mlsanityData to 7 Oct 2026

Autofocused oracles for model-based design

arXiv 2006.08052 ↗First posted 14 Jun 2020cs.LG q-bio.QM stat.MLcited by 50

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Abstract (arXiv)

Data-driven design is making headway into a number of application areas, including protein, small-molecule, and materials engineering. The design goal is to construct an object with desired properties, such as a protein that binds to a therapeutic target, or a superconducting material with a higher critical temperature than previously observed. To that end, costly experimental measurements are being replaced with calls to high-capacity regression models trained on labeled data, which can be leveraged in an in silico search for design candidates. However, the design goal necessitates moving into regions of the design space beyond where such models were trained. Therefore, one can ask: should the regression model be altered as the design algorithm explores the design space, in the absence of new data? Herein, we answer this question in the affirmative. In particular, we (i) formalize the data-driven design problem as a non-zero-sum game, (ii) develop a principled strategy for retraining the regression model as the design algorithm proceeds---what we refer to as autofocusing, and (iii) demonstrate the promise of autofocusing empirically.

Key facts. Cited by 50 papers in the map (data through 7 Oct 2026). First posted on arXiv 14 Jun 2020.

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Citing papers per year: 2021: 8; 2022: 10; 2023: 11; 2024: 12; 2025: 8; 2026: 1.

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  1. 2022Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimizationcited by 96
  2. 2021Conservative Objective Models for Effective Offline Model-Based Optimizationcited by 87
  3. 2023Diffusion Models for Black-Box Optimizationcited by 75
  4. 2022Conformal Prediction Under Feedback Covariate Shift for Biomolecular Designcited by 53
  5. 2021RoMA: Robust Model Adaptation for Offline Model-based Optimizationcited by 39
  6. 2021Offline Model-Based Optimization via Normalized Maximum Likelihood Estimationcited by 38
  7. 2022Generative Pretraining for Black-Box Optimizationcited by 36
  8. 2021Protein sequence design with deep generative modelscited by 35
  9. 2022Data-Driven Offline Decision-Making via Invariant Representation Learningcited by 31
  10. 2021Data-Driven Offline Optimization For Architecting Hardware Acceleratorscited by 29
  11. 2022Gradient-based Bi-level Optimization for Deep Learning: A Surveycited by 26
  12. 2024Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Modelscited by 24
38 more
  1. 2023Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequencescited by 23
  2. 2023ExPT: Synthetic Pretraining for Few-Shot Experimental Designcited by 22
  3. 2024Offline Model-Based Optimization via Policy-Guided Gradient Searchcited by 19
  4. 2021Deep Extrapolation for Attribute-Enhanced Generationcited by 18
  5. 2022Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMCcited by 17
  6. 2024Guided Trajectory Generation with Diffusion Models for Offline Model-based Optimizationcited by 15
  7. 2025Offline Model-Based Optimization: Comprehensive Reviewcited by 14
  8. 2021Adaptive machine learning for protein engineeringcited by 13
  9. 2024Offline Model-Based Optimization by Learning to Rankcited by 13
  10. 2025Preference-Guided Diffusion for Multi-Objective Offline Optimizationcited by 12
  11. 2024Design Editing for Offline Model-based Optimizationcited by 10
  12. 2023Design from Policies: Conservative Test-Time Adaptation for Offline Policy Optimizationcited by 8
  13. 2023Molecule Design by Latent Prompt Transformercited by 8
  14. 2024"Noisier" Noise Contrastive Eestimation is (Almost) Maximum Likelihoodcited by 8
  15. 2024Robust Guided Diffusion for Offline Black-Box Optimizationcited by 8
  16. 2021Amortized Synthesis of Constrained Configurations Using a Differentiable Surrogatecited by 6
  17. 2025Boosting Offline Optimizers with Surrogate Sensitivitycited by 6
  18. 2025Towards Universal Offline Black-Box Optimization via Learning Language Model Embeddingscited by 6
  19. 2025Incorporating Surrogate Gradient Norm to Improve Offline Optimization Techniquescited by 5
  20. 2022Fourier Representations for Black-Box Optimization over Categorical Variablescited by 4
  21. 2023Beyond the training set: an intuitive method for detecting distribution shift in model-based optimizationcited by 4
  22. 2025ROOT: Rethinking Offline Optimization as Distributional Translation via Probabilistic Bridgecited by 4
  23. 2023Conservative objective models are a special kind of contrastive divergence-based energy modelcited by 3
  24. 2024Tree Search-Based Evolutionary Bandits for Protein Sequence Optimizationcited by 3
  25. 2024Cliqueformer: Model-Based Optimization with Structured Transformerscited by 3
  26. 2025Overconfident Oracles: Limitations of In Silico Sequence Design Benchmarkingcited by 3
  27. 2022Bandit Theory and Thompson Sampling-Guided Directed Evolution for Sequence Optimizationcited by 2
  28. 2023Robust Model-Based Optimization for Challenging Fitness Landscapescited by 2
  29. 2023Is novelty predictable?cited by 2
  30. 2024Sharpness-Aware Black-Box Optimizationcited by 2
  31. 2022Augmenting Neural Networks with Priors on Function Valuescited by 1
  32. 2022Exploring validation metrics for offline model-based optimisation with diffusion modelscited by 1
  33. 2023ROMO: Retrieval-enhanced Offline Model-based Optimizationcited by 1
  34. 2024From Function to Distribution Modeling: A PAC-Generative Approach to Offline Optimizationcited by 1
  35. 2026Support-Proximity Augmented Diffusion Estimation for Offline Black-Box Optimizationcited by 1
  36. 2023An information-Theoretic Approach to Semi-supervised Transfer Learningcited by 0
  37. 2024Molecule Design by Latent Prompt Transformercited by 0
  38. 2025Leveraging Discrete Function Decomposability for Scientific Designcited by 0