awesome-offline-model-based-optimization
📰 Must-Read Papers on Offline Model-Based Optimization 🔥
https://github.com/mila-iqia/awesome-offline-model-based-optimization
Last synced: 3 days ago
JSON representation
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🎯 Surrogate Modeling
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Evaluation Metric
- **Bidirectional Learning for Offline Infinite-Width Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bdi.txt)
- **Conservative Objective Models for Effective Offline Model-Based Optimization** - baselines) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/coms.txt)
- **Bidirectional Learning for Offline Infinite-Width Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bdi.txt)
- **Bidirectional Learning for Offline Model-Based Biological Sequence Design** - ICML2023-Submission) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bib.txt)
- **Parallel-Mentoring for Offline Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/parallel_mentor.txt)
- **Learning Surrogates for Offline Black-Box Optimization via Gradient Matching** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/matchopt.txt)
- **Boosting Offline Optimizers with Surrogate Sensitivity** - dm/BOSS) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/boss.txt)
- **Incorporating Surrogate Gradient Norm to Improve Offline Optimization Techniques** - dm/IGNITE) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ignite.txt)
- **Conservative Objective Models for Effective Offline Model-Based Optimization** - baselines) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/coms.txt)
- **Offline Model-Based Optimization by Learning to Rank** - Xi Tan et al., ICLR 2025) [💻](https://github.com/lamda-bbo/Offline-RaM) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/learning2rank.txt)
- **Autofocused Oracles for Model-Based Design** - oracles) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/autofocused.txt)
- **Importance-Aware Co-Teaching for Offline Model-Based Optimization** - iqia/Importance-aware-Co-teaching) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ict.txt)
- **Offline Model-Based Optimization via Normalized Maximum Likelihood Estimation** - anonymous) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/nemo.txt)
- **Conflict-Averse Gradient Optimization of Ensembles for Effective Offline Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/conflictaverse.txt)
- **Bidirectional Learning for Offline Model-Based Biological Sequence Design** - ICML2023-Submission) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bib.txt)
- **Parallel-Mentoring for Offline Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/parallel_mentor.txt)
- **Learning Surrogates for Offline Black-Box Optimization via Gradient Matching** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/matchopt.txt)
- **Boosting Offline Optimizers with Surrogate Sensitivity** - dm/BOSS) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/boss.txt)
- **Incorporating Surrogate Gradient Norm to Improve Offline Optimization Techniques** - dm/IGNITE) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ignite.txt)
- **Offline Model-Based Optimization by Learning to Rank** - Xi Tan et al., ICLR 2025) [💻](https://github.com/lamda-bbo/Offline-RaM) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/learning2rank.txt)
- **Autofocused Oracles for Model-Based Design** - oracles) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/autofocused.txt)
- **Importance-Aware Co-Teaching for Offline Model-Based Optimization** - iqia/Importance-aware-Co-teaching) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ict.txt)
- **Functional Graphical Models: Structure Enables Offline Data-Driven Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/fgm.txt)
- **Functional Graphical Models: Structure Enables Offline Data-Driven Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/fgm.txt)
- **Offline Model-Based Optimization via Normalized Maximum Likelihood Estimation** - anonymous) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/nemo.txt)
- **Conflict-Averse Gradient Optimization of Ensembles for Effective Offline Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/conflictaverse.txt)
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🤔 Generative Modeling
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Evaluation Metric
- **Generative Flow Networks Assisted Biological Sequence Editing** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/sequence_editing.txt)
- **Improved Off-Policy Reinforcement Learning in Biological Sequence Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/delta_cs.txt)
- **Learning to Scale Logits for Temperature-Conditional GFlowNets** - 11/logit-gfn) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/logitgfn.txt)
- **Posterior Inference with Diffusion Models for High-Dimensional Black-box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/dibo.txt)
- **Biological Sequence Design with GFlowNets** - GFN-AL) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/biosequence_gflownet.txt)
- **Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences** - silab/bootgen) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bootgen.txt)
- **Generative Pretraining for Black-Box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bonet.txt)
