Featured ToC and crossref functionality. More details in the example PDF and GitHub Repo: https://github.com/Jue-Xu/Latex-Template-for-Scientific-Style-Book, YouTube Demo Preview
% !TEX root = ./notes_template.tex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%% preamble %%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[11pt,twoside]{book}
\usepackage[mono=false]{libertine} % new linux font, ignore mono
\usepackage{luatex85}
%\renewcommand{\baselinestretch}{1.05}
\usepackage{amsmath,amsthm,amssymb,mathrsfs,amsfonts,dsfont}
\usepackage{epsfig,graphicx}
\usepackage{tabularx}
\usepackage{blkarray}
\usepackage{slashed}
\usepackage{color}
\usepackage{listings}
\usepackage{caption}
% \usepackage{fullpage}
\usepackage{lipsum} % provides dummy text for testing
\usepackage[toc,title,titletoc,header]{appendix}
\usepackage{minitoc}
\usepackage{color}
\usepackage{multicol} % two-col ToC
\usepackage{bm}
\usepackage{imakeidx} % before hyperref
\usepackage{hyperref}
% link colors settings
\hypersetup{
colorlinks=true,
citecolor=magenta,
linkcolor=blue,
filecolor=green,
urlcolor=cyan,
% hypertexnames=false,
}
\usepackage[capitalise]{cleveref}
\usepackage{subcaption}
\usepackage{enumitem}
\usepackage{mathtools}
\usepackage{physics}
\usepackage[linesnumbered,ruled,vlined,algosection]{algorithm2e}
\SetCommentSty{textsf}
\usepackage{epigraph}
\epigraphwidth=1.0\linewidth
\epigraphrule=0pt
% adjust margin
\usepackage[margin=2.3cm]{geometry}
\headheight13.6pt
%%%%%%%%%%%%%%%% thmtools %%%%%%%%%%%%%%%%%%%%%
\usepackage{thmtools}
\declaretheorem[numberwithin=chapter]{theorem}
\declaretheorem[numberwithin=chapter]{axiom}
\declaretheorem[numberwithin=chapter]{lemma}
\declaretheorem[numberwithin=chapter]{proposition}
\declaretheorem[numberwithin=chapter]{claim}
\declaretheorem[numberwithin=chapter]{conjecture}
\declaretheorem[sibling=theorem]{corollary}
\declaretheorem[numberwithin=chapter, style=definition]{definition}
\declaretheorem[numberwithin=chapter, style=definition]{problem}
\declaretheorem[numberwithin=chapter, style=definition]{example}
\declaretheorem[numberwithin=chapter, style=definition]{exercise}
\declaretheorem[numberwithin=chapter, style=definition]{observation}
\declaretheorem[numberwithin=chapter, style=definition]{fact}
\declaretheorem[numberwithin=chapter, style=definition]{construction}
\declaretheorem[numberwithin=chapter, style=definition]{remark}
\declaretheorem[numberwithin=chapter, style=remark]{question}
%%%%%%%%%%%%%%%% thmtools %%%%%%%%%%%%%%%%%%%%%
\usepackage{changepage}
\newenvironment{solution}
{\renewcommand\qedsymbol{$\square$}\color{blue}\begin{adjustwidth}{0em}{2em}\begin{proof}[\textit Solution.~]}
{\end{proof}\end{adjustwidth}}
%%%%%%%%%%%%%%%% index %%%%%%%%%%%%%%%%%%%%%
\begin{filecontents}{index.ist}
% https://tex.stackexchange.com/questions/65247/index-with-an-initial-letter-of-the-group
headings_flag 1
heading_prefix "{\\centering\\large \\textbf{"
heading_suffix "}}\\nopagebreak\n"
delim_0 "\\nobreak\\dotfill"
\end{filecontents}
\newcommand{\myindex}[1]{\index{#1} \emph{#1}}
\makeindex[columns=3, intoc, title=Alphabetical Index, options= -s index.ist]
%%%%%%%%%%%%%%%% index %%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%% ToC %%%%%%%%%%%%%%%%%%%%%
% Link Chapter title to ToC: https://tex.stackexchange.com/questions/32495/linking-the-section-text-to-the-toc
\usepackage[explicit]{titlesec}
\titleformat{\chapter}[display]
{\normalfont\huge\bfseries}{\chaptertitlename\ {\thechapter}}{20pt}{\hyperlink{chap-\thechapter}{\Huge#1}
\addtocontents{toc}{\protect\hypertarget{chap-\thechapter}{}}}
\titleformat{name=\chapter,numberless}
{\normalfont\huge\bfseries}{}{-20pt}{\Huge#1}
%%%%%%%%%%%%%%%%%%% fancyhdr %%%%%%%%%%%%%%%%%
\usepackage{fancyhdr}
\pagestyle{fancy} % enable fancy page style
\renewcommand{\headrulewidth}{0.0pt} % comment if you want the rule
\fancyhf{} % clear header and footer
\fancyhead[lo,le]{\leftmark}
\fancyhead[re,ro]{\rightmark}
\fancyfoot[CE,CO]{\hyperref[toc-contents]{\thepage}}
