paperetl
SciencePlots
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| paperetl | SciencePlots | |
|---|---|---|
| 12 | 8 | |
| 316 | 6,407 | |
| 7.9% | - | |
| 6.3 | 5.9 | |
| 5 months ago | 2 months ago | |
| Python | Python | |
| Apache License 2.0 | MIT License |
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paperetl
- Show HN: Open-source Rule-based PDF parser for RAG
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Oracle of Zotero: LLM QA of Your Research Library
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.
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[P] Parse research papers into structured data
paperai | paperetl
- Parse research papers into a structured dataset
- ETL for medical and scientific papers
- Show HN: ETL for Medical and Scientific Papers
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Seeking Advice: How to extract Abstract from scientific journals (.pdfs) 10k+.
paperai and paperetl are a set of projects to consider for this task.
- paperetl: ETL processes for medical and scientific papers
SciencePlots
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Lets-Plot: An open-source plotting library by JetBrains
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.
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Resources for data visualization (free & paid) for scientific publications
What is it about matplotlib that you object to? If it’s just the number of commands needed to get it right, you can look at something like https://github.com/garrettj403/SciencePlots that will get you most of the way.
- Matplotlib Styles for Scientific Plotting
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LovelyPlots
I know a lot of academics that do, but wouldn't recommend it personally. Also, there is https://github.com/garrettj403/SciencePlots
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Struggling with Python
Seeing as you're doing bioinformatics, I recommend Juptyer notebooks and pandas if you're not already. The pandas documentation is very extensive which is helpful. I also recommend SciencePlots for publication quality plots.
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Using Python (and matplotlib) for plotting in academia
I have also found SciencePlots. Should I use this in addition to cmcrameri?
- Matplotlib style library for Scientific plots
What are some alternatives?
tika-python - Tika-Python is a Python binding to the Apache Tika™ REST services allowing Tika to be called natively in the Python community.
paperai - 📄 🤖 Semantic search and workflows for medical/scientific papers
ciscoconfparse - Parse, Audit, Query, Build, and Modify Cisco IOS-style configurations.
dufte - :chart_with_upwards_trend: Minimalistic Matplotlib style
daltonize - Simulate and correct images for dichromatic color blindness
rdm - Our regulatory documentation manager. Streamlines 62304, 14971, and 510(k) documentation for software projects.
VSCode-LaTeX-Inkscape - ✍️ A way to integrate LaTeX, VS Code, and Inkscape in macOS
dagster - An orchestration platform for the development, production, and observation of data assets.
sane_tikz - Reconquer the canvas: beautiful Tikz figures without clunky Tikz code
science-parse - Science Parse parses scientific papers (in PDF form) and returns them in structured form.
plotly.rs - Plotly for Rust