- **ExPT: Synthetic Pretraining for Few-Shot Experimental Design** - nd/ExPT) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/expt.txt)
- **RoMA: Robust Model Adaptation for Offline Model-Based Optimization** - yu/RoMA) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/roma.txt)
- **Data-Driven Offline Decision-Making via Invariant Representation Learning** - neurips) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/iom.txt)
- **Automatic Chemical Design using a Data-Driven Continuous Representation of Molecules** - Bombarelli & Jennifer N. Wei & David Duvenaud & José
- 💻 - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/automaticchem.txt)
- **Conditioning by Adaptive Sampling for Robust Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/cbas.txt)
- **RoMA: Robust Model Adaptation for Offline Model-Based Optimization** - yu/RoMA) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/roma.txt)
- **Latent Bayesian Optimization via Autoregressive Normalizing Flows** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/latentbayes.txt)
- **Conditioning by Adaptive Sampling for Robust Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/cbas.txt)
- **Latent Bayesian Optimization via Autoregressive Normalizing Flows** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/latentbayes.txt)
- **Robust Guided Diffusion for Offline Black-Box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/rgd.txt)
- **Model Inversion Networks for Model-Based Optimization** - baselines/tree/master/design_baselines/mins) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mins.txt)
- **Data-Driven Offline Decision-Making via Invariant Representation Learning** - neurips) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/iom.txt)
- **Automatic Chemical Design using a Data-Driven Continuous Representation of Molecules** - Bombarelli & Jennifer N. Wei & David Duvenaud & José
- **Generative Adversarial Model-Based Optimization via Source Critic Regularization** - s-yao/gabo) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gabo.txt)
- 💻 - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/automaticchem.txt)
- **Plug and Play Language Models: A Simple Approach to Controlled Text Generation** - research/PPLM) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/pplm.txt)
- **Model-Based Reinforcement Learning for Biological Sequence Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mbrl_bio.txt)
- **Generative Pretraining for Black-Box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bonet.txt)
- **Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences** - silab/bootgen) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bootgen.txt)
- **Model Inversion Networks for Model-Based Optimization** - baselines/tree/master/design_baselines/mins) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mins.txt)
- **Generative Adversarial Model-Based Optimization via Source Critic Regularization** - s-yao/gabo) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gabo.txt)
- **Plug and Play Language Models: A Simple Approach to Controlled Text Generation** - research/PPLM) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/pplm.txt)
- **Model-Based Reinforcement Learning for Biological Sequence Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mbrl_bio.txt)
- **Dirichlet Flow Matching with Applications to DNA Sequence Design** - flow-matching) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/dirichlet.txt)
- **ExPT: Synthetic Pretraining for Few-Shot Experimental Design** - nd/ExPT) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/expt.txt)
- **Diffusion Models for Black-Box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ddom.txt)
- **Exploring Chemical Space with Score-Based Out-of-Distribution Generation** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mood.txt)
- **Guided Trajectory Generation with Diffusion Models for Offline Model-Based Optimization** - 11/GTG) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gtg.txt)
- **Design Editing for Offline Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/demo.txt)
- **Low To High-Value Designs: Offline Optimization via Generalized Diffusion** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/low2high.txt)
- **Conservative Objective Models Are a Special Kind of Contrastive Divergence-Based Energy Model** - beckham/coms-are-energy-models) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/coms_are_energy.txt)
- **Exploring Chemical Space with Score-Based Out-of-Distribution Generation** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mood.txt)
- **Robust Guided Diffusion for Offline Black-Box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/rgd.txt)
- **Guided Trajectory Generation with Diffusion Models for Offline Model-Based Optimization** - 11/GTG) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gtg.txt)
- **Design Editing for Offline Model-Based Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/demo.txt)
- **Protein Discovery with Discrete Walk-Jump Sampling** - design/walk-jump) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/walkjump.txt)
- **Latent Energy-Based Odyssey: Black-Box Optimization via Expanded Exploration in the Energy-Based Latent Space** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/odyssey.txt)
