Autofocused oracles for model-based design
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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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38 more
- 2024Robust Guided Diffusion for Offline Black-Box Optimization1 Oct 2024
- 2024Guided Trajectory Generation with Diffusion Models for Offline Model-based Optimization29 Jun 2024
- 2024Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models30 May 2024
- 2024"Noisier" Noise Contrastive Eestimation is (Almost) Maximum Likelihood27 May 2024
- 2024Design Editing for Offline Model-based Optimization22 May 2024
- 2024Offline Model-Based Optimization via Policy-Guided Gradient Search8 May 2024
- 2024Molecule Design by Latent Prompt Transformer27 Feb 2024
- 2024Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization8 Jan 2024
- 2024From Function to Distribution Modeling: A PAC-Generative Approach to Offline Optimization4 Jan 2024
- 2023Beyond the training set: an intuitive method for detecting distribution shift in model-based optimization9 Nov 2023
- 2023ExPT: Synthetic Pretraining for Few-Shot Experimental Design30 Oct 2023
- 2023ROMO: Retrieval-enhanced Offline Model-based Optimization11 Oct 2023
- 2023Molecule Design by Latent Prompt Transformer5 Oct 2023
- 2023Design from Policies: Conservative Test-Time Adaptation for Offline Policy Optimization26 Jun 2023
- 2023Diffusion Models for Black-Box Optimization12 Jun 2023
- 2023An information-Theoretic Approach to Semi-supervised Transfer Learning11 Jun 2023
- 2023Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences5 Jun 2023
- 2023Is novelty predictable?1 Jun 2023
- 2023Robust Model-Based Optimization for Challenging Fitness Landscapes23 May 2023
- 2023Conservative objective models are a special kind of contrastive divergence-based energy model7 Apr 2023
- 2022Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC20 Dec 2022
- 2022Data-Driven Offline Decision-Making via Invariant Representation Learning21 Nov 2022
- 2022Exploring validation metrics for offline model-based optimisation with diffusion models19 Nov 2022
- 2022Gradient-based Bi-level Optimization for Deep Learning: A Survey24 Jul 2022
- 2022Generative Pretraining for Black-Box Optimization22 Jun 2022
- 2022Bandit Theory and Thompson Sampling-Guided Directed Evolution for Sequence Optimization5 Jun 2022
- 2022Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization17 Feb 2022
- 2022Augmenting Neural Networks with Priors on Function Values10 Feb 2022
- 2022Fourier Representations for Black-Box Optimization over Categorical Variables8 Feb 2022
- 2022Conformal Prediction Under Feedback Covariate Shift for Biomolecular Design8 Feb 2022
- 2021RoMA: Robust Model Adaptation for Offline Model-based Optimization27 Oct 2021
- 2021Data-Driven Offline Optimization For Architecting Hardware Accelerators20 Oct 2021
- 2021Conservative Objective Models for Effective Offline Model-Based Optimization14 Jul 2021
- 2021Deep Extrapolation for Attribute-Enhanced Generation7 Jul 2021
- 2021Amortized Synthesis of Constrained Configurations Using a Differentiable Surrogate16 Jun 2021
- 2021Adaptive machine learning for protein engineering10 Jun 2021
- 2021Protein sequence design with deep generative models9 Apr 2021
- 2021Offline Model-Based Optimization via Normalized Maximum Likelihood Estimation16 Feb 2021
- 2023Diffusion Models for Black-Box Optimizationcited by 75
- 2024Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Modelscited by 24
- 2024Guided Trajectory Generation with Diffusion Models for Offline Model-based Optimizationcited by 15
- 2025Preference-Guided Diffusion for Multi-Objective Offline Optimizationcited by 12
- 2024Design Editing for Offline Model-based Optimizationcited by 10
- 2024Robust Guided Diffusion for Offline Black-Box Optimizationcited by 8
- 2022Exploring validation metrics for offline model-based optimisation with diffusion modelscited by 1
- 2025Preference-Guided Diffusion for Multi-Objective Offline Optimization21 Mar 2025
- 2024Robust Guided Diffusion for Offline Black-Box Optimization1 Oct 2024
- 2024Guided Trajectory Generation with Diffusion Models for Offline Model-based Optimization29 Jun 2024
- 2024Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models30 May 2024
- 2024Design Editing for Offline Model-based Optimization22 May 2024
- 2023Diffusion Models for Black-Box Optimization12 Jun 2023
- 2022Exploring validation metrics for offline model-based optimisation with diffusion models19 Nov 2022
- 2022Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimizationcited by 96
- 2021Conservative Objective Models for Effective Offline Model-Based Optimizationcited by 87
- 2022Conformal Prediction Under Feedback Covariate Shift for Biomolecular Designcited by 53
- 2021RoMA: Robust Model Adaptation for Offline Model-based Optimizationcited by 39
- 2021Offline Model-Based Optimization via Normalized Maximum Likelihood Estimationcited by 38
- 2022Generative Pretraining for Black-Box Optimizationcited by 36
- 2021Protein sequence design with deep generative modelscited by 35
- 2022Data-Driven Offline Decision-Making via Invariant Representation Learningcited by 31
- 2021Data-Driven Offline Optimization For Architecting Hardware Acceleratorscited by 29
- 2022Gradient-based Bi-level Optimization for Deep Learning: A Surveycited by 26
- 2023Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequencescited by 23
- 2023ExPT: Synthetic Pretraining for Few-Shot Experimental Designcited by 22
12 most cited of 42 All 42 (JSON)
- 2026Support-Proximity Augmented Diffusion Estimation for Offline Black-Box Optimization11 May 2026
- 2025Leveraging Discrete Function Decomposability for Scientific Design4 Nov 2025
- 2025ROOT: Rethinking Offline Optimization as Distributional Translation via Probabilistic Bridge19 Sep 2025
- 2025Towards Universal Offline Black-Box Optimization via Learning Language Model Embeddings8 Jun 2025
- 2025Offline Model-Based Optimization: Comprehensive Review21 Mar 2025
- 2025Incorporating Surrogate Gradient Norm to Improve Offline Optimization Techniques6 Mar 2025
- 2025Boosting Offline Optimizers with Surrogate Sensitivity6 Mar 2025
- 2025Overconfident Oracles: Limitations of In Silico Sequence Design Benchmarking24 Feb 2025
- 2024Cliqueformer: Model-Based Optimization with Structured Transformers17 Oct 2024
- 2024Sharpness-Aware Black-Box Optimization16 Oct 2024
- 2024Offline Model-Based Optimization by Learning to Rank15 Oct 2024
- 2024"Noisier" Noise Contrastive Eestimation is (Almost) Maximum Likelihood27 May 2024
12 newest of 42 All 42 (JSON)