Elucidating the Design Space of Multimodal Protein Language Models
Fuente:
arXiv
Saved in:
| Main Authors: | Hsieh, Cheng-Yen, Wang, Xinyou, Zhang, Daiheng, Xue, Dongyu, Ye, Fei, Huang, Shujian, Zheng, Zaixiang, Gu, Quanquan |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
DPLM-2: A Multimodal Diffusion Protein Language Model
by: Wang, Xinyou, et al.
Published: (2024)
by: Wang, Xinyou, et al.
Published: (2024)
ProteinBench: A Holistic Evaluation of Protein Foundation Models
by: Ye, Fei, et al.
Published: (2024)
by: Ye, Fei, et al.
Published: (2024)
Protein Autoregressive Modeling via Multiscale Structure Generation
by: Qu, Yanru, et al.
Published: (2026)
by: Qu, Yanru, et al.
Published: (2026)
Diffusion Language Models Are Versatile Protein Learners
by: Wang, Xinyou, et al.
Published: (2024)
by: Wang, Xinyou, et al.
Published: (2024)
AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design
by: Rahman, Sahil, et al.
Published: (2026)
by: Rahman, Sahil, et al.
Published: (2026)
Beyond Protein Language Models: An Agentic LLM Framework for Mechanistic Enzyme Design
by: Jacob, Bruno, et al.
Published: (2025)
by: Jacob, Bruno, et al.
Published: (2025)
Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models
by: Liang, Po-Yu, et al.
Published: (2024)
by: Liang, Po-Yu, et al.
Published: (2024)
ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design
by: Ge, Yutang, et al.
Published: (2026)
by: Ge, Yutang, et al.
Published: (2026)
ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression
by: Shen, Yuning, et al.
Published: (2025)
by: Shen, Yuning, et al.
Published: (2025)
HMAMP: Hypervolume-Driven Multi-Objective Antimicrobial Peptides Design
by: Wang, Li, et al.
Published: (2024)
by: Wang, Li, et al.
Published: (2024)
Training Compute-Optimal Protein Language Models
by: Cheng, Xingyi, et al.
Published: (2024)
by: Cheng, Xingyi, et al.
Published: (2024)
Annotation-guided Protein Design with Multi-Level Domain Alignment
by: Yuan, Chaohao, et al.
Published: (2024)
by: Yuan, Chaohao, et al.
Published: (2024)
Design Proteins Using Large Language Models: Enhancements and Comparative Analyses
by: Zeinalipour, Kamyar, et al.
Published: (2024)
by: Zeinalipour, Kamyar, et al.
Published: (2024)
Co-Generative De Novo Functional Protein Design
by: Chen, Xinrui, et al.
Published: (2026)
by: Chen, Xinrui, et al.
Published: (2026)
Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models
by: Yazdani-Jahromi, Mehdi, et al.
Published: (2025)
by: Yazdani-Jahromi, Mehdi, et al.
Published: (2025)
Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics
by: Shoghi, Nima, et al.
Published: (2026)
by: Shoghi, Nima, et al.
Published: (2026)
Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins
by: Sinclair, Matthew, et al.
Published: (2025)
by: Sinclair, Matthew, et al.
Published: (2025)
Automated Protein Motif Localization using Concept Activation Vectors in Protein Language Model Embedding Space
by: Shamail, Ahmad, et al.
Published: (2025)
by: Shamail, Ahmad, et al.
Published: (2025)
VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design
by: Seo, Hyunjin, et al.
Published: (2026)
by: Seo, Hyunjin, et al.
Published: (2026)
Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach
by: Gao, Ziqi, et al.
Published: (2026)
by: Gao, Ziqi, et al.
Published: (2026)
Detection of circular permutations by Protein Language Models
by: Hu, Yue, et al.
Published: (2024)
by: Hu, Yue, et al.
Published: (2024)
AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering
by: Liu, Yungeng, et al.
Published: (2024)
by: Liu, Yungeng, et al.
Published: (2024)
ODBO: Bayesian Optimization with Search Space Prescreening for Directed Protein Evolution
by: Cheng, Lixue, et al.
Published: (2022)
by: Cheng, Lixue, et al.
Published: (2022)
Can Large Language Models Design Biological Weapons? Evaluating Moremi Bio
by: Hattoh, Gertrude, et al.
Published: (2025)
by: Hattoh, Gertrude, et al.
Published: (2025)
Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
by: Cao, Hanqun, et al.
Published: (2025)
by: Cao, Hanqun, et al.
Published: (2025)
The Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design
by: Armer, Chase, et al.
Published: (2023)
by: Armer, Chase, et al.
Published: (2023)
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?
by: Tan, Yang, et al.
Published: (2024)
by: Tan, Yang, et al.
Published: (2024)
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design
by: Campbell, Andrew, et al.
Published: (2024)
by: Campbell, Andrew, et al.
Published: (2024)
A Universal Space of Brain Dynamics for Unveiling Cognitive Transitions and Individual Differences
by: Zheng, Ronghua, et al.
Published: (2026)
by: Zheng, Ronghua, et al.
Published: (2026)
Large Language Model is Secretly a Protein Sequence Optimizer
by: Wang, Yinkai, et al.
Published: (2025)
by: Wang, Yinkai, et al.
Published: (2025)
Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries
by: Gu, Chunbin, et al.
Published: (2024)
by: Gu, Chunbin, et al.
Published: (2024)
General Protein Pretraining or Domain-Specific Designs? Benchmarking Protein Modeling on Realistic Applications
by: Yan, Shuo, et al.
Published: (2025)
by: Yan, Shuo, et al.
Published: (2025)
Adaptive Multimodal Protein Plug-and-Play with Diffusion-Based Priors
by: Banerjee, Amartya, et al.
Published: (2025)
by: Banerjee, Amartya, et al.
Published: (2025)
A Text-guided Protein Design Framework
by: Liu, Shengchao, et al.
Published: (2023)
by: Liu, Shengchao, et al.
Published: (2023)
LAMP-PRo: Label-aware Attention for Multi-label Prediction of DNA- and RNA-binding Proteins using Protein Language Models
by: Ghosh, Nimisha, et al.
Published: (2025)
by: Ghosh, Nimisha, et al.
Published: (2025)
A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion
by: Cheng, Chaoran, et al.
Published: (2026)
by: Cheng, Chaoran, et al.
Published: (2026)
Scaling and Data Saturation in Protein Language Models
by: Spinner, Aviv, et al.
Published: (2025)
by: Spinner, Aviv, et al.
Published: (2025)
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen
by: Tan, Cheng, et al.
Published: (2025)
by: Tan, Cheng, et al.
Published: (2025)
Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model
by: Tan, Yang, et al.
Published: (2024)
by: Tan, Yang, et al.
Published: (2024)
Protein Structure Tokenization via Geometric Byte Pair Encoding
by: Sun, Michael, et al.
Published: (2025)
by: Sun, Michael, et al.
Published: (2025)
Similar Items
-
DPLM-2: A Multimodal Diffusion Protein Language Model
by: Wang, Xinyou, et al.
Published: (2024) -
ProteinBench: A Holistic Evaluation of Protein Foundation Models
by: Ye, Fei, et al.
Published: (2024) -
Protein Autoregressive Modeling via Multiscale Structure Generation
by: Qu, Yanru, et al.
Published: (2026) -
Diffusion Language Models Are Versatile Protein Learners
by: Wang, Xinyou, et al.
Published: (2024) -
AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design
by: Rahman, Sahil, et al.
Published: (2026)