- **Low To High-Value Designs: Offline Optimization via Generalized Diffusion** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/low2high.txt)
- **ParetoFlow: Guided Flows in Multi-Objective Optimization** - iqia/ParetoFlow) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/paretoflow.txt)
- **Flow Q-Learning** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/fql.txt)
- **AffinityFlow: Guided Flows for Antibody Affinity Maturation** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/affinityflow.txt)
- **Multi-Objective GFlowNets** - objective-gfn) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mogfn.txt)
- **Latent Energy-Based Odyssey: Black-Box Optimization via Expanded Exploration in the Energy-Based Latent Space** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/odyssey.txt)
- **Biological Sequence Design with GFlowNets** - GFN-AL) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/biosequence_gflownet.txt)
- **Multi-Objective GFlowNets** - objective-gfn) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/mogfn.txt)
- **Generative Flow Networks Assisted Biological Sequence Editing** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/sequence_editing.txt)
- **Improved Off-Policy Reinforcement Learning in Biological Sequence Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/delta_cs.txt)
- **Learning to Scale Logits for Temperature-Conditional GFlowNets** - 11/logit-gfn) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/logitgfn.txt)
- **Posterior Inference with Diffusion Models for High-Dimensional Black-box Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/dibo.txt)
- **Dirichlet Flow Matching with Applications to DNA Sequence Design** - flow-matching) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/dirichlet.txt)
- **Flow Q-Learning** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/fql.txt)
- **AffinityFlow: Guided Flows for Antibody Affinity Maturation** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/affinityflow.txt)
- **Conservative Objective Models Are a Special Kind of Contrastive Divergence-Based Energy Model** - beckham/coms-are-energy-models) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/coms_are_energy.txt)
- **Protein Discovery with Discrete Walk-Jump Sampling** - design/walk-jump) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/walkjump.txt)
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🔗 Benchmark
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Task
- **A Literature Survey of Benchmark Functions for Global Optimization Problems** - She Yang, Int. Journal of Mathematical Modelling and Numerical Optimisation 2013) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/functions.txt)
- **Cases for the Nugget in Modeling Computer Experiments** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/nugget.txt)
- **A Benchmark of Kriging-Based Infill Criteria for Noisy Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/sphere.txt)
- **Scalable Test Problems for Evolutionary Multiobjective Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/deb2005.txt)
- **Omni-Optimizer: A Generic Evolutionary Algorithm for Single and Multi-Objective Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/omni.txt)
- **Virtual Library of Simulation Experiments: Test Functions and Datasets** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/simulationlib.txt)
- **BayesO Benchmarks: Benchmark Functions for Bayesian Optimization** - benchmarks) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bayeso.txt)
- **Pymoo: Multi-Objective Optimization in Python** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/pymoo.txt)
- **Evolutionary Algorithms in Theory and Practice : Evolution Strategies, Evolutionary Programming, Genetic Algorithms** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ea_book.txt)
- **Virtual Library of Simulation Experiments: Test Functions and Datasets** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/simulationlib.txt)
- **BayesO Benchmarks: Benchmark Functions for Bayesian Optimization** - benchmarks) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/bayeso.txt)
- **Pymoo: Multi-Objective Optimization in Python** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/pymoo.txt)
- **Evolutionary Algorithms in Theory and Practice : Evolution Strategies, Evolutionary Programming, Genetic Algorithms** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ea_book.txt)
- **A Literature Survey of Benchmark Functions for Global Optimization Problems** - She Yang, Int. Journal of Mathematical Modelling and Numerical Optimisation 2013) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/functions.txt)
- **Cases for the Nugget in Modeling Computer Experiments** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/nugget.txt)
- **A Benchmark of Kriging-Based Infill Criteria for Noisy Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/sphere.txt)
- **Scalable Test Problems for Evolutionary Multiobjective Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/deb2005.txt)
- **Omni-Optimizer: A Generic Evolutionary Algorithm for Single and Multi-Objective Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/omni.txt)
- **Multiobjective Evolutionary Algorithm Test Suites** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/vlmop.txt)
