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Masatoshi Uehara

Publications and source records attributed to Masatoshi Uehara.

At least 19 recordsLinked to original sources
arXiv2026

Iterative Distillation for Reward-Guided Fine-Tuning of Diffusion Models in Biomolecular Design

We address the problem of fine-tuning diffusion models for reward-guided generation in biomolecular design. While diffusion models have proven highly effective in modeling complex, high-dimensional data distributions, real-world applications often demand more than high-fidelity generation, requiring optimization with respect to potentially non-differentiable reward functions such as physics-based simulation or rewards based on scientific knowledge. Although RL methods have been explored to fine-tune diffusion models for such objectives, they often suffer from instability, low sample efficiency, and mode collapse due to their on-policy nature. In this work, we propose an iterative distillation-based fine-tuning framework that enables diffusion models to optimize for arbitrary reward functions. Our method casts the problem as policy distillation: it collects off-policy data during the roll-in phase, simulates reward-based soft-optimal policies during roll-out, and updates the model by minimizing the KL divergence between the simulated soft-optimal policy and the current model policy. Our off-policy formulation, combined with KL divergence minimization, enhances training stability and sample efficiency compared to existing RL-based methods. Empirical results demonstrate the effectiveness and superior reward optimization of our approach across diverse tasks in protein, small molecule, and regulatory DNA design. The source code is released at (https://divelab.github.io/VIDD/).

cs.LG↗
arXiv2025

Dynamic Search for Inference-Time Alignment in Diffusion Models

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

cs.LG↗
arXiv2025

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

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arXiv2025

Adding Conditional Control to Diffusion Models with Reinforcement Learning

Diffusion models are powerful generative models that allow for precise control over the characteristics of the generated samples. While these diffusion models trained on large datasets have achieved success, there is often a need to introduce additional controls in downstream fine-tuning processes, treating these powerful models as pre-trained diffusion models. This work presents a novel method based on reinforcement learning (RL) to add such controls using an offline dataset comprising inputs and labels. We formulate this task as an RL problem, with the classifier learned from the offline dataset and the KL divergence against pre-trained models serving as the reward functions. Our method, $\textbf{CTRL}$ ($\textbf{C}$onditioning pre-$\textbf{T}$rained diffusion models with $\textbf{R}$einforcement $\textbf{L}$earning), produces soft-optimal policies that maximize the abovementioned reward functions. We formally demonstrate that our method enables sampling from the conditional distribution with additional controls during inference. Our RL-based approach offers several advantages over existing methods. Compared to classifier-free guidance, it improves sample efficiency and can greatly simplify dataset construction by leveraging conditional independence between the inputs and additional controls. Additionally, unlike classifier guidance, it eliminates the need to train classifiers from intermediate states to additional controls. The code is available at https://github.com/zhaoyl18/CTRL.

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arXiv2025

Reward-Guided Iterative Refinement in Diffusion Models at Test-Time with Applications to Protein and DNA Design

To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their significance, current approaches predominantly focus on single-shot generation, transitioning from fully noised to denoised states. We propose a novel framework for inference-time reward optimization with diffusion models inspired by evolutionary algorithms. Our approach employs an iterative refinement process consisting of two steps in each iteration: noising and reward-guided denoising. This sequential refinement allows for the gradual correction of errors introduced during reward optimization. Besides, we provide a theoretical guarantee for our framework. Finally, we demonstrate its superior empirical performance in protein and cell-type-specific regulatory DNA design. The code is available at \href{https://github.com/masa-ue/ProDifEvo-Refinement}{https://github.com/masa-ue/ProDifEvo-Refinement}.

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arXiv2025

Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and Review

This tutorial provides an in-depth guide on inference-time guidance and alignment methods for optimizing downstream reward functions in diffusion models. While diffusion models are renowned for their generative modeling capabilities, practical applications in fields such as biology often require sample generation that maximizes specific metrics (e.g., stability, affinity in proteins, closeness to target structures). In these scenarios, diffusion models can be adapted not only to generate realistic samples but also to explicitly maximize desired measures at inference time without fine-tuning. This tutorial explores the foundational aspects of such inference-time algorithms. We review these methods from a unified perspective, demonstrating that current techniques -- such as Sequential Monte Carlo (SMC)-based guidance, value-based sampling, and classifier guidance -- aim to approximate soft optimal denoising processes (a.k.a. policies in RL) that combine pre-trained denoising processes with value functions serving as look-ahead functions that predict from intermediate states to terminal rewards. Within this framework, we present several novel algorithms not yet covered in the literature. Furthermore, we discuss (1) fine-tuning methods combined with inference-time techniques, (2) inference-time algorithms based on search algorithms such as Monte Carlo tree search, which have received limited attention in current research, and (3) connections between inference-time algorithms in language models and diffusion models. The code of this tutorial on protein design is available at https://github.com/masa-ue/AlignInversePro

