SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation
Fuente:
arXiv
Saved in:
| Main Authors: | He, Liang, Jin, Peiran, Min, Yaosen, Xie, Shufang, Wu, Lijun, Qin, Tao, Liang, Xiaozhuan, Gao, Kaiyuan, Jiang, Yuliang, Liu, Tie-Yan |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
by: Pei, Qizhi, et al.
Published: (2024)
by: Pei, Qizhi, et al.
Published: (2024)
Multi-scale Graph Autoregressive Modeling: Molecular Property Prediction via Next Token Prediction
by: Jiang, Zhuoyang, et al.
Published: (2026)
by: Jiang, Zhuoyang, et al.
Published: (2026)
MIN: Multi-channel Interaction Network for Drug-Target Interaction with Protein Distillation
by: Li, Shuqi, et al.
Published: (2024)
by: Li, Shuqi, et al.
Published: (2024)
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)
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
by: Xie, Jiaqing, et al.
Published: (2024)
by: Xie, Jiaqing, et al.
Published: (2024)
Co-Enrichment of Proteins in Extracellular Vesicles
by: Shen, Molly L., et al.
Published: (2023)
by: Shen, Molly L., et al.
Published: (2023)
Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
by: Reilly, Charles B
Published: (2026)
by: Reilly, Charles B
Published: (2026)
ProtT-Affinity: Sequence-Based Protein-Protein Binding Affinity Prediction Using ProtT5 Embeddings
by: Lou, Hongfu
Published: (2025)
by: Lou, Hongfu
Published: (2025)
Ankh3: Multi-Task Pretraining with Sequence Denoising and Completion Enhances Protein Representations
by: Alsamkary, Hazem, et al.
Published: (2025)
by: Alsamkary, Hazem, 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)
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)
Deep Learning Model for Amyloidogenicity Prediction using a Pre-trained Protein LLM
by: Yagoub, Zohra, et al.
Published: (2025)
by: Yagoub, Zohra, et al.
Published: (2025)
Greater than the Sum of Its Parts: Building Substructure into Protein Encoding Models
by: Calef, Robert, et al.
Published: (2025)
by: Calef, Robert, et al.
Published: (2025)
PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
by: Mahbub, Sazan, et al.
Published: (2025)
by: Mahbub, Sazan, et al.
Published: (2025)
ProT-GFDM: A Generative Fractional Diffusion Model for Protein Generation
by: Liang, Xiao, et al.
Published: (2025)
by: Liang, Xiao, et al.
Published: (2025)
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)
FoldSAE: Learning to Steer Protein Folding Through Sparse Representations
by: Zarzecki, Wojciech, et al.
Published: (2025)
by: Zarzecki, Wojciech, et al.
Published: (2025)
Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
by: Lim, Hocheol, et al.
Published: (2025)
by: Lim, Hocheol, et al.
Published: (2025)
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein
by: Chen, Bo, et al.
Published: (2024)
by: Chen, Bo, et al.
Published: (2024)
Limitations of Sequence-Based Protein Representations for Parkinson's Disease Classification: A Leakage-Free Benchmark
by: Núñez-Prado, César Jesús, et al.
Published: (2026)
by: Núñez-Prado, César Jesús, et al.
Published: (2026)
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)
A Novel Framework for Multi-Modal Protein Representation Learning
by: Zheng, Runjie, et al.
Published: (2025)
by: Zheng, Runjie, et al.
Published: (2025)
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)
Co-Generative De Novo Functional Protein Design
by: Chen, Xinrui, et al.
Published: (2026)
by: Chen, Xinrui, et al.
Published: (2026)
VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design
by: Seo, Hyunjin, et al.
Published: (2026)
by: Seo, Hyunjin, et al.
Published: (2026)
Fast and Accurate Blind Flexible Docking
by: Zhang, Zizhuo, et al.
Published: (2025)
by: Zhang, Zizhuo, et al.
Published: (2025)
Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS-CoV-2
by: Wang, Anyou
Published: (2021)
by: Wang, Anyou
Published: (2021)
Large Language Model is Secretly a Protein Sequence Optimizer
by: Wang, Yinkai, et al.
Published: (2025)
by: Wang, Yinkai, et al.
Published: (2025)
Linguistic Laws Meet Protein Sequences: A Comparative Analysis of Subword Tokenization Methods
by: Suyunu, Burak, et al.
Published: (2024)
by: Suyunu, Burak, et al.
Published: (2024)
SeqProFT: Sequence-only Protein Property Prediction with LoRA Finetuning
by: Zhang, Shuo, et al.
Published: (2024)
by: Zhang, Shuo, et al.
Published: (2024)
LiveProteinBench: A Contamination-Free Benchmark for Assessing Models' Specialized Capabilities in Protein Science
by: Rong, Dingyi, et al.
Published: (2025)
by: Rong, Dingyi, 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)
Protein design and RNA design: Perspectives
by: Xi Chen, et al.
Published: (2025)
by: Xi Chen, et al.
Published: (2025)
Seq2Bind Webserver for Decoding Binding Hotspots directly from Sequences using Fine-Tuned Protein Language Models
by: Ma, Xiang, et al.
Published: (2025)
by: Ma, Xiang, et al.
Published: (2025)
Twin Peaks: Dual-Head Architecture for Structure-Free Prediction of Protein-Protein Binding Affinity and Mutation Effects
by: Dey, Supantha, et al.
Published: (2025)
by: Dey, Supantha, et al.
Published: (2025)
Clustering for Protein Representation Learning
by: Quan, Ruijie, et al.
Published: (2024)
by: Quan, Ruijie, et al.
Published: (2024)
DANCE: Deep Learning-Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images
by: Murad, Taslim, et al.
Published: (2024)
by: Murad, Taslim, et al.
Published: (2024)
Scaling Up ESM2 Architectures for Long Protein Sequences Analysis: Long and Quantized Approaches
by: de Oliveira, Gabriel Bianchin, et al.
Published: (2025)
by: de Oliveira, Gabriel Bianchin, et al.
Published: (2025)
Identification of Capture Phases in Nanopore Protein Sequencing Data Using a Deep Learning Model
by: Martin, Annabelle, et al.
Published: (2025)
by: Martin, Annabelle, et al.
Published: (2025)
XAI-Driven Deep Learning for Protein Sequence Functional Group Classification
by: Chakraborty, Pratik, et al.
Published: (2025)
by: Chakraborty, Pratik, et al.
Published: (2025)
Similar Items
-
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
by: Pei, Qizhi, et al.
Published: (2024) -
Multi-scale Graph Autoregressive Modeling: Molecular Property Prediction via Next Token Prediction
by: Jiang, Zhuoyang, et al.
Published: (2026) -
MIN: Multi-channel Interaction Network for Drug-Target Interaction with Protein Distillation
by: Li, Shuqi, et al.
Published: (2024) -
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?
by: Tan, Yang, et al.
Published: (2024) -
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
by: Xie, Jiaqing, et al.
Published: (2024)