- **Comparison of Multiobjective Evolutionary Algorithms: Empirical Results** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/zdt.txt)
- **Multiobjective Evolutionary Algorithm Test Suites** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/vlmop.txt)
- **Local Fitness Landscape of the Green Fluorescent Protein** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gfp.txt)
- **Comparison of Multiobjective Evolutionary Algorithms: Empirical Results** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/zdt.txt)
- **Human 5 UTR Design and Variant Effect Prediction from a Massively Parallel Translation Assay** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/utr.txt)
- **An Easy-to-Use Real-World Multi-Objective Optimization Problem Suite** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/re_suite.txt)
- **GTOPX Space Mission Benchmarks** - solver.com/index.php/about/benchmarks/gtopx) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gtopx.txt)
- **Data-Driven Offline Optimization for Architecting Hardware Accelerators** - research/google-research/tree/master/prime) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hardware.txt)
- **ViennaRNA Package 2.0** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/vienna_rna.txt)
- **Comprehensive AAV Capsid Fitness Landscape Reveals a Viral Gene and Enables Machine-Guided Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/aav.txt)
- **Activity-Enhancing Mutations in an E3 Ubiquitin Ligase Identified by High-Throughput Mutagenesis** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/e4b.txt)
- **Proximal Exploration for Model-Guided Protein Sequence Design** - exploration) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/proximal.txt)
- **Single-Mutation Fitness Landscapes for an Enzyme on Multiple Substrates Reveal Specificity Is Globally Encoded** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/amie.txt)
- **Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coliC** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/lgk.txt)
- **ViennaRNA Package 2.0** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/vienna_rna.txt)
- **Local Fitness Landscape of the Green Fluorescent Protein** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gfp.txt)
- **Human 5 UTR Design and Variant Effect Prediction from a Massively Parallel Translation Assay** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/utr.txt)
- **An Easy-to-Use Real-World Multi-Objective Optimization Problem Suite** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/re_suite.txt)
- **GTOPX Space Mission Benchmarks** - solver.com/index.php/about/benchmarks/gtopx) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gtopx.txt)
- **SOO-Bench: Benchmarks for Evaluating the Stability of Offline Black-Box Optimization** - 123/SOO-Bench) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/soo.txt)
- **Comprehensive AAV Capsid Fitness Landscape Reveals a Viral Gene and Enables Machine-Guided Design** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/aav.txt)
- **Data-Driven Offline Optimization for Architecting Hardware Accelerators** - research/google-research/tree/master/prime) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hardware.txt)
- **Activity-Enhancing Mutations in an E3 Ubiquitin Ligase Identified by High-Throughput Mutagenesis** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/e4b.txt)
- **Proximal Exploration for Model-Guided Protein Sequence Design** - exploration) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/proximal.txt)
- **Single-Mutation Fitness Landscapes for an Enzyme on Multiple Substrates Reveal Specificity Is Globally Encoded** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/amie.txt)
- **Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coliC** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/lgk.txt)
- **Deep Mutational Scanning of an RRM Domain of the Saccharomyces Cerevisiae Poly(A)-Binding Protein** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/pab.txt)
- **Neural Architecture Search as Multiobjective Optimization Benchmarks: Problem Formulation and Performance Assessment** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/c10.txt)
- **Deep Mutational Scanning of an RRM Domain of the Saccharomyces Cerevisiae Poly(A)-Binding Protein** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/pab.txt)
- **A Framework for Exhaustively Mapping Functional Missense Variants** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ube.txt)
- **Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/regex.txt)
- **Survey of Variation in Human Transcription Factors Reveals Prevalent DNA Binding Changes** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/tfbind.txt)
- **Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/antigen.txt)
- **Learning Multiple Layers of Features from Tiny Images** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/nbs.txt)
- **Offline Multi-Objective Optimization** - Xi Tan et al., ICML 2024) [💻](https://github.com/lamda-bbo/offline-moo) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/offline_moo.txt)
- **Prediction-Guided Multi-Objective Reinforcement Learning for Continuous Robot Control** - gfx/PGMORL) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/robot_weight.txt)