cs.AI↗
arXiv2024

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (\textit{e.g.}, classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (\textit{e.g.}, classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at \href{https://github.com/masa-ue/SVDD}{https://github.com/masa-ue/SVDD}.

cs.LG↗
arXiv2024

Functional Graphical Models: Structure Enables Offline Data-Driven Optimization

While machine learning models are typically trained to solve prediction problems, we might often want to use them for optimization problems. For example, given a dataset of proteins and their corresponding fluorescence levels, we might want to optimize for a new protein with the highest possible fluorescence. This kind of data-driven optimization (DDO) presents a range of challenges beyond those in standard prediction problems, since we need models that successfully predict the performance of new designs that are better than the best designs seen in the training set. It is not clear theoretically when existing approaches can even perform better than the naive approach that simply selects the best design in the dataset. In this paper, we study how structure can enable sample-efficient data-driven optimization. To formalize the notion of structure, we introduce functional graphical models (FGMs) and show theoretically how they can provide for principled data-driven optimization by decomposing the original high-dimensional optimization problem into smaller sub-problems. This allows us to derive much more practical regret bounds for DDO, and the result implies that DDO with FGMs can achieve nearly optimal designs in situations where naive approaches fail due to insufficient coverage of the offline data. We further present a data-driven optimization algorithm that inferes the FGM structure itself, either over the original input variables or a latent variable representation of the inputs.

cs.LG↗
arXiv2024

Feedback Efficient Online Fine-Tuning of Diffusion Models

Diffusion models excel at modeling complex data distributions, including those of images, proteins, and small molecules. However, in many cases, our goal is to model parts of the distribution that maximize certain properties: for example, we may want to generate images with high aesthetic quality, or molecules with high bioactivity. It is natural to frame this as a reinforcement learning (RL) problem, in which the objective is to fine-tune a diffusion model to maximize a reward function that corresponds to some property. Even with access to online queries of the ground-truth reward function, efficiently discovering high-reward samples can be challenging: they might have a low probability in the initial distribution, and there might be many infeasible samples that do not even have a well-defined reward (e.g., unnatural images or physically impossible molecules). In this work, we propose a novel reinforcement learning procedure that efficiently explores on the manifold of feasible samples. We present a theoretical analysis providing a regret guarantee, as well as empirical validation across three domains: images, biological sequences, and molecules.

cs.LG↗
arXiv2024

Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review

This tutorial provides a comprehensive survey of methods for fine-tuning diffusion models to optimize downstream reward functions. While diffusion models are widely known to provide excellent generative modeling capability, practical applications in domains such as biology require generating samples that maximize some desired metric (e.g., translation efficiency in RNA, docking score in molecules, stability in protein). In these cases, the diffusion model can be optimized not only to generate realistic samples but also to explicitly maximize the measure of interest. Such methods are based on concepts from reinforcement learning (RL). We explain the application of various RL algorithms, including PPO, differentiable optimization, reward-weighted MLE, value-weighted sampling, and path consistency learning, tailored specifically for fine-tuning diffusion models. We aim to explore fundamental aspects such as the strengths and limitations of different RL-based fine-tuning algorithms across various scenarios, the benefits of RL-based fine-tuning compared to non-RL-based approaches, and the formal objectives of RL-based fine-tuning (target distributions). Additionally, we aim to examine their connections with related topics such as classifier guidance, Gflownets, flow-based diffusion models, path integral control theory, and sampling from unnormalized distributions such as MCMC. The code of this tutorial is available at https://github.com/masa-ue/RLfinetuning_Diffusion_Bioseq

