Round 2 of the bib audit, covering paper subprojects (mlsysim,
tinytorch, periodic-table, mlperf-edu) that the textbook-focused first
pass deferred. Same pattern as round 1: surname/year prefixes did not
match the entry's actual paper, plus several corrupt entries from
Crossref misidentification.
Renames:
- mlsysim/{docs,paper}: barrett2024 -> zheng2024sglang (SGLang paper,
Zheng is first author).
- mlsysim/paper: zhao2025 -> deepseek2025v3 (DeepSeek-V3 ISCA paper,
corporate author DeepSeek-AI).
- tinytorch: key499f5624 -> tanenbaum1987os (hash-fallback for
Tanenbaum OS textbook); fry1985 -> abelson1996sicp (SICP 2nd ed,
Fry is not in author list); wooster1982 -> papert1980mindstorms
(Mindstorms by Papert, Wooster not in author list); collins2018 ->
collins1989apprenticeship (Cognitive Apprenticeship paper is 1989).
- tinytorch + periodic-table: vaswani2025 -> vaswani2017attention
(Attention paper is 2017; entries had a corrupt publisher and bogus
DOI from Crossref misidentification).
Body fixes accompanying renames:
- tanenbaum1987os, abelson1996sicp, papert1980mindstorms: rebuilt as
@book entries (were @article with stale review/journal DOIs).
- vaswani2017attention: rebuilt with canonical NeurIPS 2017 metadata
(Curran Associates, vol 30, pp 5998-6008); dropped corrupt DOI.
Orphan deletions:
- tinytorch keybe9561f4 (hash-fallback, no cite sites).
- mlperf-edu vaswani2017attention (orphan).
21 cite-site updates across 4 paper subprojects. bib_lint reports 0
errors across all 5 modified bibs.
Wraps up the bib-verify sweep across vol1, vol2, and the paper sub-projects,
and corrects three citation issues introduced earlier in the branch:
- Restore tang20211bit (1-bit Adam, Tang et al. ICML 2021) in vol2 bib and
in collective_communication.qmd. The earlier sweep had renamed the cite
to li2022, which now resolved to AlphaCode or 1-Bit LAMB.
- Restore micikevicius2018mixed in vol1 bib to point at "Mixed Precision
Training" (Micikevicius et al. ICLR 2018). The entry had been overwritten
with an unrelated OpenSeq2Seq paper while the cite key stayed the same.
- Drop the unused li2022 (AlphaCode) entry and the duplicate li2022 (1-Bit
LAMB) entry from vol2 bib.
Also remove eight same-paper duplicate entries that the sweep had left
behind (vol1: lawson1979, gholami2022, lange2009, ribeiro2016; vol2:
bursztein2024, rasley2020, sevilla2022, narayanan2019).
After this commit the bibs have zero duplicate keys and zero orphan
citations across both volumes and all five paper sub-projects.
Deleted reddi2024mlsysbook from tinytorch/paper and rafailov2023direct from
periodic-table/paper. Both were identified as true orphans (not cited in
any .qmd or .tex) and out of scope for their respective papers.
The previous scope was .qmd only, which made every paper-bib entry not
cited from a chapter look orphan even when paper.tex cited it. Adds
\cite/\citep/\citet/\citeauthor/\citeyear pattern matching for the four
paper.tex files (interviews, tinytorch, periodic-table, mlsysim).
Also fixes 6 broken links in tinytorch/paper/paper.tex caused by earlier
bib-audit deletions of keys that had year/surname mismatches. Restored
these entries with corrected keys (appel2002tiger, reddi2021widening,
pfaff2009pintos, rush2020minitorch, zhang2023dive) and updated the .tex
file to match. Replaced kannan2022astrasim with won2023astrasim2.
Same regression as vol1/vol2 references.bib (commit 42bc54275 figure-audit
feat) — five auxiliary bib files (interviews/paper, mlsysim/docs,
mlsysim/paper, periodic-table/paper, tinytorch/paper) had brace patterns
mangled in titles, e.g. 'Throughput-Latency Tradeoff in {LLM} Inference'
became 'Throughput-Latency Tradeoff in {LLM}} Inference', which
bibtex-tidy refuses to parse.
Restored to the parent of 42bc54275 (state at 9ebdf77d0) and
re-formatted via the bib_apply_mechanical + bibtex-tidy hooks.
Align the MLSys·im code, docs, paper, website, workflows, and lab wheel for the 0.1.1 release. This also fixes runtime/API issues found during release review and prepares the paper PDF plus archive package.
Two bibliography fixes from the Pass 16 human-review backlog that had
unambiguous verification evidence from the Phase 2 parallel-agent sweep
and Crossref, so they did not require author judgment:
1. tinytorch/paper/references.bib: re-type tanenbaum1987minix
Entry was typed @article but the cited work is A. S. Tanenbaum's
1987 book "Operating Systems: Design and Implementation" published
by Prentice-Hall. The entry already had publisher and isbn fields
(added during the Pass 16 parallel-agent bib sweep); only the type
was wrong. One-character fix: @article → @book.
2. mlsysim/paper/references.bib: fix zhang2024llmcompass DOI collision
The Phase 2 sweep (Agent F) detected that zhang2024llmcompass and
patel2024splitwise had the same DOI in the source bib
(10.1109/ISCA59077.2024.00060) — impossible since they are
different papers. Agent F verified Splitwise's correct DOI is
10.1109/ISCA59077.2024.00019 via IEEE Xplore and applied the
correction during the sweep.
