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.

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}.

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

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 additional controls, leveraging an offline dataset comprising inputs and corresponding 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. We introduce our method, $\textbf{CTRL}$ ($\textbf{C}$onditioning pre-$\textbf{T}$rained diffusion models with $\textbf{R}$einforcement $\textbf{L}$earning), which produces soft-optimal policies that maximize the abovementioned reward functions. We formally demonstrate that our method enables sampling from the conditional distribution conditioned on additional controls during inference. Our RL-based approach offers several advantages over existing methods. Compared to commonly used classifier-free guidance, our approach improves sample efficiency, and can greatly simplify offline dataset construction by exploiting conditional independence between the inputs and additional controls. Furthermore, unlike classifier guidance, we avoid the need to train classifiers from intermediate states to additional controls.

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.

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.

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.

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.

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.

Source Condition Double Robust Inference on Functionals of Inverse Problems

We consider estimation of parameters defined as linear functionals of solutions to linear inverse problems. Any such parameter admits a doubly robust representation that depends on the solution to a dual linear inverse problem, where the dual solution can be thought as a generalization of the inverse propensity function. We provide the first source condition double robust inference method that ensures asymptotic normality around the parameter of interest as long as either the primal or the dual inverse problem is sufficiently well-posed, without knowledge of which inverse problem is the more well-posed one. Our result is enabled by novel guarantees for iterated Tikhonov regularized adversarial estimators for linear inverse problems, over general hypothesis spaces, which are developments of independent interest.