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Answer

How do I preserve footnotes when converting a PDF to EPUB?

Updated:

To preserve footnotes, the converter has to recognise them as notes and link each one from its call in the text, instead of leaving them as small text in the middle of the book. EpubCC writes them as EPUB footnotes linked from the superscript that calls them.

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Fixed layout vs. reflowable text

Original PDF
A page of the original PDF: QLoRA paper (arXiv 2305.14314)
EPUB
The same passage in the EPUB made by EpubCC
Real conversion from the case PDF footnotes to EPUB notes: an academic paper · QLoRA paper (arXiv 2305.14314)

How a footnote is recognised

  • Smaller type than the body text, in the lower half of the page, below the body text on the same page.
  • Starting with a marker (a number or a symbol) that matches a superscript call on that page.
  • Pages made only of small type, such as endnotes, are kept as normal paragraphs.

What the EPUB gets

Each note becomes an EPUB 3 footnote at the end of its chapter, and each call becomes a link to it. Readers that support pop-up notes show it without leaving the page.

Limits

Notes that don't follow those patterns stay as text and are reported. The benchmark measures text, not whether every note was linked, so this is checked by hand on the corpus.

Evidence from the benchmark

8-gram recall · Like 4-gram recall with 8 words: drops when reading order or line joins break sentences (continuity). Higher is better. Mean over the documents of the benchmark of November 3, 2026. Methodology and every result
Engine8-gram recall
EpubCC engine (EPUB output)0.767
EpubCC engine (plain text)0.765
pdf_oxide · extract_text0.726
pdf_oxide · to_plain_text (XY-cut)0.658
pdf_oxide · Markdown0.653
PDFium · text().all()0.746
OpenDataLoader PDF (local mode)0.749
pdftotext (Poppler)0.743
DocumentEpubCC engine (EPUB output)EpubCC engine (plain text)pdf_oxide · extract_textpdf_oxide · to_plain_text (XY-cut)pdf_oxide · MarkdownPDFium · text().all()OpenDataLoader PDF (local mode)pdftotext (Poppler)
QLoRA paper (arXiv 2305.14314)0.7860.7820.8170.8520.8680.9080.9170.770
Federal Register document 2026-224430.8590.8530.3340.0350.3390.8590.8010.835
Calculus textbook typeset in LaTeX (Project Gutenberg #33283)0.4870.4870.4790.4960.4810.4940.5330.511

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FAQ

How do I preserve footnotes when converting a PDF to EPUB?

To preserve footnotes, the converter has to recognise them as notes and link each one from its call in the text, instead of leaving them as small text in the middle of the book. EpubCC writes them as EPUB footnotes linked from the superscript that calls them.