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}.

Cell Morphology-Guided Small Molecule Generation with GFlowNets

High-content phenotypic screening, including high-content imaging (HCI), has gained popularity in the last few years for its ability to characterize novel therapeutics without prior knowledge of the protein target. When combined with deep learning techniques to predict and represent molecular-phenotype interactions, these advancements hold the potential to significantly accelerate and enhance drug discovery applications. This work focuses on the novel task of HCI-guided molecular design. Generative models for molecule design could be guided by HCI data, for example with a supervised model that links molecules to phenotypes of interest as a reward function. However, limited labeled data, combined with the high-dimensional readouts, can make training these methods challenging and impractical. We consider an alternative approach in which we leverage an unsupervised multimodal joint embedding to define a latent similarity as a reward for GFlowNets. The proposed model learns to generate new molecules that could produce phenotypic effects similar to those of the given image target, without relying on pre-annotated phenotypic labels. We demonstrate that the proposed method generates molecules with high morphological and structural similarity to the target, increasing the likelihood of similar biological activity, as confirmed by an independent oracle model.

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.

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.

Conformalized Deep Splines for Optimal and Efficient Prediction Sets

Uncertainty estimation is critical in high-stakes machine learning applications. One effective way to estimate uncertainty is conformal prediction, which can provide predictive inference with statistical coverage guarantees. We present a new conformal regression method, Spline Prediction Intervals via Conformal Estimation (SPICE), that estimates the conditional density using neural-network-parameterized splines. We prove universal approximation and optimality results for SPICE, which are empirically validated by our experiments. SPICE is compatible with two different efficient-to-compute conformal scores, one oracle-optimal for marginal coverage (SPICE-ND) and the other asymptotically optimal for conditional coverage (SPICE-HPD). Results on benchmark datasets demonstrate SPICE-ND models achieve the smallest average prediction set sizes, including average size reductions of nearly 50% for some datasets compared to the next best baseline. SPICE-HPD models achieve the best conditional coverage compared to baselines. The SPICE implementation is made available.

Complex Preferences for Different Convergent Priors in Discrete Graph Diffusion

Diffusion models have achieved state-of-the-art performance in generating many different kinds of data, including images, text, and videos. Despite their success, there has been limited research on how the underlying diffusion process and the final convergent prior can affect generative performance; this research has also been limited to continuous data types and a score-based diffusion framework. To fill this gap, we explore how different discrete diffusion kernels (which converge to different prior distributions) affect the performance of diffusion models for graphs. To this end, we developed a novel formulation of a family of discrete diffusion kernels which are easily adjustable to converge to different Bernoulli priors, and we study the effect of these different kernels on generative performance. We show that the quality of generated graphs is sensitive to the prior used, and that the optimal choice cannot be explained by obvious statistics or metrics, which challenges the intuitions which previous works have suggested.

RINGER: Rapid Conformer Generation for Macrocycles with Sequence-Conditioned Internal Coordinate Diffusion

Macrocyclic peptides are an emerging therapeutic modality, yet computational approaches for accurately sampling their diverse 3D ensembles remain challenging due to their conformational diversity and geometric constraints. Here, we introduce RINGER, a diffusion-based transformer model for sequence-conditioned generation of macrocycle structures based on internal coordinates. RINGER provides fast backbone sampling while respecting key structural invariances of cyclic peptides. Through extensive benchmarking and analysis against gold-standard conformer ensembles of cyclic peptides generated with metadynamics, we demonstrate how RINGER generates both high-quality and diverse geometries at a fraction of the computational cost. Our work lays the foundation for improved sampling of cyclic geometries and the development of geometric learning methods for peptides.

GraphGUIDE: interpretable and controllable conditional graph generation with discrete Bernoulli diffusion

Diffusion models achieve state-of-the-art performance in generating realistic objects and have been successfully applied to images, text, and videos. Recent work has shown that diffusion can also be defined on graphs, including graph representations of drug-like molecules. Unfortunately, it remains difficult to perform conditional generation on graphs in a way which is interpretable and controllable. In this work, we propose GraphGUIDE, a novel framework for graph generation using diffusion models, where edges in the graph are flipped or set at each discrete time step. We demonstrate GraphGUIDE on several graph datasets, and show that it enables full control over the conditional generation of arbitrary structural properties without relying on predefined labels. Our framework for graph diffusion can have a large impact on the interpretable conditional generation of graphs, including the generation of drug-like molecules with desired properties in a way which is informed by experimental evidence.