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 is authored by Minsu Kim, Jiayao Gu, Ye Yuan, Taeyoung Yun, Zixuan Liu, Yoshua Bengio, and Can Chen.
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- π: links to the
bibtex
- [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 where each design vector
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.
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Virtual Library of Simulation Experiments: Test Functions and Datasets (Sonja Surjanovic & Derek Bingham, 2013) π» π
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BayesO Benchmarks: Benchmark Functions for Bayesian Optimization (Jungtaek Kim, 2023) π» π
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Pymoo: Multi-Objective Optimization in Python (Julian Blank & Kalyanmoy Ded, IEEE Access 2020) π» π
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Evolutionary Algorithms in Theory and Practice : Evolution Strategies, Evolutionary Programming, Genetic Algorithms (Thomas BΓ€ck, Oxford University Press 1996) π
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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
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Cases for the Nugget in Modeling Computer Experiments (Robert B. Gramacy and Herbert K.H. Lee, 2010) π
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A Benchmark of Kriging-Based Infill Criteria for Noisy Optimization (Victor Picheny et al., Structural and Multidisciplinary Optimization 2013) π
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Scalable Test Problems for Evolutionary Multiobjective Optimization (Kalyanmoy Deb et al., Evolutionary Multiobjective Optimization 2005) π
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Omni-Optimizer: A Generic Evolutionary Algorithm for Single and Multi-Objective Optimization (Kalyanmoy Deb et al., European Journal of Operational Research 2008) π
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Multiobjective Evolutionary Algorithm Test Suites (David A. van Veldhuizen and Gary B. Lamont, ACM Symposium on Applied Computing 1999) π
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Comparison of Multiobjective Evolutionary Algorithms: Empirical Results (Eckart Zitzler et al., Evolutionary Computation 2000) π
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An Easy-to-Use Real-World Multi-Objective Optimization Problem Suite (Ryoji Tanabe et al., Applied Soft Computing 2020) π» π
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GTOPX Space Mission Benchmarks (Martin Schlueter et al., SoftwareX 2021) π» π
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SOO-Bench: Benchmarks for Evaluating the Stability of Offline Black-Box Optimization (Hong Qian et al., ICLR 2025) π» π
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Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Brandon Trabucco & Xinyang Geng et al., ICML 2022) π» π
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Data-Driven Offline Optimization for Architecting Hardware Accelerators (Aviral Kumar & Amir Yazdanbakhsh et al., ICLR 2022) π» π
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ViennaRNA Package 2.0 (Ronny Lorenz et al., Algorithms for Molecular Biology 2011) π» π
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Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Brandon Trabucco & Xinyang Geng et al., ICML 2022) π» π
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Local Fitness Landscape of the Green Fluorescent Protein (Karen S. Sarkisyan et al., Nature 2016) π
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Human 5 UTR Design and Variant Effect Prediction from a Massively Parallel Translation Assay (Paul J. Sample et al., Nature Biotechnology 2019) π
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Comprehensive AAV Capsid Fitness Landscape Reveals a Viral Gene and Enables Machine-Guided Design (Pierce J. Ogden et al., Science 2019) π
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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
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Proximal Exploration for Model-Guided Protein Sequence Design (Zhizhou Ren & Jiahan Li et al., ICML 2022) π» π
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Single-Mutation Fitness Landscapes for an Enzyme on Multiple Substrates Reveal Specificity Is Globally Encoded (Emily E. Wrenbeck et al., Nature Communications 2017) π
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Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coliC (Justin R. Klesmith et al., ACS Synthetic Biology 2015) π
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Deep Mutational Scanning of an RRM Domain of the Saccharomyces Cerevisiae Poly(A)-Binding Protein (Daniel Melamed et al., RNA 2013) π
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A Framework for Exhaustively Mapping Functional Missense Variants (Jochen Weile et al., Molecular Systems Biology 2017) π
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Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders (Samuel Stanton et al., ICML 2022) π
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Survey of Variation in Human Transcription Factors Reveals Prevalent DNA Binding Changes (Luis A Barrera et al., Science 2016) π
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Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (Shitong Luo & Yufeng Su et al., NeurIPS 2022) π» π
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Offline Multi-Objective Optimization (Ke Xue & Rong-Xi Tan et al., ICML 2024) π» π
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Latent Conservative Objective Models for Offline Data-Driven Crystal Structure Prediction (Han Qi & Xinyang Geng et al., ICLR ML4Materials 2023) π
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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
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Dirichlet Flow Matching with Applications to DNA Sequence Design (Hannes Stark & Bowen Jing et al., ICML 2024) π» π
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ParetoFlow: Guided Flows in Multi-Objective Optimization (Ye Yuan & Can Chen et al., ICLR 2025) π» π
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Flow Q-Learning (Seohong Park et al., 2025) π» π
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AffinityFlow: Guided Flows for Antibody Affinity Maturation (Can Chen et al., 2025) π
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Conservative Objective Models Are a Special Kind of Contrastive Divergence-Based Energy Model (Christopher Beckham et al., 2023) π» π
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Protein Discovery with Discrete Walk-Jump Sampling (Nathan C. Frey & Daniel Berenberg et al., ICLR 2024) π» π
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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:
@misc{kim2025offline,
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},
year={2025},
eprint={2503.17286},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/2503.17286},
}