Top 6 Python scientific-paper Projects

SciencePlots

8 6,407 5.9 Python

Matplotlib styles for scientific plotting

Project mention: Lets-Plot: An open-source plotting library by JetBrains | news.ycombinator.com | 2023-07-15

This seems quite similar to plotnine [0], which also provides a grammar of graphics interface for Python. That said, I love ggplot and I can't wait to use this in my research! I hope we can port/re-implement ggthemes, scientificplots [1], and other ggplot libraries for lets-plot.
0: https://plotnine.readthedocs.io/en/stable/
1: https://github.com/garrettj403/SciencePlots

scibert

2 1,402 0.0 Python

A BERT model for scientific text.
InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
paperai

19 1,189 5.9 Python

📄 🤖 Semantic search and workflows for medical/scientific papers

Project mention: Oracle of Zotero: LLM QA of Your Research Library | news.ycombinator.com | 2023-11-26

Nice project!
I've spent quite a lot of time in the medical/scientific literature space. With regards to LLMs, specifically RAG, how the data is chunked is quite important. With that, I have a couple projects that might be beneficial additions.
paperetl (https://github.com/neuml/paperetl) - supports parsing arXiv, PubMed and integrates with GROBID to handle parsing metadata and text from arbitrary papers.
paperai (https://github.com/neuml/paperai) - builds embeddings databases of medical/scientific papers. Supports LLM prompting, semantic workflows and vector search. Built with txtai (https://github.com/neuml/txtai).
While arbitrary chunking/splitting can work, I've found that integrating parsing that has knowledge of medical/scientific paper structure increases the overall accuracy and experience of downstream applications.

paperetl

12 315 6.3 Python

📄 ⚙️ ETL processes for medical and scientific papers

Project mention: Show HN: Open-source Rule-based PDF parser for RAG | news.ycombinator.com | 2024-01-23

findpapers

1 177 4.0 Python

Findpapers: A tool for helping researchers who are looking for related works

Project mention: Findpapers | news.ycombinator.com | 2023-12-31

abstracts-search

1 66 6.0 Python

Semantic search engine indexing 95 million academic publications

Project mention: [P] abstracts-search: A semantic search engine indexing 95 million academic publications | /r/MachineLearning | 2023-05-15

I'm releasing the entire project as open code and open data. All ~600 lines of Python, 69 GB in embeddings, and raw faiss index can be found through https://github.com/colonelwatch/abstracts-search

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020). The latest post mention was on 2024-01-23.