Cover Image

Repurposing Protein Language Models for Latent Flow-Based Fitness Optimization

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Arroyo, Amaru Caceres, Bogensperger, Lea, Allam, Ahmed, Krauthammer, Michael, Schindler, Konrad, Narnhofer, Dominik
Format:	Preprint
Published:	2026
Subjects:	Machine Learning Quantitative Methods
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

A Variational Perspective on Generative Protein Fitness Optimization
by: Bogensperger, Lea, et al.
Published: (2025)

Binary Latent Protein Fitness Landscapes for Quantum Annealing Optimization
by: Hy, Truong-Son
Published: (2026)

DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm
by: Schwarz, Kyriakos, et al.
Published: (2022)

Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space
by: Lee, Minji, et al.
Published: (2024)

Improving Protein Optimization with Smoothed Fitness Landscapes
by: Kirjner, Andrew, et al.
Published: (2023)

No Generation without Representation: Efficient Causal Protein Language Models Enable Zero-Shot Fitness Estimation
by: Eris, Furkan
Published: (2026)

TriFit: Trimodal Fusion with Protein Dynamics for Mutation Fitness Prediction
by: Cho, Seungik
Published: (2026)

Towards AI-Based Precision Oncology: A Machine Learning Framework for Personalized Counterfactual Treatment Suggestions based on Multi-Omics Data
by: Schürch, Manuel, et al.
Published: (2024)

Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models
by: Liang, Po-Yu, et al.
Published: (2024)

Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction
by: Weitzman, Ruben, et al.
Published: (2025)

Drug Repurposing Using Deep Embedded Clustering and Graph Neural Networks
by: Delzer, Luke, et al.
Published: (2025)

Learning Personalized Treatment Decisions in Precision Medicine: Disentangling Treatment Assignment Bias in Counterfactual Outcome Prediction and Biomarker Identification
by: Vollenweider, Michael, et al.
Published: (2024)

Large Language Model is Secretly a Protein Sequence Optimizer
by: Wang, Yinkai, et al.
Published: (2025)

Evolutionary Profiles for Protein Fitness Prediction
by: Fan, Jigang, et al.
Published: (2025)

DPLM-2: A Multimodal Diffusion Protein Language Model
by: Wang, Xinyou, et al.
Published: (2024)

Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design
by: Campbell, Andrew, et al.
Published: (2024)

Learning the Language of Protein Structure
by: Gaujac, Benoit, et al.
Published: (2024)

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
by: Geffner, Tomas, et al.
Published: (2025)

Driving Accurate Allergen Prediction with Protein Language Models and Generalization-Focused Evaluation
by: Wong, Brian Shing-Hei, et al.
Published: (2025)

Endowing Protein Language Models with Structural Knowledge
by: Chen, Dexiong, et al.
Published: (2024)

Low-N Protein Activity Optimization with FolDE
by: Roberts, Jacob B., et al.
Published: (2025)

ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals
by: Mitra, Shania, et al.
Published: (2024)

Ankh3: Multi-Task Pretraining with Sequence Denoising and Completion Enhances Protein Representations
by: Alsamkary, Hazem, et al.
Published: (2025)

PGraphDTA: Improving Drug Target Interaction Prediction using Protein Language Models and Contact Maps
by: Bal, Rakesh, et al.
Published: (2023)

Self-Improvement Imitation with Biologically Guided Search for Protein Design Under Oracle Budgets
by: Khanna, Ashima, et al.
Published: (2026)

EPO: Diverse and Realistic Protein Ensemble Generation via Energy Preference Optimization
by: Sun, Yuancheng, et al.
Published: (2025)

Molecular Embedding-Based Algorithm Selection in Protein-Ligand Docking
by: Wang, Jiabao Brad, et al.
Published: (2025)

HGTDR: Advancing Drug Repurposing with Heterogeneous Graph Transformers
by: Gharizadeh, Ali, et al.
Published: (2024)

Sleep Apnea Detection on a Wireless Multimodal Wearable Device Without Oxygen Flow Using a Mamba-based Deep Learning Approach
by: Luszczynski, Dominik, et al.
Published: (2025)

Training Compute-Optimal Protein Language Models
by: Cheng, Xingyi, et al.
Published: (2024)

Better Protein Function Prediction by Modeling Survivorship Bias
by: Chao, Zhongmou, et al.
Published: (2026)

Protein-Mamba: Biological Mamba Models for Protein Function Prediction
by: Xu, Bohao, et al.
Published: (2024)

A Diffusion Model to Shrink Proteins While Maintaining Their Function
by: Baron, Ethan, et al.
Published: (2025)

Elucidating the Design Space of Multimodal Protein Language Models
by: Hsieh, Cheng-Yen, et al.
Published: (2025)

Drug Repurposing for Parkinson's Disease Using Random Walk With Restart Algorithm and the Parkinson's Disease Ontology Database
by: Kankariya, Pratham, et al.
Published: (2024)

Flow-Matching Based Refiner for Molecular Conformer Generation
by: Xu, Xiangyang, et al.
Published: (2025)

Improving AlphaFlow for Efficient Protein Ensembles Generation
by: Li, Shaoning, et al.
Published: (2024)

Accelerating the Generation of Molecular Conformations with Progressive Distillation of Equivariant Latent Diffusion Models
by: Lacombe, Romain, et al.
Published: (2024)

ProteinZero: Self-Improving Protein Generation via Online Reinforcement Learning
by: Wang, Ziwen, et al.
Published: (2025)

ODBO: Bayesian Optimization with Search Space Prescreening for Directed Protein Evolution
by: Cheng, Lixue, et al.
Published: (2022)