Niksa Praljak's repositories
RefineGNNplus
Make innovations onto the RefineGNN model. For example, one innovation is to replace the GRU used for the framework region with a Transformer encoder.
LatentCondDDPM
Final project for fundamentals of deep learning at Toyota Tech. Institute Chicago with Professor David A. McAllester.
ProtWaveVAE_model
A fully featured autoregressive (AR) Variational autoencoder (VAE) using a WaveNet decoder for data-driven protein design (ProtWave-VAE).
atom3d
Atomic tasks on molecules in three dimensions
bioformats
Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
CV
Curriculum Vitae (Version: November 5th, 2022)
gitignore
A collection of useful .gitignore templates
keras_lstm_vae
Keras implementation of LSTM Variational Autoencoder
lightning
Build and train PyTorch models and connect them to the ML lifecycle using Lightning App templates, without handling DIY infrastructure, cost management, scaling, and other headaches.
Auto-GPT
An experimental open-source attempt to make GPT-4 fully autonomous.
chemcrow-public
Chemcrow
galai
Model API for GALACTICA
GearNet
GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
llama-qrlhf
Implementation of the Llama architecture with RLHF + Q-learning
MatLab-Video-2-Gif
Converts videos to gif directly frame by frame (modification to Moshe Lindner's code)
Minimalist_Codon_Translation
Hat tip to Bryan Andrews, the most minimalist code for reverse aa translation and specie codon optimization.
PraljakReps.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
pySCA_temp
Python3 implementation of Statistical Coupling Analysis (SCA)
TMalign_for_design_predictions
Tmalign algorithm for high-throughput TMscore retrieval for a library of design sequences with structure predictions
tmux
tmux source code
toolformer-pytorch
Implementation of Toolformer, Language Models That Can Use Tools, by MetaAI
tutorials
PyTorch tutorials.