update introduction etc.

Author: nkrusch

.github/readme.md

@@ -1,18 +1,17 @@
 # Dissertation
 
 [![Compile](https://github.com/nkrusch/thesis/actions/workflows/compile.yaml/badge.svg)](https://github.com/nkrusch/thesis/actions/workflows/compile.yaml)
-[![Status](https://img.shields.io/badge/review-FF5722?style=flat-square&logo=%20&logoColor=ffffff&label=Status&labelColor=333333)](https://github.com/nkrusch/dissertation/releases)
 
 Repository to host, compile, and share my dissertation.
 
-### Formatting references 
-
+### Formatting guides 
+    
 * [Augusta University ETD Guides](https://guides.augusta.edu/etd)
 * [AU Dissertation Guide Booklet v.2024](https://augustauniversity.app.box.com/s/vj0ygpy8tvyqmsbae8y0qp9767ta7jb9)
 * [Dissertation template](https://github.com/aubertc/au_ccs_dissertation_template/) (LaTeX/markdown)
 * [Preparing Your Manuscript for Submission (ProQuest)](https://about.proquest.com/globalassets/proquest/files/pdf-files/preparing-your-manuscript.pdf)
 
-### 📁 Repository Organization
+### Repository Organization
 
     .
     ├─ 🗀 .github/         : Automated workflows
@@ -31,15 +30,18 @@ Repository to host, compile, and share my dissertation.
     ├─ Makefile            : Build commands
     └─ *                   : Configuration files
 
-### 🐳 Docker environment for compilation
+### Compilation with Docker
+
+From the repository root, pull the latest [texlive-full][texlive] image, then launch the container.
+
+    export DOCKER_DEFAULT_PLATFORM=linux/amd64
+    docker pull ghcr.io/xu-cheng/texlive-full:latest 
+    docker run -v "$(pwd):/dissertation" -it --rm ghcr.io/xu-cheng/texlive-full
+
+Insider the container, compile the dissertation by running:
 
-Pull latest [texlive-full image](https://github.com/xu-cheng/latex-docker/pkgs/container/texlive-full), 
-then launch the container.
-Run the container from the root of this repository.
+    cd dissertation && make
 
-```
-docker pull ghcr.io/xu-cheng/texlive-full:latest 
-docker run -v "$(pwd):/dissertation" -it --rm ghcr.io/xu-cheng/texlive-full
-```
+The output should be a `main.pdf` at the repository root.
 
-Insider the container run `cd dissertation && make` to compile the dissertation.
+[texlive]: https://github.com/xu-cheng/latex-docker/pkgs/container/texlive-full

main.mst

@@ -1,6 +1,6 @@
 %% LaTeX2e file `main.mst'
 %% generated by the `filecontents' environment
-%% from source `main' on 2025/06/24.
+%% from source `main' on 2025/06/25.
 %%
 headings_flag 1
 heading_prefix "\{\\normalsize\\textbf\{"

