SciencePlots
paperai
SciencePlots | paperai | |
---|---|---|
8 | 19 | |
6,471 | 1,196 | |
- | 1.3% | |
5.9 | 5.9 | |
3 months ago | 5 months ago | |
Python | Python | |
MIT License | Apache License 2.0 |
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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.
0: https://plotnine.readthedocs.io/en/stable/
1: https://github.com/garrettj403/SciencePlots
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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
paperai
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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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Build Personal ChatGPT Using Your Data
https://github.com/neuml/paperai
Disclaimer: I am the author of both
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[P] Parse research papers into structured data
paperai | paperetl
- Show HN: Semantic search and workflows for medical/scientific papers
- Semantic search and workflows for medical/scientific papers
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# Run txtai in native code
action: translate input: txtai executes machine-learning workflows to transform data and build AI-powered semantic search applications. output: txtai exécute des workflows d'apprentissage automatique pour transformer les données et construire des applications de recherche sémantique alimentées par l'IA. action: translate input: Traditional search systems use keywords to find data output: Les systèmes de recherche traditionnels utilisent des mots-clés pour trouver des données action: summary input: https://github.com/neuml/txtai output: txtai executes machine-learning workflows to transform data and build AI-powered semantic search applications. Semantic search applications have an understanding of natural language and identify results that have the same meaning, not necessarily the same keywords. API bindings for JavaScript, Java, Rust and Go. Cloud-native architecture scales out with container orchestration systems (e. g. Kubernetes) action: summary input: https://github.com/neuml/paperai output: paperai is an AI-powered literature discovery and review engine for medical/scientific papers. Paperai was used to analyze the COVID-19 Open Research Dataset (CORD-19) paperai and NeuML have been recognized in the following articles: Cord-19 Kaggle Challenge Awards Machine-Learning Experts Delve Into 47,000 Papers on Coronavirus Family. real 0m22.478s user 0m13.776s sys 0m3.218s
What are some alternatives?
paperetl - 📄 ⚙️ ETL processes for medical and scientific papers
txtai - đź’ˇ All-in-one open-source embeddings database for semantic search, LLM orchestration and language model workflows
dufte - :chart_with_upwards_trend: Minimalistic Matplotlib style
tika-python - Tika-Python is a Python binding to the Apache Tika™ REST services allowing Tika to be called natively in the Python community.
daltonize - Simulate and correct images for dichromatic color blindness
sentence-transformers - Multilingual Sentence & Image Embeddings with BERT
sane_tikz - Reconquer the canvas: beautiful Tikz figures without clunky Tikz code
faiss - A library for efficient similarity search and clustering of dense vectors.
VSCode-LaTeX-Inkscape - ✍️ A way to integrate LaTeX, VS Code, and Inkscape in macOS
scibert - A BERT model for scientific text.
plotly.rs - Plotly for Rust
science-parse - Science Parse parses scientific papers (in PDF form) and returns them in structured form.