π° Must-Read Papers on Offline Model-Based Optimization π₯
This repository collects important papers for our latest survey: "Offline Model-Based Optimization: Comprehensive Review", which accepted by the Transactions of Machine Learning Research (TMLR 2026) with the Survey Certification. This survey is authored by Minsu Kim, Jiayao Gu, Ye Yuan, Taeyoung Yun, Zixuan Liu, Yoshua Bengio, and Can Chen.
- π»: links to the
code - π: links to the
bibtex
- [2026/01/05] Our Survey is accepted by the Transactions of Machine Learning Research with the survey certification! accessible here
- [2025/03/23] Our Survey is Publicly Accessible Now: See Our ArXiv Preprint here!
- [2025/03/04] First Release of Awesome-Offline-Model-Based Optimization!
- π What is Offline Model-Based Optimization?
- π Benchmark
- π― Surrogate Modeling
- π€ Generative Modeling
- π Citing This Survey!
In offline optimization, the goal is to discover a new design, denoted by 
In offline single-objective optimization, only one objective is considered (i.e.,
We review recent benchmarks, highlighting key tasks and evaluation metrics. We then categorize existing approaches into two key areas: surrogate modeling, which emphasizes accurate function approximation in out-of-distribution regions, and generative modeling, which explores high-dimensional design spaces to identify high-performing designs.
-
Virtual Library of Simulation Experiments: Test Functions and Datasets (Sonja Surjanovic & Derek Bingham, 2013) π» π
-
BayesO Benchmarks: Benchmark Functions for Bayesian Optimization (Jungtaek Kim, 2023) π» π
-
Pymoo: Multi-Objective Optimization in Python (Julian Blank & Kalyanmoy Ded, IEEE Access 2020) π» π
-
Evolutionary Algorithms in Theory and Practice : Evolution Strategies, Evolutionary Programming, Genetic Algorithms (Thomas BΓ€ck, Oxford University Press 1996) π
-
A Literature Survey of Benchmark Functions for Global Optimization Problems (Momin Jamil and Xin-She Yang, Int. Journal of Mathematical Modelling and Numerical Optimisation 2013) π
-
Cases for the Nugget in Modeling Computer Experiments (Robert B. Gramacy and Herbert K.H. Lee, 2010) π
-
A Benchmark of Kriging-Based Infill Criteria for Noisy Optimization (Victor Picheny et al., Structural and Multidisciplinary Optimization 2013) π
-
Scalable Test Problems for Evolutionary Multiobjective Optimization (Kalyanmoy Deb et al., Evolutionary Multiobjective Optimization 2005) π
-
Omni-Optimizer: A Generic Evolutionary Algorithm for Single and Multi-Objective Optimization (Kalyanmoy Deb et al., European Journal of Operational Research 2008) π
-
Multiobjective Evolutionary Algorithm Test Suites (David A. van Veldhuizen and Gary B. Lamont, ACM Symposium on Applied Computing 1999) π
-
Comparison of Multiobjective Evolutionary Algorithms: Empirical Results (Eckart Zitzler et al., Evolutionary Computation 2000) π
-
An Easy-to-Use Real-World Multi-Objective Optimization Problem Suite (Ryoji Tanabe et al., Applied Soft Computing 2020) π» π
-
GTOPX Space Mission Benchmarks (Martin Schlueter et al., SoftwareX 2021) π» π
-
SOO-Bench: Benchmarks for Evaluating the Stability of Offline Black-Box Optimization (Hong Qian et al., ICLR 2025) π» π
-
Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Brandon Trabucco & Xinyang Geng et al., ICML 2022) π» π
-
Data-Driven Offline Optimization for Architecting Hardware Accelerators (Aviral Kumar & Amir Yazdanbakhsh et al., ICLR 2022) π» π
-
ViennaRNA Package 2.0 (Ronny Lorenz et al., Algorithms for Molecular Biology 2011) π» π
-
Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Brandon Trabucco & Xinyang Geng et al., ICML 2022) π» π
-
Local Fitness Landscape of the Green Fluorescent Protein (Karen S. Sarkisyan et al., Nature 2016) π
-
Human 5 UTR Design and Variant Effect Prediction from a Massively Parallel Translation Assay (Paul J. Sample et al., Nature Biotechnology 2019) π
-
Comprehensive AAV Capsid Fitness Landscape Reveals a Viral Gene and Enables Machine-Guided Design (Pierce J. Ogden et al., Science 2019) π
-
Activity-Enhancing Mutations in an E3 Ubiquitin Ligase Identified by High-Throughput Mutagenesis (Lea M. Starita et al., Proceedings of the National Academy of Sciences 2013) π
-
Proximal Exploration for Model-Guided Protein Sequence Design (Zhizhou Ren & Jiahan Li et al., ICML 2022) π» π
-
Single-Mutation Fitness Landscapes for an Enzyme on Multiple Substrates Reveal Specificity Is Globally Encoded (Emily E. Wrenbeck et al., Nature Communications 2017) π
-
Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coliC (Justin R. Klesmith et al., ACS Synthetic Biology 2015) π
-
Deep Mutational Scanning of an RRM Domain of the Saccharomyces Cerevisiae Poly(A)-Binding Protein (Daniel Melamed et al., RNA 2013) π
-
A Framework for Exhaustively Mapping Functional Missense Variants (Jochen Weile et al., Molecular Systems Biology 2017) π
-
Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders (Samuel Stanton et al., ICML 2022) π
-
Survey of Variation in Human Transcription Factors Reveals Prevalent DNA Binding Changes (Luis A Barrera et al., Science 2016) π
-
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (Shitong Luo & Yufeng Su et al., NeurIPS 2022) π» π
-
Offline Multi-Objective Optimization (Ke Xue & Rong-Xi Tan et al., ICML 2024) π» π
-
Latent Conservative Objective Models for Offline Data-Driven Crystal Structure Prediction (Han Qi & Xinyang Geng et al., ICLR ML4Materials 2023) π
-
Bayesian Optimization of Active Materials for Lithium-Ion Batteries (Homero Valladares et al., IEEE IECON 2021) π
- Neural Architecture Search with Reinforcement Learning (Barret Zoph et al., ICLR 2017) π
- Neural Architecture Search as Multiobjective Optimization Benchmarks: Problem Formulation and Performance Assessment (Zhichao Lu et al., IEEE Transactions on Evolutionary Computation 2023) π
- Learning Multiple Layers of Features from Tiny Images (Alex Krizhevsky, 2009) π
- Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Brandon Trabucco & Xinyang Geng et al., ICML 2022) π» π
- Offline Multi-Objective Optimization (Ke Xue & Rong-Xi Tan et al., ICML 2024) π» π
- Prediction-Guided Multi-Objective Reinforcement Learning for Continuous Robot Control (Jie Xu et al., ICML 2020) π» π
- HPOBench: A Collection of Reproducible Multi-Fidelity Benchmark Problems for HPO (Katharina Eggensperger et al., NeurIPS Datasets and Benchmarks Track 2021) π» π
- Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Brandon Trabucco & Xinyang Geng et al., ICML 2022) π» π
- Biological Sequence Design with GFlowNets (Moksh Jain et al., ICML 2022) π» π
- Multiobjective Optimization Using Evolutionary Algorithms β A Comparative Case Study (Eckart Zitzler and Lothar Thiele, Parallel Problem Solving from Nature β PPSN V 1998) π
- The Balance between Proximity and Diversity in Multiobjective Evolutionary Algorithms (P.A.N. Bosman and D. Thierens, IEEE Transactions on Evolutionary Computation 2003) π
- Biological Sequence Design with GFlowNets (Moksh Jain et al., ICML 2022) π» π
- Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences (Minsu Kim et al., NeurIPS 2023) π» π
