Poor Markdown conversion quality for academic paper

Description

I used MarkItDown to convert the following paper from PDF to Markdown:

• PDF: [AutoSOTA](https://arxiv.org/pdf/2604.05550)
• Converted Markdown: [AutoSOTA.md](https://github.com/user-attachments/files/30193595/AutoSOTA.md)

However, the generated Markdown has very poor formatting and structure. For example, the reading order, headings, equations, tables, and multi-column content are not preserved correctly, making the output difficult to read and use.

Is this an expected limitation when converting academic papers with complex layouts, or could this indicate an issue with the conversion process?

Expected behavior

The converted Markdown should preserve the document structure and reading order as accurately as possible, including:

• Section headings
• Paragraph order
• Mathematical equations
• Tables and figures
• Multi-column layouts

Actual behavior

The generated Markdown contains significant formatting and structural issues, resulting in content that is difficult to read.

Start by reproducing the conversion using the linked AutoSOTA PDF and compare the result with AutoSOTA.md. Investigate the conversion path responsible for reading order, headings, equations, tables, figures, and multi-column content; done means the issue is either resolved with improved structure or documented as an established limitation.