Paper Siphon

Paper Siphon — PDF to Markdown

Convert academic PDFs into clean Markdown using paper-siphon. Runs via uvx — no installation needed.

Quick Start

# Local PDF
uvx paper-siphon paper.pdf

# Remote PDF (e.g. arXiv)
uvx paper-siphon https://arxiv.org/pdf/1706.03762.pdf

# Custom output path
uvx paper-siphon paper.pdf -o paper-notes.md

By default, output is written to the same filename with a .md extension (e.g. paper.pdf → paper.md).

Choosing the Right Extraction Approach

Paper Siphon has multiple extraction pipelines. Pick the right one based on the paper's complexity.

Default pipeline (Docling-based)

Best for: most papers — standard single/double-column text, simple tables, no heavy math.

uvx paper-siphon paper.pdf

This is the fastest option. It uses Docling to parse PDF structure, strips margin line numbers (common in journal proofs), and normalizes whitespace. Start here — it handles the majority of papers well.

VLM pipeline (--vlm)

Best for: papers with complex layouts — multi-column figures interleaved with text, unusual formatting, scanned documents, or when the default pipeline produces garbled output.

uvx paper-siphon --vlm paper.pdf

This uses a vision-language model to interpret page images directly. It is significantly slower but handles visual complexity that pure text extraction misses. Use this when:

• The default output has mangled paragraphs or missing sections
• The paper has complex figure/table/text interleaving
• The PDF is a scan rather than born-digital

On Apple Silicon (M-series), this automatically uses MLX acceleration. To disable it:

uvx paper-siphon --vlm --no-mlx paper.pdf

To use the VLM pipeline with MLX dependencies explicitly included:

uvx --with 'paper-siphon[mlx]' paper-siphon --vlm paper.pdf

Formula enrichment (--enrich-formula)

Best for: nudging the default pipeline's math when you want to stay on the fast text-extraction path.

uvx paper-siphon --enrich-formula paper.pdf

This post-processes the default pipeline's extracted math expressions for better fidelity. Warning: resource-intensive — only enable when the paper's math content is important for the task at hand.

For genuinely math-heavy papers, prefer --vlm. In our backend benchmark the default (Docling) pipeline frequently drops display equations (emitting formula-not-decoded), scoring far lower on math than the VLM backends, which read equations off the page image as LaTeX. --enrich-formula improves the default path but does not close that gap.

Decision guide

Rule of thumb: try the default pipeline first. Escalate to --vlm if the output is garbled or incomplete, or if the paper is math-heavy — the default pipeline tends to drop display equations, and the VLM path reads them off the page far more reliably.

CLI Reference

uvx paper-siphon [OPTIONS] INPUT

Input Formats

• Local PDF files: uvx paper-siphon ./downloads/paper.pdf
• Remote URLs: uvx paper-siphon https://arxiv.org/pdf/1706.03762.pdf

For arXiv, use the /pdf/ URL (not /abs/). For example:

• Correct: https://arxiv.org/pdf/1706.03762.pdf
• Wrong: https://arxiv.org/abs/1706.03762

Common Workflows

Download and read a paper someone linked

1. Extract the PDF:

   uvx paper-siphon https://arxiv.org/pdf/1706.03762.pdf -o attention.md
   

2. Read the resulting Markdown file to answer questions or summarize.

Batch-convert a folder of PDFs

for f in papers/*.pdf; do uvx paper-siphon "$f"; done

Combine with scholar-search

1. Find a paper with scholar-search skill
2. Get the PDF URL from the search results (look for arXiv or open-access links)
3. Convert to Markdown:

   uvx paper-siphon https://arxiv.org/pdf/<id>.pdf -o paper.md
   

When to Use

Use this skill when:

• You encounter a PDF of a paper (local or URL) and need to read its contents
• A user shares a PDF link and asks about its content
• You need to extract text from an academic paper for summarization, analysis, or reference
• A user asks you to "download", "read", "extract", or "convert" a paper PDF
• You need to work with paper content that is only available as PDF