Introduction}
\label{sec:intro}

Convolutional neural networks \parencite{lecun1998} have revolutionized
computer vision. Recent advances include transformers \parencite{vaswani2017}.

\section{Methods}
\label{sec:methods}

As discussed in \cref{sec:intro}, we use a CNN architecture.

Our model is defined by:
\begin{equation}
  y = \sigma(Wx + b)
  \label{eq:model}
\end{equation}

where $\sigma$ is the activation function.

\section{Results}
\label{sec:results}

\Cref{fig:accuracy,tab:performance} show our results.

\begin{figure}[htbp]
  \centering
  \includegraphics[width=0.6\textwidth]{accuracy_plot}
  \caption{Training and validation accuracy over epochs}
  \label{fig:accuracy}
\end{figure}

\begin{table}[htbp]
  \centering
  \caption{Performance comparison}
  \label{tab:performance}
  \begin{tabular}{lcc}
    \toprule
    Model & Accuracy & Params (M) \\
    \midrule
    Baseline & 92.3\% & 1.2 \\
    Ours & 95.7\% & 2.1 \\
    \bottomrule
  \end{tabular}
\end{table}

\Cref{eq:model} defines our architecture, which achieves 95.7\% accuracy
(see \cref{tab:performance}).

\section{Conclusion}

We presented a method that improves upon prior work \parencite{lecun1998}.
Future work will explore transformers \parencite{vaswani2017}.

\printbibliography

\end{document}

Best Practices¶

Label everything: Sections, figures, tables, equations
Use descriptive labels: fig:network_architecture not fig:1
Prefix labels: sec:, fig:, tab:, eq:
Label after caption: For figures/tables, \label comes after \caption
Use cleveref: Automatic "Figure", "Table", etc.
Organize .bib files: One file per project, or one master file
Complete .bib entries: Include DOI, URL when available
Use tools: Zotero, Mendeley for bibliography management
Run enough passes: pdflatex → bibtex → pdflatex → pdflatex
Check broken references: LaTeX warns "Reference undefined"

Troubleshooting¶

"Reference undefined" warning¶

Cause: Referenced label doesn't exist or hasn't been processed Solution: Check label spelling, run pdflatex again

"Citation undefined" warning¶

Cause: .bib entry not processed or key misspelled Solution: Run bibtex/biber, check .bib file

Wrong reference numbers¶

Cause: \label in wrong position Solution: Move \label after \caption (figures/tables) or inside environment (equations)

Bibliography not appearing¶

Cause: No citations or bibtex not run Solution: Add at least one \cite{}, run bibtex/biber

"Empty bibliography" warning¶

Cause: No .bib file or no cited entries Solution: Check \bibliography{} or \addbibresource{} path

Exercises¶

Exercise 1: Cross-References¶

Create a document with: - 3 sections - 2 figures - 2 tables - 3 equations - References to all of the above using \autoref or \cref

Exercise 2: Bibliography¶

Create a .bib file with at least 5 entries (different types: article, book, inproceedings). Write a document citing all of them using \cite, \citet, and \citep.

Exercise 3: BibLaTeX¶

Convert your Exercise 2 document to use BibLaTeX with the IEEE style. Compare the output.

Exercise 4: Multiple Reference Types¶

Create a document that references: - A section by number and by name - A page number where a figure appears - An equation range: "equations (1)–(3)" - Multiple figures: "figures 1, 2, and 3"

Exercise 5: Hyperref Customization¶

Configure hyperref with: - Colored links (custom colors) - PDF metadata (title, author, keywords) - Bookmarks for sections

Exercise 6: Index¶

Create a document with at least 20 index entries, including: - Main entries - Subentries - Cross-references ("see also") - Formatted page numbers (bold for definitions)

Exercise 7: Glossary¶

Create a glossary with 5 technical terms and 3 acronyms. Use them throughout a document and generate the glossary.

Exercise 8: Complete Academic Paper¶

Write a full academic paper (3+ pages) with: - Title, author, abstract - Table of contents - Multiple sections with cross-references - At least 3 figures and 2 tables - At least 5 bibliography citations - Proper use of cleveref throughout

Summary¶

This lesson covered: - Basic labels and references with \label{} and \ref{} - Page references with \pageref{} - Smart references with hyperref and \autoref{} - Advanced references with cleveref - BibTeX workflow and .bib file format - Citation commands with natbib - Modern bibliography management with BibLaTeX and Biber - BibTeX vs BibLaTeX comparison - Bibliography management tools - Hyperlinks with \url{} and \href{} - Creating indexes with makeidx - Glossaries and acronyms with the glossaries package

Mastering cross-references and citations is essential for producing professional academic and technical documents.

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