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Simple and efficient pytorch-native transformer text generation in <1000 LOC of python.
A generalized computational framework for biomolecular modeling.
A comprehensive JAX/NNX library for diffusion and flow matching generative algorithms, featuring DiT (Diffusion Transformer) and its variants as the primary backbone with support for ImageNet train…
A partially latent flow matching model for the joint generation of a protein’s amino acid sequence and full atomistic structure, including both the backbone and side chain.
The Family of Diffusion Protein Language Models (DPLM)
IntelliFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction.
Protein Engineering via Exploration of an Energy Landscape
Proteina is a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture.
A standardized protein design benchmark for motif-scaffolding problems
[ICLR 2025 Oral] Block Diffusion: Interpolating Between Autoregressive and Diffusion Language Models
[NeurIPS 2024]OmniTokenizer: one model and one weight for image-video joint tokenization.
A trainable PyTorch reproduction of AlphaFold 3.
Fast protein backbone generation with SE(3) flow matching.
A PyTorch implementation of MAGE: MAsked Generative Encoder to Unify Representation Learning and Image Synthesis
Protein structure datasets for machine learning.
Pretrainable geometric graph neural network for antibody affinity maturation
🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2025).
Protein Ligand INteraction Dataset and Evaluation Resource
Implementation of Alphafold 3 from Google Deepmind in Pytorch
Vabs-Net: Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains
🧬 Advanced hybrid language model for directed protein evolution. (NeurIPS 2024)
Official code for Score-Based Generative Modeling through Stochastic Differential Equations (ICLR 2021, Oral)
Elucidating the Design Space of Diffusion-Based Generative Models (EDM)
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
Multi-Scale Representation Learning on Proteins (NeurIPS 2021)