references/references.bib

@@ -199,7 +199,9 @@ @article{brockschmidt2016
     number       = {4},
     pages        = {1--50},
     doi          = {10.1145/2866575},
-    issn         = {1558-4593}
+    issn         = {1558-4593},
+    articleno    = {13},
+    numpages     = {50}
 }
 @article{chang2005,
     title        = {{Inferring Object Invariants: Extended Abstract}},
@@ -490,6 +492,21 @@ @article{hainry2023
     doi          = {10.1145/3571221},
     issn         = {2475-1421}
 }
+@article{haselwarter2023,
+    title        = {{SSProve: A Foundational Framework for Modular Cryptographic Proofs in Coq}},
+    author       = {Haselwarter, Philipp G. and Rivas, Exequiel and Van Muylder, Antoine and Winterhalter, Th\'{e}o and Abate, Carmine and Sidorenco, Nikolaj and Hri\c{t}cu, C\u{a}t\u{a}lin and Maillard, Kenji and Spitters, Bas},
+    year         = {2023},
+    month        = {7},
+    journal      = {{ACM Transactions on Programming Languages and Systems}},
+    publisher    = {{ACM}},
+    volume       = {45},
+    number       = {3},
+    doi          = {10.1145/3594735},
+    issn         = {0164-0925},
+    issue_date   = {September 2023},
+    articleno    = {15},
+    numpages     = {61}
+}
 @article{hoare1969,
     title        = {{An axiomatic basis for computer programming}},
     author       = {Hoare, C. A. R.},
@@ -2410,7 +2427,8 @@ @misc{aws2024
     author       = {Byron Cook},
     year         = {2024},
     url          = {https://aws.amazon.com/blogs/security/an-unexpected-discovery-automated-reasoning-often-makes-systems-more-efficient-and-easier-to-maintain/},
-    note         = {AWS Security Blog, 17 October 2024 (accessed: 2025-04-17)}
+    annote       = {AWS Security Blog, 17 October 2024},
+    note         = {Accessed: 2025-04-17},
 }
 @misc{casc,
     title        = {{The CADE ATP System Competition}},
@@ -2419,6 +2437,13 @@ @misc{casc
     url          = {https://tptp.org/CASC/},
     note         = {Accessed: 2025-04-15}
 }
+@misc{core,
+    title        = {{ICORE Conference Portal}},
+    author       = {{Computing Research and Education (CORE)}},
+    year         = {2025},
+    url          = {https://portal.core.edu.au/conf-ranks/},
+    note         = {Accessed: 2025-06-25}
+}
 @misc{cinteger,
     title        = {{C Integer Programs}},
     author       = {{Termination Portal},},
@@ -2435,10 +2460,19 @@ @misc{crowdstrike
 }
 @misc{etaps2025,
     title        = {{Ina Schaefer on X-by-Construction}},
-    author       = {{ETAPS} Blog},
+    author       = {Benjamin Kaminski},
     year         = {2025},
+    month        = {3},
     url          = {https://etaps.org/blog/031-ina-schaefer/},
-    note         = {Published on 25 March 2025 (Accessed: 2025-04-27)}
+    note         = {Accessed: 2025-04-27},
+    annote       = {ETAPS Blog, Published on 25 March 2025 }
+}
+@misc{complexityzoo,
+    title        = {{Complexity Zoo}},
+    author       = {Scott Aaronson and Greg Kuperberg and Oliver Habryka},
+    year         = {2025},
+    url          = {https://complexityzoo.net/Complexity_Zoo},
+    note         = {Accessed: 2025-06-25}
 }
 @misc{flores_experiments,
     title        = {{Experimental evaluation of Cost Analysis of Programs Based on the Refinement of Cost Relations}},
@@ -2452,7 +2486,8 @@ @misc{furia2014b
     author       = {Furia, Carlo A.},
     year         = {2014},
     url          = {https://se.inf.ethz.ch/courses/2014b_fall/sv/slides/06-AssertionInference.pdf},
-    note         = {Lecture notes of Software Verification course, ETH Zürich, Fall 2014 (Accessed: 2025-04-19)}
+    note         = {Accessed: 2025-04-19},
+    annote       = {Lecture notes of Software Verification course, ETH Zürich, Fall 2014},
 }
 @misc{hundredtheorems,
     title        = {{Formalizing 100 Theorems}},
@@ -2467,46 +2502,52 @@ @misc{kristiansen2017
     year         = {2017},
     month        = {4},
     url          = {https://zenodo.org/records/15288399},
-    note         = {Presentation slides at DICE-FOPARA 2017, Uppsala, Sweden (Accessed: 2025-01-06)}
+    note         = {Accessed: 2025-01-06},
+    annote       = {Presentation slides at DICE-FOPARA 2017, Uppsala, Sweden}
 }
 @misc{leino2010b,
     title        = {{Dafny An automatic program verifier for functional correctness}},
     author       = {Leino, K Rustan M},
     year         = {2010},
     month        = {4},
     url          = {https://www.microsoft.com/en-us/research/publication/dafny-automatic-program-verifier-functional-correctness/},
