Reward Weighted Classifier-Free Guidance as Policy Improvement in Autoregressive Models

Goal-directed optimization is essential for steering molecular generators to propose candidates with desired properties. However, it is often implemented with policy-gradient reinforcement learning, which requires a generation-trajectory log-probability whose form depends on the model architecture and generation procedure. This makes an optimizer difficult to reuse across architectures and conditional generative designs. Supervised fine-tuning needs none of that machinery, but its update is driven by a fixed dataset, so the reward never enters the update. We introduce Elite-Weighted Supervised Fine-tuning (EW-SFT), which uses reward to guide elite selection of high-scoring molecules, and updates the model by its own pretraining loss on that set. Ablations show that reward information is passed primarily through elite selection, rather than through continuous weighting within the selected set. Because the update consumes only scored molecules and the model's native loss, the same rule applies across autoregressive, masked-diffusion, and discrete-flow generators, and across de novo, motif-extension, and linker-design tasks. Under a fixed budget of 3D shape alignment oracle calls on two kinase reference compounds, EW-SFT consistently outperforms the corresponding native optimizers. It further improves goal-directed optimization under a 2D similarity oracle on four held-out references and achieves comparable performance on a sample-efficiency benchmark without a trajectory-level RL formulation. These results demonstrate that EW-SFT is a unified and effective optimizer across molecular generators, design constraints, references, and oracles.

A major bottleneck in scientific discovery consists of narrowing an exponentially large set of objects, such as proteins or molecules, to a small set of promising candidates with desirable properties. While this process can rely on expert knowledge, recent methods leverage reinforcement learning (RL) guided by a proxy reward function to enable this filtering. By employing various forms of entropy regularization, these methods aim to learn samplers that generate diverse candidates that are highly rated by the proxy function. In this work, we make two main contributions. First, we show that these methods are liable to generate overly diverse, suboptimal candidates in large search spaces. To address this issue, we introduce a novel unified operator that combines several regularized RL operators into a general framework that better targets peakier sampling distributions. Secondly, we offer a novel, robust RL perspective of this filtering process. The regularization can be interpreted as robustness to a compositional form of uncertainty in the proxy function (i.e., the true evaluation of a candidate differs from the proxy's evaluation). Our analysis leads us to a novel, easy-to-use algorithm we name trajectory general mellowmax (TGM): we show it identifies higher quality, diverse candidates than baselines in both synthetic and real-world tasks. Code: https://github.com/marcojira/tgm.

Recent advances in reward modeling show a paradigm shift from discriminative reward models to generative reward models. However, despite their strong capabilities in response ranking, generative reward models have not realized their potential in reinforcement learning (RL). Our analysis reveals that this limitation arises from a mismatch between the comparative nature of generative reward modeling and the scalar scoring paradigm adopted by existing RL algorithms. To bridge this gap, we propose a Ranking-based Reward Construction (RRC) approach, which enables generative reward models to provide more effective RL learning signals by deriving rewards from relative preference rankings. RRC introduces two complementary strategies: self-competitive ranking, which exploits comparisons among sampled responses, and anchor-guided ranking, which enables scalable ranking-based reward construction with a small set of reference responses. Experiments across open-ended chat and reasoning benchmarks demonstrate that RRC substantially improves RL training with generative reward models, achieving consistent gains over existing reward construction approaches. Our code can be found at https://github.com/wangclnlp/RRC.