From Sentences to Sequences: Rethinking Languages in Biological System
Fuente:
arXiv
Saved in:
| Main Authors: | Liu, Ke, Shen, Shuaike, Chen, Hao |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models
by: He, Haonan, et al.
Published: (2024)
by: He, Haonan, et al.
Published: (2024)
Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
by: Wei, Chen, et al.
Published: (2026)
by: Wei, Chen, et al.
Published: (2026)
COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models
by: Ren, Yuchen, et al.
Published: (2024)
by: Ren, Yuchen, et al.
Published: (2024)
Reinforcement Learning for Sequence Design Leveraging Protein Language Models
by: Subramanian, Jithendaraa, et al.
Published: (2024)
by: Subramanian, Jithendaraa, et al.
Published: (2024)
TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation
by: Zongying, Lin, et al.
Published: (2024)
by: Zongying, Lin, et al.
Published: (2024)
TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering
by: Shen, Yiqing, et al.
Published: (2024)
by: Shen, Yiqing, et al.
Published: (2024)
BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature
by: Yan, Jiaxian, et al.
Published: (2026)
by: Yan, Jiaxian, et al.
Published: (2026)
AMix-2: Establishing Protein as a Native Modality in Large Language Models
by: Qiu, Keyue, et al.
Published: (2026)
by: Qiu, Keyue, et al.
Published: (2026)
Floating Anchor Diffusion Model for Multi-motif Scaffolding
by: Liu, Ke, et al.
Published: (2024)
by: Liu, Ke, et al.
Published: (2024)
S$^2$ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning
by: Yin, Mingze, et al.
Published: (2024)
by: Yin, Mingze, et al.
Published: (2024)
RTMol: Rethinking Molecule-text Alignment in a Round-trip View
by: Chen, Letian, et al.
Published: (2025)
by: Chen, Letian, et al.
Published: (2025)
PharmAgents: Building a Virtual Pharma with Large Language Model Agents
by: Gao, Bowen, et al.
Published: (2025)
by: Gao, Bowen, et al.
Published: (2025)
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models
by: Ma, Zicheng, et al.
Published: (2025)
by: Ma, Zicheng, et al.
Published: (2025)
Do Protein Transformers Have Biological Intelligence?
by: Lin, Fudong, et al.
Published: (2025)
by: Lin, Fudong, et al.
Published: (2025)
AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction
by: Yuan, Zhongju, et al.
Published: (2023)
by: Yuan, Zhongju, et al.
Published: (2023)
MoleCode unlocks structural intelligence in large language models
by: Yan, Zhiyuan, et al.
Published: (2026)
by: Yan, Zhiyuan, et al.
Published: (2026)
Controlling Repetition in Protein Language Models
by: Zhang, Jiahao, et al.
Published: (2026)
by: Zhang, Jiahao, et al.
Published: (2026)
Are Protein Language Models Compute Optimal?
by: Serrano, Yaiza, et al.
Published: (2024)
by: Serrano, Yaiza, et al.
Published: (2024)
OmniESI: A unified framework for enzyme-substrate interaction prediction with progressive conditional deep learning
by: Nie, Zhiwei, et al.
Published: (2025)
by: Nie, Zhiwei, et al.
Published: (2025)
From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?
by: Cao, Hanqun, et al.
Published: (2025)
by: Cao, Hanqun, et al.
Published: (2025)
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings
by: Kong, Zitai, et al.
Published: (2025)
by: Kong, Zitai, et al.
Published: (2025)
Improving Protein Sequence Design through Designability Preference Optimization
by: Xue, Fanglei, et al.
Published: (2025)
by: Xue, Fanglei, et al.
Published: (2025)
Generative AI for Controllable Protein Sequence Design: A Survey
by: Zhu, Yiheng, et al.
Published: (2024)
by: Zhu, Yiheng, et al.
Published: (2024)
FROGENT: An End-to-End Full-process Drug Design Multi-Agent System
by: Pan, Qihua, et al.
Published: (2025)
by: Pan, Qihua, et al.
Published: (2025)
DeepPNI: Language- and graph-based model for mutation-driven protein-nucleic acid energetics
by: Mondal, Somnath, et al.
Published: (2025)
by: Mondal, Somnath, et al.
Published: (2025)
Unifying Sequences, Structures, and Descriptions for Any-to-Any Protein Generation with the Large Multimodal Model HelixProtX
by: Chen, Zhiyuan, et al.
Published: (2024)
by: Chen, Zhiyuan, et al.
Published: (2024)
Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling
by: Qiu, Keyue, et al.
Published: (2026)
by: Qiu, Keyue, et al.
Published: (2026)
PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs
by: Zheng, Xinzhe, et al.
Published: (2025)
by: Zheng, Xinzhe, et al.
Published: (2025)
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction
by: Wu, Lirong, et al.
Published: (2024)
by: Wu, Lirong, et al.
Published: (2024)
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
by: Ko, Eunji, et al.
Published: (2024)
by: Ko, Eunji, et al.
Published: (2024)
Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks
by: Qiu, Keyue, et al.
Published: (2024)
by: Qiu, Keyue, et al.
Published: (2024)
OmegAMP: Targeted AMP Discovery through Biologically Informed Generation
by: Soares, Diogo, et al.
Published: (2025)
by: Soares, Diogo, et al.
Published: (2025)
Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design
by: Yang, Zaifei, et al.
Published: (2026)
by: Yang, Zaifei, et al.
Published: (2026)
MolTextNet: A Two-Million Molecule-Text Dataset for Multimodal Molecular Learning
by: Zhu, Yihan, et al.
Published: (2025)
by: Zhu, Yihan, et al.
Published: (2025)
AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model
by: Lv, Changze, et al.
Published: (2025)
by: Lv, Changze, et al.
Published: (2025)
Gradient Propagation in Retrosynthetic Space: An Efficient Framework for Synthesis Plan Generation
by: Tian, Chengyang, et al.
Published: (2024)
by: Tian, Chengyang, et al.
Published: (2024)
Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure
by: Wang, Zhicong, et al.
Published: (2025)
by: Wang, Zhicong, et al.
Published: (2025)
RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
by: Kshirsagar, Meghana, et al.
Published: (2026)
by: Kshirsagar, Meghana, et al.
Published: (2026)
TEMPO: Temporal Multi-scale Autoregressive Generation of Protein Conformational Ensembles
by: Xu, Yaoyao, et al.
Published: (2025)
by: Xu, Yaoyao, et al.
Published: (2025)
Flows, straight but not so fast: Exploring the design space of Rectified Flows in Protein Design
by: Chen, Junhua, et al.
Published: (2025)
by: Chen, Junhua, et al.
Published: (2025)
Similar Items
-
Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models
by: He, Haonan, et al.
Published: (2024) -
Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
by: Wei, Chen, et al.
Published: (2026) -
COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models
by: Ren, Yuchen, et al.
Published: (2024) -
Reinforcement Learning for Sequence Design Leveraging Protein Language Models
by: Subramanian, Jithendaraa, et al.
Published: (2024) -
TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation
by: Zongying, Lin, et al.
Published: (2024)