:: Library Catalog

Cover Image

Saved in:

Bibliographic Details
Main Authors:	Dilip, Rohit, Zhang, Evan, Varshney, Ayush, Van Valen, David
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Biomolecules
Online Access:	https://arxiv.org/abs/2510.00351
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Adaptive Protein Tokenization
by: Dilip, Rohit, et al.
Published: (2026)

Interpreting and Steering Protein Language Models through Sparse Autoencoders
by: Garcia, Edith Natalia Villegas, et al.
Published: (2025)

Reverse Distillation: Consistently Scaling Protein Language Model Representations
by: Catrina, Darius, et al.
Published: (2026)

Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
by: Parsan, Nithin, et al.
Published: (2025)

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
by: Wu, Lirong, et al.
Published: (2024)

AlphaFold Meets Flow Matching for Generating Protein Ensembles
by: Jing, Bowen, et al.
Published: (2024)

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation
by: Huguet, Guillaume, et al.
Published: (2024)

Token-Mol 1.0: Tokenized drug design with large language model
by: Wang, Jike, et al.
Published: (2024)

Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
by: Zhou, Xiangxin, et al.
Published: (2025)

FoldToken: Learning Protein Language via Vector Quantization and Beyond
by: Gao, Zhangyang, et al.
Published: (2024)

ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings
by: Kong, Zitai, et al.
Published: (2025)

Mechanisms of AI Protein Folding in ESMFold
by: Lu, Kevin, et al.
Published: (2026)

Tokenizing Loops of Antibodies
by: Fang, Ada, et al.
Published: (2025)

Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
by: Dunn, Ian, et al.
Published: (2023)

Structure-Informed Protein Language Model
by: Zhang, Zuobai, et al.
Published: (2024)

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction
by: Tan, Cheng, et al.
Published: (2024)

FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generation
by: Dunn, Ian, et al.
Published: (2025)

Attention Based Molecule Generation via Hierarchical Variational Autoencoder
by: Sivanesan, Divahar
Published: (2024)

Flexibility-Conditioned Protein Structure Design with Flow Matching
by: Viliuga, Vsevolod, et al.
Published: (2025)

ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design
by: Ma, Yiming, et al.
Published: (2024)

Open-Source Protein Language Models for Function Prediction and Protein Design
by: Pandi, Shivasankaran Vanaja, et al.
Published: (2024)

Automated Neuron Labelling Enables Generative Steering and Interpretability in Protein Language Models
by: Banerjee, Arjun, et al.
Published: (2025)

Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction
by: Yu, Ziyang, et al.
Published: (2024)

Hierarchical Multi-Label Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms
by: Liu, Shiyi, et al.
Published: (2025)

ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
by: Halfon, Matan, et al.
Published: (2024)

ProteinGuide: On-the-fly property guidance for protein sequence generative models
by: Xiong, Junhao, et al.
Published: (2025)

Multi-Scale Representation Learning for Protein Fitness Prediction
by: Zhang, Zuobai, et al.
Published: (2024)

Steering Protein Language Models
by: Huang, Long-Kai, et al.
Published: (2025)

Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
by: Qiu, Jiahao, et al.
Published: (2024)

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction
by: Alsamkary, Hazem, et al.
Published: (2025)

Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation
by: Shah, Aayush, et al.
Published: (2024)

Exploring Discrete Flow Matching for 3D De Novo Molecule Generation
by: Dunn, Ian, et al.
Published: (2024)

ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
by: Zhang, Zuobai, et al.
Published: (2024)

Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2
by: Lin, Yeqing, et al.
Published: (2024)

Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics
by: Tang, Haocheng, et al.
Published: (2026)

Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering
by: Jiao, Shujian, et al.
Published: (2024)

Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation
by: Dunn, Ian, et al.
Published: (2024)

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates
by: Gao, Kaiyuan, et al.
Published: (2024)

Protein Inverse Folding From Structure Feedback
by: Xu, Junde, et al.
Published: (2025)

Peptide Sequencing Via Protein Language Models
by: Pham, Thuong Le Hoai, et al.
Published: (2024)