-    note         = {Presentation slides of LPAR-16 on 27 April 2010 (Accessed: 2025-04-14)}
+    annote       = {Presentation slides of LPAR-16, on 27 April 2010},
+    note         = {Accessed: 2025-04-14},
 }
 @misc{moller2024,
     title        = {{Static Program Analysis}},
     author       = {Møller, Anders},
     year         = {2024},
     month        = {8},
     url          = {https://zenodo.org/records/15288399},
-    note         = {Lecture notes from Marktoberdorf Summer School 2024, Herrsching am Ammersee, Germany (Accessed: 2025-02-08)}
+    annote       = {Lecture notes from Marktoberdorf Summer School 2024, Herrsching am Ammersee, Germany},
+    note         = {Accessed: 2025-02-08},
 }
 @misc{muller2024,
     title        = {{Ownership in program verification -- from separation logic to Rust and back}},
     author       = {Müller, Peter},
     year         = {2024},
     month        = {8},
     url          = {https://zenodo.org/records/15288399},
-    note         = {Lecture notes from Marktoberdorf Summer School 2024, Herrsching am Ammersee, Germany (Accessed: 2025-04-19)}
+    note         = {Accessed: 2025-04-19},
+    annote       = {Lecture notes from Marktoberdorf Summer School 2024, Herrsching am Ammersee, Germany}
 }
 @misc{oak-slides,
     title        = {{Introduction to OpenMP Offload: Part I}},
     author       = {Pophale, Swaroop},
     year         = {2023},
     url          = {https://www.olcf.ornl.gov/wp-content/uploads/OpenMP_Introduction_to_Offload_Part1.pdf},
-    note         = {OpenMP training series at the National Energy Research Scientific Computing Center (NERSC) (Accessed: 2025-03-08)}
+    note         = {Accessed: 2025-03-08},
+    annote       = {OpenMP training series at the National Energy Research Scientific Computing Center (NERSC)}
 }
 @misc{piessens2024,
     title        = {{Software security across abstraction layers}},
     author       = {Piessens, Frank},
     year         = {2024},
     month        = {8},
     url          = {https://zenodo.org/records/15288399},
-    note         = {Lecture notes from Marktoberdorf Summer School 2024, Herrsching am Ammersee, Germany (Accessed: 2025-02-15)}
+    note         = {Accessed: 2025-02-15},
+    annote       = {Lecture notes from Marktoberdorf Summer School 2024, Herrsching am Ammersee, Germany}
 }
 @misc{rocq-community,
     title        = {{The Rocq Community}},
@@ -2521,15 +2562,17 @@ @misc{shankar2023
     year         = {2023},
     month        = {5},
     url          = {https://fm.csl.sri.com/SSFT23/speaklogicV12.pdf},
-    note         = {Lecture notes from the Twelfth Summer School on Formal Techniques, Menlo College, California (Accessed: 2025-04-19)}
+    note         = {Accessed: 2025-04-19},
+    annote       = {Lecture notes from the Twelfth Summer School on Formal Techniques, Menlo College, California}
 }
 @misc{torlak2015,
     title        = {{Static Analysis}},
     author       = {Torlak, Emina},
     year         = {2015},
     month        = {5},
     url          = {https://courses.cs.washington.edu/courses/cse403/15sp/lectures/L19.pdf},
-    note         = {Lecture notes from CSE 403: Software Engineering, Spring 2015 (Accessed: 2025-02-09)}
+    note         = {Accessed: 2025-02-09},
+    annote       = {Lecture notes from CSE 403: Software Engineering, Spring 2015}
 }
 @misc{usg2024,
     title        = {{Notice of Data Breach}},
@@ -2563,15 +2606,17 @@ @misc{zave2023
     year         = {2023},
     month        = {5},
     url          = {https://fm.csl.sri.com/SSFT23/aLecture1.pdf},
-    note         = {Lecture notes from the Twelfth Summer School on Formal Techniques, Menlo College, California (Accessed: 2025-04-19)}
+    note         = {Accessed: 2025-04-19},
+    annote       = {Lecture notes from the Twelfth Summer School on Formal Techniques, Menlo College, California}
 }
 @misc{zave2023b,
     title        = {{No More Garbage In: Validating Formal Models - A Short Course (Reference)}},
     author       = {Zave, Pamela and Nelson, Tim},
     year         = {2023},
     month        = {5},
     url          = {https://fm.csl.sri.com/SSFT23/reference.pdf},
-    note         = {Lecture notes from the Twelfth Summer School on Formal Techniques, Menlo College, California (Accessed: 2025-04-19)}
+    note         = {Accessed: 2025-04-19},
+    annote       = {Lecture notes from the Twelfth Summer School on Formal Techniques, Menlo College, California}
 }
 @phdthesis{carbonneaux2018,
     title        = {{Modular and Certified Resource-Bound Analyses}},

