library supporting NLP and CV research on scientific papers

papermage

Setup

conda create -n papermage python=3.9
conda activate papermage
pip install -e '.[dev,predictors,visualizers]'

If you're on MacOSX, you'll also want to run:

conda install poppler

Unit testing

python -m pytest

for latest failed test

python -m pytest --lf --no-cov -n0

for specific test name of class name

python -m pytest -k 'TestPDFPlumberParser' --no-cov -n0

Quick start

1. Create a Document for the first time from a PDF

from papermage.recipes import CoreRecipe

recipe = CoreRecipe()
doc = recipe.run("tests/fixtures/papermage.pdf")

2. Understanding the output: the Document class

What is a Document? At minimum, it is some text, saved under the .symbols field, which is just a <str>. For example:

> doc.symbols
"PaperMage: A Unified Toolkit for Processing, Representing, and\nManipulating Visually-..."

But this library is really useful when you have multiple different ways of segmenting .symbols. For example, segmenting the paper into Pages, and then each page into Rows:

for page in doc.pages:
    print(f'\n=== PAGE: {page.id} ===\n\n')
    for row in page.rows:
        print(row.text)
        
...
=== PAGE: 5 ===

4
Vignette: Building an Attributed QA
System for Scientific Papers
How could researchers leverage papermage for
their research? Here, we walk through a user sce-
nario in which a researcher (Lucy) is prototyping
an attributed QA system for science.
System Design.
Drawing inspiration from Ko
...

This shows two nice aspects of this library:

• Document provides iterables for different segmentations of symbols. Options include things like pages, tokens, rows, sentences, paragraphs, sections, .... Not every Parser will provide every segmentation, though.

• Each one of these segments (in our library, we call them Entity objects) is aware of (and can access) other segment types. For example, you can call page.rows to get all Rows that intersect a particular Page. Or you can call sent.tokens to get all Tokens that intersect a particular Sentence. Or you can call sent.rows to get the Row(s) that intersect a particular Sentence. These indexes are built dynamically when the Document is created and each time a new Entity type is added. In the extreme, as long as those fields are available in the Document, you can write:

for page in doc.pages:
    for paragraph in page.paragraphs:
        for sent in paragraph.sentences:
            for row in sent.rows: 
                ...

You can check which fields are available in a Document via:

> doc.fields
['tokens',
 'rows',
 'pages',
 'words',
 'sentences',
 'blocks',
 'vila_entities',
 'titles',
 'paragraphs',
 'authors',
 'abstracts',
 'keywords',
 'sections',
 'lists',
 'bibliographies',
 'equations',
 'algorithms',
 'figures',
 'tables',
 'captions',
 'headers',
 'footers',
 'footnotes',
 'symbols',
 'images',
 'metadata',
 'entities',
 'relations']

3. Understanding intersection of Entities

Note that Entitys don't necessarily perfectly nest each other. For example, what happens if you run:

for sent in doc.sentences:
    for row in sent.rows:
        print([token.text for token in row.tokens])

Tokens that are outside each sentence can still be printed. This is because when we jump from a sentence to its rows, we are looking for all rows that have any overlap with the sentence. Rows can extend beyond sentence boundaries, and as such, can contain tokens outside that sentence.

Here's another example:

for page in doc.pages:
    print([sent.text for sent in page.sentences])

Sentences can cross page boundaries. As such, adjacent pages may end up printing the same sentence.

But rows and tokens adhere strictly to page boundaries, and thus will not repeat when printed across pages:

for page in doc.pages:
    print([row.text for row in page.rows])
    print([token.text for token in page.tokens])

A key aspect of using this library is understanding how these different fields are defined & anticipating how they might interact with each other. We try to make decisions that are intuitive, but we do ask users to experiment with fields to build up familiarity.

4. What's in an Entity?

Each Entity object stores information about its contents and position:

• .spans: List[Span], A Span is a pointer into Document.symbols (that is, Span(start=0, end=5) corresponds to symbols[0:5]). By default, when you iterate over an Entity, you iterate over its .spans.

• .boxes: List[Box], A Box represents a rectangular region on the page. Each span is associated a Box.

• .metadata: Metadata, A free form dictionary-like object to store extra metadata about that Entity. These are usually empty.

5. How can I manually create my own Document?

A Document is created by stitching together 3 types of tools: Parsers, Rasterizers and Predictors.

• Parsers take a PDF as input and return a Document compared of .symbols and other fields. The example one we use is a wrapper around PDFPlumber - MIT License utility.

• Rasterizers take a PDF as input and return an Image per page that is added to Document.images. The example one we use is PDF2Image - MIT License.

• Predictors take a Document and apply some operation to compute a new set of Entity objects that we can insert into our Document. These are all built in-house and can be either simple heuristics or full machine-learning models.

6. How can I save my Document?

import json
with open('filename.json', 'w') as f_out:
    json.dump(doc.to_json(with_images=True), f_out, indent=4)

will produce something akin to:

{
    "symbols": "PaperMage: A Unified Toolkit for Processing, Representing, an...",
    "entities": {
        "images": [...],
        "rows": [...],
        "tokens": [...],
        "words": [...],
        "blocks": [...],
        "sentences": [...]
    },
    "metadata": {...}
}

Note that Images are serialized to base64 if you include with_images flag. Otherwise, it's left out of JSON serialization by default.

7. How can I load my Document?

These can be used to reconstruct a Document again via:

with open('filename.json') as f_in:
    doc_dict = json.load(f_in)
    doc = Document.from_json(doc_dict)

Note: A common pattern for adding fields to a document is to load in a previously saved document, run some additional Predictors on it, and save the result.

See papermage/predictors/README.md for more information about training custom predictors on your own data.

See papermage/examples/quick_start_demo.ipynb for a notebook walking through some more usage patterns.