Julius Cathalina's Projects
A tool for retrosynthetic planning
Base16 for Vim
A personal project entailing a remake of Daniel Lowe's code for chemical reaction extraction from (USPTO) patent application and grants, written in Rust.
Covariance Data Frames for Predictive M/EEG Pipelines
My configuration files
De Novo Design of Drug Molecule by Pareto-based Multi-Objective Reinforcement Learning in Polypharmacology
A reduced and simplified version of the deep reinforcement learning-based drug molecule generator, DrugEx created by Xuhan Liu. Created to facilitate experimentation and expansion.
Python tools for standardizing drug names to generic names.
Repository for a project on standardizing drug name entries in spontaneous reporting system databases.
GFlowNet related training and environment code
Generative Flow Networks
A polars based fork of Denis Engemann's coffeine library implementing covariance dataframes for predictive M/EEG pipelines.
A launch point for your personal nvim configuration
A Docker Compose template that builds a interactive development environment for PySpark with Jupyter Lab, MinIO as object storage, Hive Metastore, Trino and Kafka
Blazing fast Neovim config providing solid defaults and a beautiful UI, enhancing your neovim experience.
Text mining of chemical reactions
Multi-target de novo molecular generator conditioned on AlphaFold latent embeddings.
Rust bindings for the C++ API of RDKit.
Rust wrapper for the RDKit using CFFI
A collection of deep reinforcement learning-based & GFlowNet drug molecule generators focused on generation of molecules using Graphs/SELFIES guided by modern retrosynthesis tools to increase synthetic accessibility of de-novo designed drugs.
RXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/content/7/15/eabe4166).
A Rust port of Self-Referencing Embedded Strings (SELFIES), for learning purposes.
Modeling, simulation and analysis of Boolean networks applied to Systems Pharmacology.
nothing to see here.
GFlowNet library
Repo for the uspto downloader util to automatically and asynchronously (optional) download uspto files for data collection purposes.
The ultimate Vim configuration (vimrc)