AlphaFold Meets Flow Matching for Generating Protein Ensembles - bjing2016/alphaflow

Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel antibodies to bind a specific epitope on a target. Instead, antibody discovery...

[NeurIPS'22] Tokenized Graph Transformer (TokenGT), in PyTorch - jw9730/tokengt

gRNAde: Geometric Deep Learning for RNA Design. Contribute to chaitjo/geometric-rna-design development by creating an account on GitHub.

Pretraining on a large number of unlabeled 3D molecules has showcased superiority in various scientific applications. However, prior efforts typically focus on pretraining models on a specific...

The source code of "Equivariant Spatio-Temporal Attentive Graph Networks to Simulate Physical Dynamics" - ManlioWu/ESTAG

Contribute to GFNOrg/conf-gfn development by creating an account on GitHub.

Flow matching is a more general method than diffusion and serves as the basis for models like Stable Diffusion 3.Paper: https://arxiv.org/abs/2210.02747Abstr...

Valence Labs is a research engine within Recursion committed to advancing the frontier of AI in drug discovery. Learn more about our open roles: https://www....

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations (EMNLP 2023) - QizhiPei/BioT5

Proteomics has been revolutionized by large pre-trained protein language models, which learn unsupervised representations from large corpora of sequences. The parameters of these models are then...

Accurately mapping protein-protein interactions (PPIs) is critical for elucidating cellular functions and has significant implications for health and disease. Conventional experimental approaches,...

Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials - mir-group/allegro

Recent research, such as BitNet, is paving the way for a new era of 1-bit Large Language Models (LLMs). In this work, we introduce a 1-bit LLM variant, namely BitNet b1.58, in which every single...

Introduction to Riemannian Manifolds (Graduate Texts in Mathematics)

Code for AAAI24 paper Text-Guided Molecule Generation with Diffusion Language Model - GitHub - Deno-V/tgm-dlm: Code for AAAI24 paper Text-Guided Molecule Generation with Diffusion Language Model

Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer) - flyark/AFM-LIS

Learning to represent and simulate the dynamics of physical systems is a crucial yet challenging task. Existing equivariant Graph Neural Network (GNN) based methods have encapsulated the symmetry...

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in...

Accurately mapping protein-protein interactions (PPIs) is critical for elucidating cellular functions and has significant implications for health and disease. Conventional experimental approaches,...

Most language models (LMs) are trained and applied in an autoregressive left-to-right fashion, assuming that the next token only depends on the preceding ones. However, this assumption ignores the...

Accurately mapping protein-protein interactions (PPIs) is critical for elucidating cellular functions and has significant implications for health and disease. Conventional experimental approaches,...

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in...

Moderna deployed ChatGPT Enterprise to thousands of employees, seeing remarkable adoption across the company. They’ve created hundreds of custom versions of ...

Machine learning is frequently listed among the most promising applications for quantum computing. This is in fact a curious choice: Today's machine learning algorithms are notoriously powerful in...

Contribute to oxpig/binding-sites development by creating an account on GitHub.

Evolutionary velocity with protein language models - brianhie/evolocity

Bioelectric networks as targets for regenerative medicine

Boltzmann Generators and Normalizing Flows in PyTorch - noegroup/bgflow

In this work, we discuss building performant Multimodal Large Language Models (MLLMs). In particular, we study the importance of various architecture components and data choices. Through careful...

Nature Communications - Most globular proteins are selected to fold into one unique structure. Schafer and Porter demonstrate that some proteins are selected to assume two stable folds; they...

Token-free language models learn directly from raw bytes and remove the inductive bias of subword tokenization. Operating on bytes, however, results in significantly longer sequences. In this...

(Unofficial) GET for proteins. Contribute to amelie-iska/u_GET development by creating an account on GitHub.

Machine learning is frequently listed among the most promising applications for quantum computing. This is in fact a curious choice: Today's machine learning algorithms are notoriously powerful in...

Implementation of Nougat Neural Optical Understanding for Academic Documents - facebookresearch/nougat

Transformer-based Large Language Models (LLMs) have become a fixture in modern machine learning. Correspondingly, significant resources are allocated towards research that aims to further advance...

Transformer-based Large Language Models (LLMs) have become a fixture in modern machine learning. Correspondingly, significant resources are allocated towards research that aims to further advance...