Protify 0.0.2

Low code chemcial property prediction

Protify

A low code solution for computationally predicting the properties of chemicals.
Explore the docs »

View Demo · Report Bug · Request Feature

Table of Contents

1. About The Project
   • Why Protify?
   • Current Key Features
   • Support Protify's Development
2. Getting Started
   • Installation
3. Usage
4. Contributing
5. Built With
6. License
7. Contact
8. Cite

About The Project

Protify is an open source platform designed to simplify and democratize workflows for chemical language models. With Protify, deep learning models can be trained to predict chemical properties at the click of a button, without requiring extensive coding knowledge or computational resources.

Why Protify?

• Benchmark multiple models efficiently: Need to evaluate 10 different protein language models against 15 diverse datasets with publication-ready figures? Protify makes this possible without writing a single line of code.
• Flexible for all skill levels: Build custom pipelines with code or use our no-code interface depending on your needs and expertise.
• Accessible computing: No GPU? No problem. Synthyra offers precomputed embeddings for many popular datasets, which Protify can download for analysis with scikit-learn on your laptop.
• Cost-effective solutions: The upcoming Synthyra API integration will offer affordable GPU training options, while our Colab notebook provides an accessible entry point for GPU-reliant analysis.

Protify is currently in beta. We're actively working to enhance features and documentation to meet our ambitious goals.

Current Key Features

• Multiple interfaces: Run experiments via an intuitive GUI, CLI, or prepared YAML files
• Efficient embeddings: Leverage fast and efficient embeddings from ESM2 and ESMC via FastPLMs
  • Coming soon: Additional protein, SMILES, SELFIES, codon, and nucleotide language models
• Flexible model probing: Use efficient MLPs for sequence-wise tasks or transformer probes for token-wise tasks
  • Coming soon: Full model fine-tuning, hybrid probing, and LoRA
• Automated model selection: Find optimal scikit-learn models for your data with LazyPredict, enhanced by automatic hyperparameter optimization
  • Coming soon: GPU acceleration
• Complete reproducibility: Every session generates a detailed log that can be used to reproduce your entire workflow
• Publication-ready visualizations: Generate cross-model and dataset comparisons with radar and bar plots, embedding analysis with PCA, t-SNE, and UMAP, and statistically sound confidence interval plots
• Extensive dataset support: Access 25 protein datasets by default, or easily integrate your own local or private datasets
  • Coming soon: Additional protein, SMILES, SELFIES, codon, and nucleotide property datasets
• Advanced interaction modeling: Support for protein-protein interaction datasets
  • Coming soon: Protein-small molecule interaction capabilities

Support Protify's Development

Help us grow by sharing online, starring our repository, or contributing through our bounty program.

(back to top)

Getting Started

Installation

From pip pip install Protify

To get started locally

git clone https://@github.com/Synthyra/Protify.git
cd Protify
python -m pip install -r docs/requirements.txt
git submodule update --init --remote --recursive
cd src/protify

(back to top)

Usage

Examples coming soon.

(back to top)

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

We work with a bounty system. You can find bounties on this page. Contributing bounties will get you listed on the Protify consortium and potentially coauthorship on published papers involving the framework.

Simply open a pull request with the bounty ID in the title to claim one. For additional features not on the bounty list simply use a descriptive title.

For bugs and general suggestions please use GitHub issues.

Top contributors:

(back to top)

Built With

• 
• 
• 
• 
• 
• 
• 
• 
• 
• 

(back to top)

License

Distributed under the Protify License. See LICENSE.md for more information.

(back to top)

Contact

Email: [e-mail]
Website: https://synthyra.com

(back to top)

Cite

If you use this package, please cite the following papers. (Coming soon)