cs.LG↗
arXiv2024

Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models

AI-driven design problems, such as DNA/protein sequence design, are commonly tackled from two angles: generative modeling, which efficiently captures the feasible design space (e.g., natural images or biological sequences), and model-based optimization, which utilizes reward models for extrapolation. To combine the strengths of both approaches, we adopt a hybrid method that fine-tunes cutting-edge diffusion models by optimizing reward models through RL. Although prior work has explored similar avenues, they primarily focus on scenarios where accurate reward models are accessible. In contrast, we concentrate on an offline setting where a reward model is unknown, and we must learn from static offline datasets, a common scenario in scientific domains. In offline scenarios, existing approaches tend to suffer from overoptimization, as they may be misled by the reward model in out-of-distribution regions. To address this, we introduce a conservative fine-tuning approach, BRAID, by optimizing a conservative reward model, which includes additional penalization outside of offline data distributions. Through empirical and theoretical analysis, we demonstrate the capability of our approach to outperform the best designs in offline data, leveraging the extrapolation capabilities of reward models while avoiding the generation of invalid designs through pre-trained diffusion models.

cs.LG↗
arXiv2024

Provable Reward-Agnostic Preference-Based Reinforcement Learning

Preference-based Reinforcement Learning (PbRL) is a paradigm in which an RL agent learns to optimize a task using pair-wise preference-based feedback over trajectories, rather than explicit reward signals. While PbRL has demonstrated practical success in fine-tuning language models, existing theoretical work focuses on regret minimization and fails to capture most of the practical frameworks. In this study, we fill in such a gap between theoretical PbRL and practical algorithms by proposing a theoretical reward-agnostic PbRL framework where exploratory trajectories that enable accurate learning of hidden reward functions are acquired before collecting any human feedback. Theoretical analysis demonstrates that our algorithm requires less human feedback for learning the optimal policy under preference-based models with linear parameterization and unknown transitions, compared to the existing theoretical literature. Specifically, our framework can incorporate linear and low-rank MDPs with efficient sample complexity. Additionally, we investigate reward-agnostic RL with action-based comparison feedback and introduce an efficient querying algorithm tailored to this scenario.

cs.LG↗
arXiv2024

Regularized DeepIV with Model Selection

In this paper, we study nonparametric estimation of instrumental variable (IV) regressions. While recent advancements in machine learning have introduced flexible methods for IV estimation, they often encounter one or more of the following limitations: (1) restricting the IV regression to be uniquely identified; (2) requiring minimax computation oracle, which is highly unstable in practice; (3) absence of model selection procedure. In this paper, we present the first method and analysis that can avoid all three limitations, while still enabling general function approximation. Specifically, we propose a minimax-oracle-free method called Regularized DeepIV (RDIV) regression that can converge to the least-norm IV solution. Our method consists of two stages: first, we learn the conditional distribution of covariates, and by utilizing the learned distribution, we learn the estimator by minimizing a Tikhonov-regularized loss function. We further show that our method allows model selection procedures that can achieve the oracle rates in the misspecified regime. When extended to an iterative estimator, our method matches the current state-of-the-art convergence rate. Our method is a Tikhonov regularized variant of the popular DeepIV method with a non-parametric MLE first-stage estimator, and our results provide the first rigorous guarantees for this empirically used method, showcasing the importance of regularization which was absent from the original work.

cs.LG↗
arXiv2024

Fine-Tuning of Continuous-Time Diffusion Models as Entropy-Regularized Control

Diffusion models excel at capturing complex data distributions, such as those of natural images and proteins. While diffusion models are trained to represent the distribution in the training dataset, we often are more concerned with other properties, such as the aesthetic quality of the generated images or the functional properties of generated proteins. Diffusion models can be finetuned in a goal-directed way by maximizing the value of some reward function (e.g., the aesthetic quality of an image). However, these approaches may lead to reduced sample diversity, significant deviations from the training data distribution, and even poor sample quality due to the exploitation of an imperfect reward function. The last issue often occurs when the reward function is a learned model meant to approximate a ground-truth "genuine" reward, as is the case in many practical applications. These challenges, collectively termed "reward collapse," pose a substantial obstacle. To address this reward collapse, we frame the finetuning problem as entropy-regularized control against the pretrained diffusion model, i.e., directly optimizing entropy-enhanced rewards with neural SDEs. We present theoretical and empirical evidence that demonstrates our framework is capable of efficiently generating diverse samples with high genuine rewards, mitigating the overoptimization of imperfect reward models.