% https://tex.stackexchange.com/questions/550520/making-each-page-number-link-back-to-beginning-of-chapter-or-section
\makeatletter
\def\chaptermark#1{\markboth{\protect\hyper@linkstart{link}{\@currentHref}{Chapter \thechapter ~ #1}\protect\hyper@linkend}{}}
\def\sectionmark#1{\markright{\protect\hyper@linkstart{link}{\@currentHref}{\thesection ~ #1}\protect\hyper@linkend}}
\makeatother
%%%%%%%%%%%%%%%%%%% fancyhdr %%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%% biblatex %%%%%%%%%%%%%%%%%
\usepackage[doi=false,url=false,isbn=false,style=alphabetic,backend=biber,backref=true]{biblatex}
\addbibresource{bib.bib}
\newbibmacro{string+doiurlisbn}[1]{%
\iffieldundef{doi}{%
\iffieldundef{url}{%
\iffieldundef{isbn}{%
\iffieldundef{issn}{%
#1%
}{%
\href{http://books.google.com/books?vid=ISSN\thefield{issn}}{#1}%
}%
}{%
\href{http://books.google.com/books?vid=ISBN\thefield{isbn}}{#1}%
}%
}{%
\href{\thefield{url}}{#1}%
}%
}{%
\href{http://dx.doi.org/\thefield{doi}}{#1}%
}%
}
% https://tex.stackexchange.com/questions/94089/remove-quotes-from-inbook-reference-title-with-biblatex
\DeclareFieldFormat[article,incollection,inproceedings,book,misc]{title}{\usebibmacro{string+doiurlisbn}{\mkbibemph{#1}}}
% https://tex.stackexchange.com/questions/454672/biblatex-journal-name-non-italic
\DeclareFieldFormat{journaltitle}{#1\isdot}
\DeclareFieldFormat{booktitle}{#1\isdot}
% https://tex.stackexchange.com/questions/10682/suppress-in-biblatex
\renewbibmacro{in:}{}
% add video field: https://tex.stackexchange.com/questions/111846/biblatex-2-custom-fields-only-one-is-working
\DeclareSourcemap{
\maps[datatype=bibtex]{
\map{
\step[fieldsource=video]
\step[fieldset=usera,origfieldval]
}
}
}
\DeclareFieldFormat{usera}{\href{#1}{\textsc{Online video}}}
\AtEveryBibitem{
\csappto{blx@bbx@\thefield{entrytype}}{% put at end of entry
\iffieldundef{usera}{}{\space \printfield{usera}}
}
}
%%%%%%%%%%%%%%%%%%% biblatex %%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%% glossaries %%%%%%%%%%%%%%%%%
\input{./glossaries.tex}
%%%%%%%%%%%%%%%%%%%%% glossaries %%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%% glossaries-extra %%%%%%%%%%%%%%%%%
% \usepackage[record,abbreviations,symbols,stylemods={list,tree,mcols}]{glossaries-extra}
%%%%%%%%%%%%%%%%%%%%% glossaries-extra %%%%%%%%%%%%%%%%%
\input{./macros.tex}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%% begin of document %%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\title{\bf \huge Study Notes}
\author{Jue Xu}
\date{Update on \today}
\maketitle
\setcounter{tocdepth}{2}
\setcounter{minitocdepth}{1}
\begin{multicols}{2}
\dominitoc% Initialization
\adjustmtc[2]% chp number shift for mini-toc
\tableofcontents
\label{toc-contents}
\end{multicols}
\listoffigures
% \listoftables
\begin{multicols}{2}
\listoftheorems[ignoreall,show={theorem}]
\end{multicols}
\renewcommand{\listtheoremname}{List of Definitions}
\begin{multicols}{2}
\listoftheorems[ignoreall,show={definition}]
\end{multicols}
% \printglossaries
% \printglossary[type=\acronymtype]
\printglossary
% \printglossary[title=List of terms, toctitle=List of terms]
% bib2gls
% \printunsrtglossaries % print all types
% \printunsrtglossary[type={abbreviations},title=List of Abbreviations,style=listgroup]
% \printunsrtglossary[type={abbreviations},title=List of Abbreviations,style=listhypergroup] % doesn't work
% \printunsrtglossary[type={symbols},title=List of Symbols,style=listgroup]
% \printunsrtglossary % main entry
%%%%%%%%%%%%%%%Content%%%%%%%%%%%%%%%
% \mainmatter % separat the number of toc and mainmatter
\input{./chapter/preface.tex}
\part{Mathematics}
\input{./chapter/discrete_math.tex}
\part{Computer Science}
% \input{./chapter/complexity.tex}
\input{./chapter/machine_learning.tex}
% \input{./chapter/algorithms.tex}
\part{Physics}
\input{./chapter/quantum_mechanics.tex}
% \input{./chapter/quantum_field_theory.tex}
\begin{appendices}
\input{./chapter/appendix_formula.tex}
\end{appendices}
\backmatter
%%%%%%%%%%%%%%% Reference %%%%%%%%%%%%%%%
\printbibliography[heading=bibintoc]
\printindex
\end{document}