- Improving Protein Optimization with Smoothed Fitness Landscapes (Andrew Kirjner & Jason Yim et al., ICLR 2024) π» π
- Diversity By Design: Leveraging Distribution Matching for Offline Model-Based Optimization (Michael S. Yao et al., 2025) π» π
- Biological Sequence Design with GFlowNets (Moksh Jain et al., ICML 2022) π» π
- Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences (Minsu Kim et al., NeurIPS 2023) π» π
- Improving Protein Optimization with Smoothed Fitness Landscapes (Andrew Kirjner & Jason Yim et al., ICLR 2024) π» π
- SOO-Bench: Benchmarks for Evaluating the Stability of Offline Black-Box Optimization (Hong Qian et al., ICLR 2025) π» π
- Conservative Objective Models for Effective Offline Model-Based Optimization (Brandon Trabucco & Aviral Kumar et al., ICML 2021) π» π
- RoMA: Robust Model Adaptation for Offline Model-Based Optimization (Sihyun Yu et al., NeurIPS 2021) π» π
- Bidirectional Learning for Offline Infinite-Width Model-Based Optimization (Can Chen et al., NeurIPS 2022) π» π
- Data-Driven Offline Decision-Making via Invariant Representation Learning (Han Qi & Yi Su & Aviral Kumar et al., NeurIPS 2022) π» π
- Bidirectional Learning for Offline Model-Based Biological Sequence Design (Can Chen et al., ICML 2023) π» π
- Parallel-Mentoring for Offline Model-Based Optimization (Can Chen et al., NeurIPS 2023) π» π
- Learning Surrogates for Offline Black-Box Optimization via Gradient Matching (Minh Hoang et al., ICML 2024) π» π
- Boosting Offline Optimizers with Surrogate Sensitivity (Manh Cuong Dao et al., ICML 2024) π» π
- Incorporating Surrogate Gradient Norm to Improve Offline Optimization Techniques (Manh Cuong Dao et al., NeurIPS 2024) π» π
- Offline Model-Based Optimization by Learning to Rank (Rong-Xi Tan et al., ICLR 2025) π» π
- Autofocused Oracles for Model-Based Design (Clara Fannjiang et al., NeurIPS 2020) π» π
- Conservative Objective Models for Effective Offline Model-Based Optimization (Brandon Trabucco & Aviral Kumar et al., ICML 2021) π» π
- Bidirectional Learning for Offline Model-Based Biological Sequence Design (Can Chen et al., ICML 2023) π» π
- Parallel-Mentoring for Offline Model-Based Optimization (Can Chen et al., NeurIPS 2023) π» π
- Importance-Aware Co-Teaching for Offline Model-Based Optimization (Ye Yuan & Can Chen et al., NeurIPS 2023) π» π
- Functional Graphical Models: Structure Enables Offline Data-Driven Optimization (Jakub Grudzien Kuba et al., AISTATS 2024) π
- Offline Model-Based Optimization via Normalized Maximum Likelihood Estimation (Justin Fu et al., ICLR 2021) π» π
- Conflict-Averse Gradient Optimization of Ensembles for Effective Offline Model-Based Optimization (Sathvik Kolli, 2023) π
- Parallel-Mentoring for Offline Model-Based Optimization (Can Chen et al., NeurIPS 2023) π» π
- Importance-Aware Co-Teaching for Offline Model-Based Optimization (Ye Yuan & Can Chen et al., NeurIPS 2023) π» π
- Autofocused Oracles for Model-Based Design (Clara Fannjiang et al., NeurIPS 2020) π» π
- Data-Driven Offline Decision-Making via Invariant Representation Learning (Han Qi & Yi Su & Aviral Kumar et al., NeurIPS 2022) π» π
- Robust Guided Diffusion for Offline Black-Box Optimization (Can Chen et al., TMLR 2024) π» π
- Automatic Chemical Design using a Data-Driven Continuous Representation of Molecules (Rafael GΓ³mez-Bombarelli & Jennifer N. Wei & David Duvenaud & JosΓ© Miguel HernΓ‘ndez-Lobato et al., ACS central science 2018) π» π
- Conditioning by Adaptive Sampling for Robust Design (David H. Brookes et al., ICML 2019) π» π