text/bg-formal.tex

@@ -318,15 +318,6 @@ \subsubsection{The Rocq Theorem Prover}
 The successes of Rocq have also created abundant interest in dependent type theory;
 the core logic of Rocq~\cite{coquand1988}.
 
-%\paragraph*{Logical foundations.}
-%All Rocq expressions, including logical claims, have a type describing what it computes.
-%Calculus of inductive constructions
-%a version of dependent type theory with a countable hierarchy of non-cumulative universes and inductive types.
-%By the Curry-Howard correspondence, Rocq can be seen at the same time as a pure functional programming language and a rich proof system.
-%For all formula there exists a proof of this formula in natural deduction if and only if there exists a term that has this formula as type.
-%Theorem statement \(\leftrightarrow\) Type
-%Proof \(\leftrightarrow\) Program
-
 \paragraph*{Technical overview.}
 As a guiding example, consider simple proof in~\autoref{lst:rocq-basic}.
 The \pr|lemma| keywords starts a statement we wish to prove.
@@ -399,20 +390,50 @@ \subsubsection{The Rocq Theorem Prover}
 \toprule
 \textbf{Formalization target} & \textbf{Authors} \\
 \midrule
-\href{https://users.dimi.uniud.it/~ivan.scagnetto/pi-calculus.html}{\(\pi\)-calculus in (Co)inductive-type theory} & \textcite{honsell2001} \\
-\href{https://github.com/rocq-community/goedel}{Gödel-Rosser 1st incompleteness theorem} & \textcite{oconnor2005} \\
-Modal model of impredicative semantics & \textcite{appel2007} \\
-\href{https://github.com/rocq-community/fourcolor}{Four Color theorem}\smtabularnote{based on~\cite{robertson1997} and~\cite{appel1989}} & \textcite{gonthier2008} \\
-\href{https://github.com/AbsInt/CompCert}{Verified Optimizing C Compiler, CompCert}\index{CompCert}\smtabularnote{A verifying compiler is one of the grand challenges for computing research posed in~\textcite{hoare2003}}\smtabularnote{CompCert received the ACM Software System Award in 2021.} & \textcite{leroy2009} \\
-\href{https://gitlab.inria.fr/flocq/flocq}{Flocq: floating-point numbers} & \textcite{boldo2011} \\
-\href{http://plv.csail.mit.edu/bedrock/}{Bedrock: low-level programming library} & \textcite{chlipala2011} \\
-\href{https://github.com/davidnowak/bellantonicook}{Safe Recursion} -- \autoref{safe-rec} & \textcite{heraud2011} \\
-\href{https://github.com/ProjectiveGeometry/ProjectiveGeometry}{Desargues's theorem in projective geometry} & \textcite{magaud2012} \\
-\href{https://github.com/math-comp/odd-order}{Feit-Thompson's Odd Order theorem} & \textcite{gonthier2013} \\
-\href{https://github.com/HoTT/Coq-HoTT}{Homotopy Type Theory} & \textcite{bauer2017} \\
-\href{https://github.com/rocq-community/reglang}{Regular Language representations} & \textcite{doczkal2018} \\
-\href{https://github.com/DeepSpec/InteractionTrees}{Recursive and impure programs} & \textcite{xia2019} \\
-\href{https://github.com/uds-psl/coq-library-undecidability}{Undecidable Problems} & \textcite{forster2020b} \\
+\href{https://users.dimi.uniud.it/~ivan.scagnetto/pi-calculus.html}%
+{\ndx{\(\pi\)-calculus} in (Co)inductive-type theory}\index{coinduction} & \textcite{honsell2001}
+\\
+\href{https://github.com/rocq-community/goedel}%
+{\ndx{Gödel-Rosser incompleteness theorem}} & \textcite{oconnor2005}
+\\
+Modal model of impredicative semantics & \textcite{appel2007}
+\\
+\href{https://github.com/rocq-community/fourcolor}%
+{\ndx{Four Color theorem}}\smtabularnote{based on~\cite{robertson1997} and~\cite{appel1989}} & \textcite{gonthier2008}
+\\
+\href{https://github.com/AbsInt/CompCert}%
+{Verified Optimizing C Compiler, \ndx{CompCert}}%
+\smtabularnote{A verifying compiler is one of the grand challenges for computing research posed in~\textcite{hoare2003}}%
+\smtabularnote{CompCert received the ACM Software System Award in 2021.} & \textcite{leroy2009}
+\\
+\href{https://gitlab.inria.fr/flocq/flocq}%
+{\ndx{Flocq}: floating-point numbers} & \textcite{boldo2011}
+\\
+\href{http://plv.csail.mit.edu/bedrock/}%
+{\ndx{Bedrock}: low-level programming library} & \textcite{chlipala2011}
+\\
+\href{https://github.com/davidnowak/bellantonicook}%
+{Safe Recursion\index{safe recursion}} -- \autoref{safe-rec} & \textcite{heraud2011} \\
+\href{https://github.com/ProjectiveGeometry/ProjectiveGeometry}
+{\ndx{Desargues's theorem} in projective geometry} & \textcite{magaud2012}
+\\
+\href{https://github.com/math-comp/odd-order}%
+{Feit-Thompson's \ndx{Odd Order theorem}} & \textcite{gonthier2013}
+\\
+\href{https://github.com/HoTT/Coq-HoTT}%
+{\ndx{Homotopy Type Theory}} & \textcite{bauer2017}
+\\
+\href{https://github.com/rocq-community/reglang}%
+{Regular Language representations} & \textcite{doczkal2018}
+\\
+\href{https://github.com/DeepSpec/InteractionTrees}%
+{Interaction Trees: Recursive and impure programs} & \textcite{xia2019}
+\\
+\href{https://github.com/uds-psl/coq-library-undecidability}%
+{Undecidable\index{undecidability} Problems} & \textcite{forster2020b}
+\\
+\href{https://github.com/SSProve/ssprove}%
+{\ndx{SSProve}: modular cryptographic proofs} & \textcite{haselwarter2023} \\
 \bottomrule
 \end{NiceTabularX}
 \caption[The Rocq prover formalization results]{A small sample of results formalized with the Rocq prover.}
@@ -449,18 +470,18 @@ \subsubsection{Dafny: The Verification Aware Programming Language}
 \end{figure}
 
