Xin Dai's repositories
alphafold
Open source code for AlphaFold.
Ca-Backbone-Prediction
Deep Learning for Ca Backbone Prediction from High Resolution CryoEM Data
deepEMhancer
Deep learning for cryo-EM maps post-processing
DeepSurvivalMachines
Deep Survival Machines - Fully Parametric Survival Regression
DPIR
Plug-and-Play Image Restoration with Deep Denoiser Prior (IEEE TPAMI 2021) (PyTorch)
EM-GAN
EM-GAN is a computational tool, which enables capturing protein structure information from cryo-EM maps more effectively than raw maps. It is based on 3D deep learning. It is aimed to help protein structure modeling from cryo-EM maps.
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
FIDDLE
FlexIble Data-Driven pipeLinE – a preprocessing pipeline that transforms structured EHR data into feature vectors to be used with ML algorithms. https://doi.org/10.1093/jamia/ocaa139
GeoDiff
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
gradient-boosting-survival-embeddings
Improving gradient boosting survival analysis with embeddings and debiased estimators
GRU-D
Gated Recurrent Unit with a Decay mechanism for Multivariate Time Series with Missing Values
Kaggle-PANDA-1st-place-solution
1st place solution for the Kaggle PANDA Challenge
LMetalSite
MetalSite: alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
mimic3-benchmarks
Python suite to construct benchmark machine learning datasets from the MIMIC-III clinical database.
NAFNet
The state-of-the-art image restoration model without nonlinear activation functions.
NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
ngboost
Natural Gradient Boosting for Probabilistic Prediction
OmegaFold
OmegaFold Release Code
openfold
Trainable PyTorch reproduction of AlphaFold 2
ProteinMPNN
Code for the ProteinMPNN paper
RepLKNet-pytorch
Scaling Up Your Kernels to 31x31: Revisiting Large Kernel Design in CNNs (CVPR 2022)
SiamDiff
Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
StageNet
Source code for StageNet: Stage-Aware Neural Networks for Health Risk Prediction
VIME
Codebase for VIME: Extending the Success of Self- and Semi-supervised Learning to Tabular Domain - NeurIPS 2020