However, zhang2024llmcompass was left with the original DOI
10.1109/ISCA59077.2024.00060 pending verification. Crossref
confirms that DOI belongs to "HEAP: A Fully Homomorphic Encryption
Accelerator with Parallelized Bootstrapping" by Agrawal et al.,
NOT LLMCompass.
Crossref returns the correct DOI for LLMCompass as
10.1109/ISCA59077.2024.00082
("LLMCompass: Enabling Efficient Hardware Design for Large
Language Model Inference").
This commit updates zhang2024llmcompass.doi to the verified
Crossref value.
Both files are now at 0 open bibliography-hygiene findings.
The 6 remaining bibliography-hygiene human-review items still in
the audit (3 fabricated entries + 3 wrong-author attributions) are
NOT touched by this commit — they require author judgment about
delete-vs-replace and re-attribution that only the author can make.
Parallel-agent bibliography verification sweep applied to the paper
bibliography files outside the book proper. These are academic papers
that live in the repo (mlsysim tutorial paper, tinytorch paper,
interviews paper, periodic-table paper) and were previously only subject
to bibtex-tidy formatting, not §5 hygiene validation.
Batches F and G of the Pass 16 parallel sweep processed 77 entries
total across 6 files; 73 auto-applied at HIGH+MEDIUM confidence.
Per-file summary:
mlsysim/paper/references.bib 50 entries applied (0 open)
mlsysim/docs/references.bib 15 entries applied (0 open)
tinytorch/paper/references.bib 7 entries applied (1 open)
interviews/paper/references.bib 3 entries applied (0 open)
periodic-table/paper/ref.bib 11 entries applied (0 open)
Each applied entry carries:
publisher or journal (primary field) + doi (when present on source)
+ x-verified = "2026-04-08"
+ x-verified-by = "pass-16-bib-sweep"
+ x-verified-source = <authoritative URL from DBLP, Crossref, arXiv, etc.>
One open finding (intentional skip):
tanenbaum1987minix — typed @article but the actual publication is
A. S. Tanenbaum's 1987 book "Operating Systems: Design and
Implementation" (Prentice-Hall), not a journal article. The fix is
to re-type as @book, not fill a wrong `journal` field. Flagged for
a future type-refactor pass.
Cross-file duplicate keys are expected and correct: dao2022flashattention,
mattson2020mlperf, and vaswani2017attention each appear in multiple
paper .bib files because each paper independently cites these
foundational works. Each copy was verified and annotated separately.
This is the first pass that the repo-wide bib_lint + bibtex-tidy
pre-commit hooks have been applied to these paper .bib files.
Consistent layout for StaffML, mlsysim, and TinyTorch papers:
- figures/ for all visual assets (SVGs, PDFs, PNGs)
- scripts/ for utility scripts (analysis, validation, benchmarks)
- tables/ for standalone table .tex files (StaffML only)
- Makefile at root for building (created one for mlsysim)
Removed redundant build scripts (compile_paper.sh, build.sh) in
favor of Makefiles. Deleted sort_app_matrix.py (no longer needed).
Merged mlsysim images/ into figures/. Updated all references in
paper.tex, Makefiles, and CI workflows.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- StaffML paper: staffml.ai on title/footnote, drop author email, hyperref black refs + blue URLs
- TinyTorch paper: same hyperref styling for neutral PDF links
- StaffML app: clarify MLSysBook ecosystem and link mlsysbook.ai/staffml
- Vol1/Vol2 about: TinyTorch and ecosystem URL wording
Refines the explanation of K,V computation savings in the memoization module,
quantifying redundant computations and highlighting the efficiency gain.
The paper and module now specify that generating 100 tokens requires 5,050
total K,V computations, but only 100 are necessary, resulting in 4,950
redundant calculations.
Add new subsection describing function decomposition pattern used within
modules. Documents how complex operations (attention, convolution, training)
are split into focused helper functions with individual unit tests before
composition into exported functions. Updates pedagogical justification to
cover both inter-module and intra-module progressive disclosure.
Escape unescaped & characters in references.bib (Taylor & Francis,
AI & Machine-Learning) and replace Unicode em-dashes (U+2014) with
LaTeX --- ligatures in paper.tex for T1 font compatibility.
- Name the problem: "algorithm-systems divide"
- Name the approach: "implementation-based systems pedagogy"
- Add concrete systems examples (O(N^2), Adam 3x memory)
- Include MLPerf-style benchmarking in milestones
- Strengthen citable terminology throughout
- Switch from fontspec/TeX Gyre to standard fonts (mathpazo, helvet, courier)
- Replace emoji package with no-op (title is just "TinyTorch")
- Switch from biblatex/biber to natbib/bibtex
- Works with both lualatex (local) and pdflatex (arXiv)
- Acknowledge CS249r students whose feedback shaped the curriculum
- Acknowledge global mlsysbook.ai community
- Expand GenAI statement to cover framework development
- Frame AI assistance as enabling democratization (single author, 20 modules)
- Remove em-dashes throughout for cleaner prose
Reverts arXiv-specific changes to work with compile_paper.sh:
- Restored fontspec with TeX Gyre fonts
- Restored emoji package
- Restored biblatex with biber backend
- Works with lualatex as expected by compile script
