Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language
Fuente:
arXiv
Saved in:
| Main Authors: | Zhong, Zhiqiang, Larsen, Simon Sataa-Yu, Guo, Haoyu, Tang, Tao, Zhou, Kuangyu, Mottin, Davide |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Benchmarking Large Language Models for Molecule Prediction Tasks
by: Zhong, Zhiqiang, et al.
Published: (2024)
by: Zhong, Zhiqiang, et al.
Published: (2024)
Efficiently Predicting Mutational Effect on Homologous Proteins by Evolution Encoding
by: Zhong, Zhiqiang, et al.
Published: (2024)
by: Zhong, Zhiqiang, 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)
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining
by: Liu, Shengchao, et al.
Published: (2023)
by: Liu, Shengchao, et al.
Published: (2023)
NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
by: Guo, Tao, et al.
Published: (2025)
by: Guo, Tao, et al.
Published: (2025)
JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data
by: Kalia, Apurva, et al.
Published: (2024)
by: Kalia, Apurva, et al.
Published: (2024)
Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization
by: Liu, Zequn, et al.
Published: (2026)
by: Liu, Zequn, et al.
Published: (2026)
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey
by: Pei, Qizhi, et al.
Published: (2024)
by: Pei, Qizhi, et al.
Published: (2024)
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)
AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization
by: Jiang, Zixuan, et al.
Published: (2025)
by: Jiang, Zixuan, et al.
Published: (2025)
t-SMILES: A Scalable Fragment-based Molecular Representation Framework for De Novo Molecule Generation
by: Wu, Juan-Ni, et al.
Published: (2023)
by: Wu, Juan-Ni, et al.
Published: (2023)
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)
TwinBooster: Synergising Large Language Models with Barlow Twins and Gradient Boosting for Enhanced Molecular Property Prediction
by: Schuh, Maximilian G., et al.
Published: (2024)
by: Schuh, Maximilian G., et al.
Published: (2024)
From Words to Molecules: A Survey of Large Language Models in Chemistry
by: Liao, Chang, et al.
Published: (2024)
by: Liao, Chang, et al.
Published: (2024)
Contextual Molecule Representation Learning from Chemical Reaction Knowledge
by: Tang, Han, et al.
Published: (2024)
by: Tang, Han, et al.
Published: (2024)
End-to-End Reverse Screening Identifies Protein Targets of Small Molecules Using HelixFold3
by: Xu, Shengjie, et al.
Published: (2026)
by: Xu, Shengjie, et al.
Published: (2026)
Conditioned Generative Modeling of Molecular Glues: A Realistic AI Approach for Synthesizable Drug-like Molecules
by: Islam, Naeyma N., et al.
Published: (2026)
by: Islam, Naeyma N., et al.
Published: (2026)
Auxiliary Discrminator Sequence Generative Adversarial Networks (ADSeqGAN) for Few Sample Molecule Generation
by: Tang, Haocheng, et al.
Published: (2025)
by: Tang, Haocheng, et al.
Published: (2025)
RTMol: Rethinking Molecule-text Alignment in a Round-trip View
by: Chen, Letian, et al.
Published: (2025)
by: Chen, Letian, et al.
Published: (2025)
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation
by: Tang, Xiangru, et al.
Published: (2024)
by: Tang, Xiangru, et al.
Published: (2024)
Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures
by: Liu, Ce, et al.
Published: (2024)
by: Liu, Ce, et al.
Published: (2024)
Crossing New Frontiers: Knowledge-Augmented Large Language Model Prompting for Zero-Shot Text-Based De Novo Molecule Design
by: Srinivas, Sakhinana Sagar, et al.
Published: (2024)
by: Srinivas, Sakhinana Sagar, et al.
Published: (2024)
Can Large Language Models Understand Molecules?
by: Sadeghi, Shaghayegh, et al.
Published: (2024)
by: Sadeghi, Shaghayegh, et al.
Published: (2024)
Repurformer: Transformers for Repurposing-Aware Molecule Generation
by: Lee, Changhun, et al.
Published: (2024)
by: Lee, Changhun, et al.
Published: (2024)
WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking
by: Liu, Yunchao, et al.
Published: (2024)
by: Liu, Yunchao, et al.
Published: (2024)
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)
Unraveling the Potential of Diffusion Models in Small Molecule Generation
by: Zhang, Peining, et al.
Published: (2025)
by: Zhang, Peining, et al.
Published: (2025)
Open-Source Molecular Processing Pipeline for Generating Molecules
by: Shreyas, V, et al.
Published: (2024)
by: Shreyas, V, et al.
Published: (2024)
TAGMol: Target-Aware Gradient-guided Molecule Generation
by: Dorna, Vineeth, et al.
Published: (2024)
by: Dorna, Vineeth, et al.
Published: (2024)
Hierarchical Structure Enhances the Convergence and Generalizability of Linear Molecular Representation
by: Wu, Juan-Ni, et al.
Published: (2024)
by: Wu, Juan-Ni, et al.
Published: (2024)
TEMPO: Temporal Multi-scale Autoregressive Generation of Protein Conformational Ensembles
by: Xu, Yaoyao, et al.
Published: (2025)
by: Xu, Yaoyao, et al.
Published: (2025)
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models
by: Yoo, Kiwoong, et al.
Published: (2024)
by: Yoo, Kiwoong, et al.
Published: (2024)
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
by: Lin, Haitao, et al.
Published: (2024)
by: Lin, Haitao, et al.
Published: (2024)
PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion
by: Tang, Sophia, et al.
Published: (2024)
by: Tang, Sophia, et al.
Published: (2024)
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules
by: Feng, Shikun, et al.
Published: (2024)
by: Feng, Shikun, et al.
Published: (2024)
Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation
by: Xu, Can, et al.
Published: (2024)
by: Xu, Can, et al.
Published: (2024)
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
by: Zhang, Zuobai, et al.
Published: (2024)
by: Zhang, Zuobai, et al.
Published: (2024)
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)
ControllableGPT: A Ground-Up Designed Controllable GPT for Molecule Optimization
by: Liu, Xuefeng, et al.
Published: (2025)
by: Liu, Xuefeng, et al.
Published: (2025)
Similar Items
-
Benchmarking Large Language Models for Molecule Prediction Tasks
by: Zhong, Zhiqiang, et al.
Published: (2024) -
Efficiently Predicting Mutational Effect on Homologous Proteins by Evolution Encoding
by: Zhong, Zhiqiang, et al.
Published: (2024) -
Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks
by: Qiu, Keyue, et al.
Published: (2024) -
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining
by: Liu, Shengchao, et al.
Published: (2023) -
NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
by: Guo, Tao, et al.
Published: (2025)