 \paragraph*{Technical overview.}
-Dafny is a hybrid language, influenced by Java and C\#.
+Dafny is a hybrid language, influenced by \ndx{Java} and \ndx{C\#}.
 It has both functional and object-oriented features;
-including: curly-bracket block-style, (mathematical) functions, and inductive and co-inductive data types.
+including: curly-bracket block-style, (mathematical) functions, and inductive and co-inductive\index{coinduction} data types.
 The programming constructs include loops, \pr|if|-statements, arrays, classes and methods;
 variables, types, generics, lambdas, inheritance, \etc~\cite{dafnydoc}
-The real power of Dafny comes from the ability to annotate methods to specify their behavior.
-For verification tasks, the idea is to define specifications and write proofs aside the implementation, in deductive verification-style.
+The real power of \ndx{Dafny} comes from the ability to annotate methods to specify their behavior.
+For verification tasks, the idea is to define specifications and write proofs aside the implementation, in \ndx{deductive verification}-style.
 The built-in verification constructs include pre- and postconditions;
-loop invariants, termination metrics, lemmas, and ghost constructs\footnote{
+loop invariants, termination metrics, lemmas, and \ndx{ghost construct}s\footnote{
 A \emph{ghost} is any construct that is used for verification only; they are erased during compilation~\cite[p. 19]{leino2023}.}.
-This language design enables writing functionally-correct verified programs fully in Dafny~\cite{leino2023}.
-Dafny programs can be compiled to various target languages, like C\#, Java, and Go~\cite{dafnydoc}.
+This language design enables writing functionally-correct verified programs fully in \ndx{Dafny}~\cite{leino2023}.
+Dafny programs can be compiled to various target languages, like \ndx{C\#}, \ndx{Java}, and \ndx{Go}~\cite{dafnydoc}.
 
 Dafny has an associated static program verifier.
 The role of the verifier is to check a program's specification constructs\footnote{These are Eiffel-like contracts from~\cite{meyer1988}.}.
@@ -896,9 +917,3 @@ \subsubsection{Connecting Formal Methods and ICC}
 Another perspective is to use ICC systems in assisting formal methods tools in program verification efforts.
 This is the motivating idea in the manuscript of~\autoref{sec:postcond}.
 The central idea is that inferred mwp-bounds can be used as postconditions in Dafny-style deductive verification.
-
-%The third goal is to strengthen the hypothesis that implicit computational complexity is naturally suited to formal reasoning.
-%Classic complexity theory is predicated on machine models that are difficult to represent formally~\footnote{
-%For example, a formal model of TMs in~\textcite{forster2020} took five years to complete.}.
-%In contrast, the programming languages-based approach of implicit computational complexity makes formal reasoning more accessible.
-%The findings of this dissertation are sufficient to motivate and justify the effort for undertaking rigorous formalization projects.