Self-Improvement Imitation with Biologically Guided Search for Protein Design Under Oracle Budgets
Fuente:
arXiv
Saved in:
| Main Authors: | Khanna, Ashima, Grimm, Dominik |
|---|---|
| Format: | Preprint |
| Published: |
2026
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Hashing for Protein Structure Similarity Search
by: Han, Jin, et al.
Published: (2024)
by: Han, Jin, et al.
Published: (2024)
A Text-guided Protein Design Framework
by: Liu, Shengchao, et al.
Published: (2023)
by: Liu, Shengchao, et al.
Published: (2023)
Elucidating the Design Space of Multimodal Protein Language Models
by: Hsieh, Cheng-Yen, et al.
Published: (2025)
by: Hsieh, Cheng-Yen, et al.
Published: (2025)
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)
Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
by: Cao, Hanqun, et al.
Published: (2025)
by: Cao, Hanqun, et al.
Published: (2025)
A Comprehensive Review of Transformer-based language models for Protein Sequence Analysis and Design
by: Ghosh, Nimisha, et al.
Published: (2025)
by: Ghosh, Nimisha, 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)
Iterative Distillation for Reward-Guided Fine-Tuning of Diffusion Models in Biomolecular Design
by: Su, Xingyu, et al.
Published: (2025)
by: Su, Xingyu, et al.
Published: (2025)
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
by: Xie, Jiaqing, et al.
Published: (2024)
by: Xie, Jiaqing, et al.
Published: (2024)
Artificial Intelligence for CRISPR Guide RNA Design: Explainable Models and Off-Target Safety
by: Abbaszadeh, Alireza, et al.
Published: (2025)
by: Abbaszadeh, Alireza, et al.
Published: (2025)
Self-Supervised Learning on Molecular Graphs: A Systematic Investigation of Masking Design
by: Yang, Jiannan, et al.
Published: (2025)
by: Yang, Jiannan, et al.
Published: (2025)
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)
FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation
by: Chen, Jiameng, et al.
Published: (2025)
by: Chen, Jiameng, et al.
Published: (2025)
HyboWaveNet: Hyperbolic Graph Neural Networks with Multi-Scale Wavelet Transform for Protein-Protein Interaction Prediction
by: Yu, Qingzhi, et al.
Published: (2025)
by: Yu, Qingzhi, et al.
Published: (2025)
LLMs Outperform Experts on Challenging Biology Benchmarks
by: Justen, Lennart
Published: (2025)
by: Justen, Lennart
Published: (2025)
Protein Structure Tokenization: Benchmarking and New Recipe
by: Yuan, Xinyu, et al.
Published: (2025)
by: Yuan, Xinyu, et al.
Published: (2025)
Training Compute-Optimal Protein Language Models
by: Cheng, Xingyi, et al.
Published: (2024)
by: Cheng, Xingyi, et al.
Published: (2024)
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)
Improving AlphaFlow for Efficient Protein Ensembles Generation
by: Li, Shaoning, et al.
Published: (2024)
by: Li, Shaoning, et al.
Published: (2024)
Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling
by: Wu, Fang, et al.
Published: (2026)
by: Wu, Fang, et al.
Published: (2026)
DCFold: Efficient Protein Structure Generation with Single Forward Pass
by: Zhang, Zhe, et al.
Published: (2026)
by: Zhang, Zhe, 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)
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 Novel Framework for Multi-Modal Protein Representation Learning
by: Zheng, Runjie, et al.
Published: (2025)
by: Zheng, Runjie, et al.
Published: (2025)
Large Language Model is Secretly a Protein Sequence Optimizer
by: Wang, Yinkai, et al.
Published: (2025)
by: Wang, Yinkai, et al.
Published: (2025)
Empowering Chemical Structures with Biological Insights for Scalable Phenotypic Virtual Screening
by: Lian, Xiaoqing, et al.
Published: (2026)
by: Lian, Xiaoqing, et al.
Published: (2026)
BioArc: Discovering Optimal Neural Architectures for Biological Foundation Models
by: Fang, Yi, et al.
Published: (2025)
by: Fang, Yi, et al.
Published: (2025)
PhaGO: Protein function annotation for bacteriophages by integrating the genomic context
by: Guan, Jiaojiao, et al.
Published: (2024)
by: Guan, Jiaojiao, et al.
Published: (2024)
XAI-Driven Deep Learning for Protein Sequence Functional Group Classification
by: Chakraborty, Pratik, et al.
Published: (2025)
by: Chakraborty, Pratik, et al.
Published: (2025)
Reward-Guided Iterative Refinement in Diffusion Models at Test-Time with Applications to Protein and DNA Design
by: Uehara, Masatoshi, et al.
Published: (2025)
by: Uehara, Masatoshi, et al.
Published: (2025)
BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning
by: Zhao, Haiteng, et al.
Published: (2025)
by: Zhao, Haiteng, et al.
Published: (2025)
Injecting Hierarchical Biological Priors into Graph Neural Networks for Flow Cytometry Prediction
by: Mojarrad, Fatemeh Nassajian, et al.
Published: (2024)
by: Mojarrad, Fatemeh Nassajian, et al.
Published: (2024)
Optimizing the Design of an Artificial Pancreas to Improve Diabetes Management
by: Khanna, Ashok, et al.
Published: (2024)
by: Khanna, Ashok, et al.
Published: (2024)
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)
ProteinBench: A Holistic Evaluation of Protein Foundation Models
by: Ye, Fei, et al.
Published: (2024)
by: Ye, Fei, et al.
Published: (2024)
Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning
by: Caranzano, Isabella, et al.
Published: (2025)
by: Caranzano, Isabella, et al.
Published: (2025)
DualBind: A Dual-Loss Framework for Protein-Ligand Binding Affinity Prediction
by: Liu, Meng, et al.
Published: (2024)
by: Liu, Meng, et al.
Published: (2024)
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)
Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A Hemagglutinin
by: Barkan, Ella, et al.
Published: (2025)
by: Barkan, Ella, et al.
Published: (2025)
Similar Items
-
Hashing for Protein Structure Similarity Search
by: Han, Jin, et al.
Published: (2024) -
A Text-guided Protein Design Framework
by: Liu, Shengchao, et al.
Published: (2023) -
Elucidating the Design Space of Multimodal Protein Language Models
by: Hsieh, Cheng-Yen, et al.
Published: (2025) -
Annotation-guided Protein Design with Multi-Level Domain Alignment
by: Yuan, Chaohao, et al.
Published: (2024) -
Design Proteins Using Large Language Models: Enhancements and Comparative Analyses
by: Zeinalipour, Kamyar, et al.
Published: (2024)