- **Latent Conservative Objective Models for Offline Data-Driven Crystal Structure Prediction** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/latent_crystal.txt)
- **HPOBench: A Collection of Reproducible Multi-Fidelity Benchmark Problems for HPO** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hpobench.txt)
- **Bayesian Optimization of Active Materials for Lithium-Ion Batteries** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/battery.txt)
- **Neural Architecture Search with Reinforcement Learning** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/NAS.txt)
- **A Framework for Exhaustively Mapping Functional Missense Variants** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ube.txt)
- **Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/regex.txt)
- **Survey of Variation in Human Transcription Factors Reveals Prevalent DNA Binding Changes** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/tfbind.txt)
- **Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/antigen.txt)
- **Offline Multi-Objective Optimization** - Xi Tan et al., ICML 2024) [💻](https://github.com/lamda-bbo/offline-moo) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/offline_moo.txt)
- **Latent Conservative Objective Models for Offline Data-Driven Crystal Structure Prediction** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/latent_crystal.txt)
- **Bayesian Optimization of Active Materials for Lithium-Ion Batteries** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/battery.txt)
- **Neural Architecture Search with Reinforcement Learning** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/NAS.txt)
- **Neural Architecture Search as Multiobjective Optimization Benchmarks: Problem Formulation and Performance Assessment** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/c10.txt)
- **Learning Multiple Layers of Features from Tiny Images** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/nbs.txt)
- **Prediction-Guided Multi-Objective Reinforcement Learning for Continuous Robot Control** - gfx/PGMORL) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/robot_weight.txt)
- **HPOBench: A Collection of Reproducible Multi-Fidelity Benchmark Problems for HPO** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hpobench.txt)
- **A Benchmark of Kriging-Based Infill Criteria for Noisy Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/sphere.txt)
- **Scalable Test Problems for Evolutionary Multiobjective Optimization** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/deb2005.txt)
- **Local Fitness Landscape of the Green Fluorescent Protein** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/gfp.txt)
- **Human 5 UTR Design and Variant Effect Prediction from a Massively Parallel Translation Assay** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/utr.txt)
- **Single-Mutation Fitness Landscapes for an Enzyme on Multiple Substrates Reveal Specificity Is Globally Encoded** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/amie.txt)
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Evaluation Metric
- **SOO-Bench: Benchmarks for Evaluating the Stability of Offline Black-Box Optimization** - 123/SOO-Bench) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/soo.txt)
- **Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization** - bench) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/design_bench.txt)
- **Multiobjective Optimization Using Evolutionary Algorithms — A Comparative Case Study** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hv.txt)
- **The Balance between Proximity and Diversity in Multiobjective Evolutionary Algorithms** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/igd.txt)
- **Improving Protein Optimization with Smoothed Fitness Landscapes** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ggs.txt)
- **Multiobjective Optimization Using Evolutionary Algorithms — A Comparative Case Study** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hv.txt)
- **The Balance between Proximity and Diversity in Multiobjective Evolutionary Algorithms** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/igd.txt)
- **Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization** - bench) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/design_bench.txt)
- **Improving Protein Optimization with Smoothed Fitness Landscapes** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/ggs.txt)
- **Diversity By Design: Leveraging Distribution Matching for Offline Model-Based Optimization** - s-yao/DynAMO) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/diversitybydesign.txt)
- **Diversity By Design: Leveraging Distribution Matching for Offline Model-Based Optimization** - s-yao/DynAMO) [📖](https://github.com/mila-iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/diversitybydesign.txt)
- **Multiobjective Optimization Using Evolutionary Algorithms — A Comparative Case Study** - iqia/Awesome-Offline-Model-Based-Optimization/blob/main/bibtex/hv.txt)
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Latest Updates
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🌟 What is Offline Model-Based Optimization?
- Offline Dataset - dimensional objective value vector.
- Offline Dataset - dimensional objective value vector.
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