Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model
Fuente:
arXiv
Saved in:
| Main Authors: | Tan, Yang, Wang, Ruilin, Wu, Banghao, Hong, Liang, Zhou, Bingxin |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning
by: Tan, Yang, et al.
Published: (2025)
by: Tan, Yang, et al.
Published: (2025)
Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction
by: Tan, Yang, et al.
Published: (2026)
by: Tan, Yang, et al.
Published: (2026)
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)
Self-evolving AI agents for protein discovery and directed evolution
by: Tan, Yang, et al.
Published: (2026)
by: Tan, Yang, et al.
Published: (2026)
Fast and Interpretable Protein Substructure Alignment via Optimal Transport
by: Wang, Zhiyu, et al.
Published: (2025)
by: Wang, Zhiyu, et al.
Published: (2025)
ProtSolM: Protein Solubility Prediction with Multi-modal Features
by: Tan, Yang, et al.
Published: (2024)
by: Tan, Yang, et al.
Published: (2024)
RadDiff: Retrieval-Augmented Denoising Diffusion for Protein Inverse Folding
by: Han, Jin, et al.
Published: (2025)
by: Han, Jin, et al.
Published: (2025)
Integrating Chain-of-Thought and Retrieval Augmented Generation Enhances Rare Disease Diagnosis from Clinical Notes
by: Wang, Zhanliang, et al.
Published: (2025)
by: Wang, Zhanliang, et al.
Published: (2025)
ProtSAE: Disentangling and Interpreting Protein Language Models via Semantically-Guided Sparse Autoencoders
by: Liu, Xiangyu, et al.
Published: (2025)
by: Liu, Xiangyu, et al.
Published: (2025)
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)
VenusX: Unlocking Fine-Grained Functional Understanding of Proteins
by: Tan, Yang, et al.
Published: (2025)
by: Tan, Yang, et al.
Published: (2025)
Computational Imaging Meets LLMs: Zero-Shot IDH Mutation Prediction in Brain Gliomas
by: Mahmood, Syed Muqeem, et al.
Published: (2025)
by: Mahmood, Syed Muqeem, et al.
Published: (2025)
Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions
by: Sun, Rui, et al.
Published: (2024)
by: Sun, Rui, et al.
Published: (2024)
TemPL: A Novel Deep Learning Model for Zero-Shot Prediction of Protein Stability and Activity Based on Temperature-Guided Language Modeling
by: Tan, Pan, et al.
Published: (2023)
by: Tan, Pan, et al.
Published: (2023)
Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
by: Wu, Lirong, et al.
Published: (2024)
by: Wu, Lirong, et al.
Published: (2024)
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation
by: He, Liang, et al.
Published: (2024)
by: He, Liang, et al.
Published: (2024)
MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction
by: Liu, Yuyan, et al.
Published: (2024)
by: Liu, Yuyan, et al.
Published: (2024)
BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers
by: Xu, Ran, et al.
Published: (2024)
by: Xu, Ran, et al.
Published: (2024)
Knowledge-Driven Agentic Scientific Corpus Distillation Framework for Biomedical Large Language Models Training
by: Xiao, Meng, et al.
Published: (2025)
by: Xiao, Meng, et al.
Published: (2025)
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)
A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding
by: Shen, Yiqing, et al.
Published: (2024)
by: Shen, Yiqing, 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)
Can Large Language Models Replace Data Scientists in Biomedical Research?
by: Wang, Zifeng, et al.
Published: (2024)
by: Wang, Zifeng, et al.
Published: (2024)
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)
MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval
by: Jin, Qiao, et al.
Published: (2023)
by: Jin, Qiao, et al.
Published: (2023)
CellVerse: Do Large Language Models Really Understand Cell Biology?
by: Zhang, Fan, et al.
Published: (2025)
by: Zhang, Fan, et al.
Published: (2025)
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)
A Hybrid Machine Learning Model for Classifying Gene Mutations in Cancer using LSTM, BiLSTM, CNN, GRU, and GloVe
by: Aburass, Sanad, et al.
Published: (2023)
by: Aburass, Sanad, et al.
Published: (2023)
Gene Set Summarization using Large Language Models
by: Joachimiak, Marcin P., et al.
Published: (2023)
by: Joachimiak, Marcin P., et al.
Published: (2023)
VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data
by: Zhang, Liang, et al.
Published: (2025)
by: Zhang, Liang, et al.
Published: (2025)
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)
Distilling and Adapting: A Topology-Aware Framework for Zero-Shot Interaction Prediction in Multiplex Biological Networks
by: Deng, Alana, et al.
Published: (2026)
by: Deng, Alana, et al.
Published: (2026)
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)
A Multimodal Foundation Model to Enhance Generalizability and Data Efficiency for Pan-cancer Prognosis Prediction
by: Zhou, Huajun, et al.
Published: (2025)
by: Zhou, Huajun, et al.
Published: (2025)
ViroGym: Realistic Large-Scale Benchmarks for Evaluating Viral Proteins
by: Zhou, Yichen, et al.
Published: (2026)
by: Zhou, Yichen, et al.
Published: (2026)
Prompting Decision Transformers for Zero-Shot Reach-Avoid Policies
by: Li, Kevin, et al.
Published: (2025)
by: Li, Kevin, et al.
Published: (2025)
Training Compute-Optimal Protein Language Models
by: Cheng, Xingyi, et al.
Published: (2024)
by: Cheng, Xingyi, et al.
Published: (2024)
PUMA: Discovery of Protein Units via Mutation-Aware Merging
by: Suyunu, Burak, et al.
Published: (2025)
by: Suyunu, Burak, et al.
Published: (2025)
NaNa and MiGu: Semantic Data Augmentation Techniques to Enhance Protein Classification in Graph Neural Networks
by: Lan, Yi-Shan, et al.
Published: (2024)
by: Lan, Yi-Shan, et al.
Published: (2024)
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health
by: Tian, Shubo, et al.
Published: (2023)
by: Tian, Shubo, et al.
Published: (2023)
Similar Items
-
VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning
by: Tan, Yang, et al.
Published: (2025) -
Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction
by: Tan, Yang, et al.
Published: (2026) -
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?
by: Tan, Yang, et al.
Published: (2024) -
Self-evolving AI agents for protein discovery and directed evolution
by: Tan, Yang, et al.
Published: (2026) -
Fast and Interpretable Protein Substructure Alignment via Optimal Transport
by: Wang, Zhiyu, et al.
Published: (2025)