cs.LG↗
arXiv2023

Distributional Offline Policy Evaluation with Predictive Error Guarantees

We study the problem of estimating the distribution of the return of a policy using an offline dataset that is not generated from the policy, i.e., distributional offline policy evaluation (OPE). We propose an algorithm called Fitted Likelihood Estimation (FLE), which conducts a sequence of Maximum Likelihood Estimation (MLE) and has the flexibility of integrating any state-of-the-art probabilistic generative models as long as it can be trained via MLE. FLE can be used for both finite-horizon and infinite-horizon discounted settings where rewards can be multi-dimensional vectors. Our theoretical results show that for both finite-horizon and infinite-horizon discounted settings, FLE can learn distributions that are close to the ground truth under total variation distance and Wasserstein distance, respectively. Our theoretical results hold under the conditions that the offline data covers the test policy's traces and that the supervised learning MLE procedures succeed. Experimentally, we demonstrate the performance of FLE with two generative models, Gaussian mixture models and diffusion models. For the multi-dimensional reward setting, FLE with diffusion models is capable of estimating the complicated distribution of the return of a test policy.

cs.LG↗
arXiv2023

Future-Dependent Value-Based Off-Policy Evaluation in POMDPs

We study off-policy evaluation (OPE) for partially observable MDPs (POMDPs) with general function approximation. Existing methods such as sequential importance sampling estimators and fitted-Q evaluation suffer from the curse of horizon in POMDPs. To circumvent this problem, we develop a novel model-free OPE method by introducing future-dependent value functions that take future proxies as inputs. Future-dependent value functions play similar roles as classical value functions in fully-observable MDPs. We derive a new Bellman equation for future-dependent value functions as conditional moment equations that use history proxies as instrumental variables. We further propose a minimax learning method to learn future-dependent value functions using the new Bellman equation. We obtain the PAC result, which implies our OPE estimator is consistent as long as futures and histories contain sufficient information about latent states, and the Bellman completeness. Finally, we extend our methods to learning of dynamics and establish the connection between our approach and the well-known spectral learning methods in POMDPs.

cs.LG↗
arXiv2023

Offline Minimax Soft-Q-learning Under Realizability and Partial Coverage

In offline reinforcement learning (RL) we have no opportunity to explore so we must make assumptions that the data is sufficient to guide picking a good policy, taking the form of assuming some coverage, realizability, Bellman completeness, and/or hard margin (gap). In this work we propose value-based algorithms for offline RL with PAC guarantees under just partial coverage, specifically, coverage of just a single comparator policy, and realizability of soft (entropy-regularized) Q-function of the single policy and a related function defined as a saddle point of certain minimax optimization problem. This offers refined and generally more lax conditions for offline RL. We further show an analogous result for vanilla Q-functions under a soft margin condition. To attain these guarantees, we leverage novel minimax learning algorithms to accurately estimate soft or vanilla Q-functions with $L^2$-convergence guarantees. Our algorithms' loss functions arise from casting the estimation problems as nonlinear convex optimization problems and Lagrangifying.

cs.LG↗
arXiv2023

Provable Offline Preference-Based Reinforcement Learning

In this paper, we investigate the problem of offline Preference-based Reinforcement Learning (PbRL) with human feedback where feedback is available in the form of preference between trajectory pairs rather than explicit rewards. Our proposed algorithm consists of two main steps: (1) estimate the implicit reward using Maximum Likelihood Estimation (MLE) with general function approximation from offline data and (2) solve a distributionally robust planning problem over a confidence set around the MLE. We consider the general reward setting where the reward can be defined over the whole trajectory and provide a novel guarantee that allows us to learn any target policy with a polynomial number of samples, as long as the target policy is covered by the offline data. This guarantee is the first of its kind with general function approximation. To measure the coverage of the target policy, we introduce a new single-policy concentrability coefficient, which can be upper bounded by the per-trajectory concentrability coefficient. We also establish lower bounds that highlight the necessity of such concentrability and the difference from standard RL, where state-action-wise rewards are directly observed. We further extend and analyze our algorithm when the feedback is given over action pairs.

cs.LG↗