- RoMA: Robust Model Adaptation for Offline Model-Based Optimization (Sihyun Yu et al., NeurIPS 2021) π» π
- Latent Bayesian Optimization via Autoregressive Normalizing Flows (Seunghun Lee et al., ICLR 2025) π» π
- Model Inversion Networks for Model-Based Optimization (Aviral Kumar et al., NeurIPS 2019) π» π
- Data-Driven Offline Decision-Making via Invariant Representation Learning (Han Qi & Yi Su & Aviral Kumar et al., NeurIPS 2022) π» π
- Generative Adversarial Model-Based Optimization via Source Critic Regularization (Michael S. Yao et al., NeurIPS 2024) π» π
- Plug and Play Language Models: A Simple Approach to Controlled Text Generation (Sumanth Dathathri et al., ICLR 2020) π» π
- Model-Based Reinforcement Learning for Biological Sequence Design (Christof Angermueller et al., ICLR 2020) π
- Generative Pretraining for Black-Box Optimization (Satvik Mashkaria & Siddarth Krishnamoorthy et al., ICML 2022) π» π
- Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences (Minsu Kim et al., NeurIPS 2023) π» π
- ExPT: Synthetic Pretraining for Few-Shot Experimental Design (Tung Nguyen et al., NeurIPS 2023) π» π
- Diffusion Models for Black-Box Optimization (Siddarth Krishnamoorthy et al., ICML 2023) π» π
- Exploring Chemical Space with Score-Based Out-of-Distribution Generation (Seul Lee et al., ICML 2023) π» π
- Robust Guided Diffusion for Offline Black-Box Optimization (Can Chen et al., TMLR 2024) π» π
- Guided Trajectory Generation with Diffusion Models for Offline Model-Based Optimization (Taeyoung Yun et al., NeurIPS 2024) π» π
- Design Editing for Offline Model-Based Optimization (Ye Yuan & Youyuan Zhang et al., 2024) π
- Low To High-Value Designs: Offline Optimization via Generalized Diffusion (Manh Cuong Dao et al., 2025) π
-
Dirichlet Flow Matching with Applications to DNA Sequence Design (Hannes Stark & Bowen Jing et al., ICML 2024) π» π
-
ParetoFlow: Guided Flows in Multi-Objective Optimization (Ye Yuan & Can Chen et al., ICLR 2025) π» π
-
Flow Q-Learning (Seohong Park et al., 2025) π» π
-
AffinityFlow: Guided Flows for Antibody Affinity Maturation (Can Chen et al., 2025) π
-
Conservative Objective Models Are a Special Kind of Contrastive Divergence-Based Energy Model (Christopher Beckham et al., 2023) π» π
-
Protein Discovery with Discrete Walk-Jump Sampling (Nathan C. Frey & Daniel Berenberg et al., ICLR 2024) π» π
-
Latent Energy-Based Odyssey: Black-Box Optimization via Expanded Exploration in the Energy-Based Latent Space (Peiyu Yu & Dinghuai Zhang et al., 2024) π
- Biological Sequence Design with GFlowNets (Moksh Jain et al., ICML 2022) π» π
- Multi-Objective GFlowNets (Moksh Jain et al., ICML 2023) π» π
- Generative Flow Networks Assisted Biological Sequence Editing (Pouya M. Ghari et al., NeurIPS GenBio 2023) π
- Improved Off-Policy Reinforcement Learning in Biological Sequence Design (Hyeonah Kim et al., NeurIPS AI for New Drug Modalities 2024) π» π
- Learning to Scale Logits for Temperature-Conditional GFlowNets (Minsu Kim & Joohwan Ko et al., ICML 2024) π» π
- Posterior Inference with Diffusion Models for High-Dimensional Black-box Optimization (Taeyoung Yun et al., 2025) π» π
If you found our survey paper is useful for your research, please consider cite our work:
@article{kim2026offline,
title={Offline Model-Based Optimization: Comprehensive Review},
author={Minsu Kim and Jiayao Gu and Ye Yuan and Taeyoung Yun and Zixuan Liu and Yoshua Bengio and Can Chen},
journal={Transactions on Machine Learning Research},
issn={2835-8856},
year={2026},
url={https://openreview.net/forum?id=QcSZWo1TLl},
note={Survey Certification}
}