A.1 Equations for Conformational Energy Landscape Overlap Analysis To quantify the similarity between the protein conformations generated by AI-based models and those in the ProteinConformers dataset, the following three commonly used overlap metrics are employed: Interaction overlap, coverage, and the Jaccard index. These metrics evaluate the extent of agreement in low-energy regions between the protein conformers from different models of the same protein, based on a specified energy threshold. Let A = {Ai,j} and B = {Bi,j} where i,j [0,N], denote the two-dimensional free energy landscapes corresponding of two conformational ensembles. Each element Ai,j and Bi,j represents the free energy value at a specific grid point in the conformational energy landscape. For a given energy threshold τ (e.g., 40 kJ/mol), the number of shared low-energy conformations is defined as: |A B| = Figure 6: Comparison of conformational landscapes for protein T1030, generated by ProteinConformers and protein conformation generative models.

Guidance techniques are commonly used in diffusion and flow models to improve image quality and input consistency for conditional generative tasks such as classconditional and text-to-image generation. In particular, classifier-free guidance (CFG) is the most widely adopted guidance technique. It results, however, in trade-offs across quality, diversity and consistency: improving some at the expense of others. While recent work has shown that it is possible to disentangle thesefactors to some extent, such methods come with an overhead of requiring an additional (weaker) model, or require more forward passes per sampling step. In this paper, we propose Entropy Rectifying Guidance (ERG), a simple and effective guidance method based on inference-time changes in the attention mechanism of state-of-the-art diffusion transformer architectures, which allows for simultaneousimprovements over image quality, diversity and prompt consistency. ERG is more general than CFG and similar guidance techniques, as it extends to unconditional sampling. We show that ERG results in significant improvements in various tasks, including text-to-image, class-conditional and unconditional image generation. We also show that ERG can be seamlessly combined with other recent guidance methods such as CADS and APG, further improving generation results.

Generalization is a key challenge in machine learning, specifically in reasoning tasks, where models are expected to solve problems more complex than those encountered during training. Existing approaches typically train reasoning models in an end-to-end fashion, directly mapping input instances to solutions. While this allows models to learn useful heuristics from data, it often results in limited generalization beyond the training distribution. In this work, we propose a novel approach to reasoning generalization by learning energy landscapes over the solution spaces of smaller, more tractable subproblems. At test time, we construct a global energy landscape for a given problem by combining the energy functions of multiple subproblems. This compositional approach enables the incorporation of additional constraints during inference, allowing the construction of energy landscapes for problems of increasing difficulty. To improve the sample quality from this newly constructed energy landscape, we introduce Parallel Energy Minimization (PEM). We evaluate our approach on a wide set of reasoning problems. Our method outperforms existing state-of-the-art methods, demonstrating its ability to generalize to larger and more complex problems.

While energy-based models have recently proven to be a powerful framework for learning to reason with neural networks, their practical application is still limited by computational cost. That is, existing methods for energy-based iterative reasoning suffer from computational bottlenecks by relying on expensive optimization routines during training and especially during inference.

We address the challenge of training diffusion models to sample from unnormalized energy distributions in the absence of data, the so-called diffusion samplers. Although these approaches have shown promise, they struggle to scale in more demanding scenarios where energy evaluations are expensive and the sampling space is high-dimensional. To address this limitation, we propose a scalable and sample-efficient framework that properly harmonizes the powerful classical sampling method and the diffusion sampler. Specifically, we utilize Monte Carlo Markov chain (MCMC) samplers with a novelty-based auxiliary energy as a Searcher to collect off-policy samples, using an auxiliary energy function to compensate for exploring modes the diffusion sampler rarely visits. These off-policy samples are then combined with on-policy data to train the diffusion sampler, thereby expanding its coverage of the energy landscape. Furthermore, we identify primacy bias, i.e., the preference of samplers for early experience during training, as the main cause of mode collapse during training, and introduce a periodic re-initialization trick to resolve this issue. Our method significantly improves sample efficiency on standard benchmarks for diffusion samplers and also excels at higher-dimensional problems and real-world molecular conformer generation.

Generalization is a key challenge in machine learning, specifically in reasoning tasks, where models are expected to solve problems more complex than those encountered during training. Existing approaches typically train reasoning models in an end-to-end fashion, directly mapping input instances to solutions. While this allows models to learn useful heuristics from data, it often results in limited generalization beyond the training distribution. In this work, we propose a novel approach to reasoning generalization by learning energy landscapes over the solution spaces of smaller, more tractable subproblems. At test time, we construct a global energy landscape for a given problem by combining the energy functions of multiple subproblems. This compositional approach enables the incorporation of additional constraints during inference, allowing the construction of energy landscapes for problems of increasing difficulty. To improve the sample quality from this newly constructed energy landscape, we introduce Parallel Energy Minimization (PEM). We evaluate our approach on a wide set of reasoning problems. Our method outperforms existing state-of-the-art methods, demonstrating its ability to generalize to larger and more complex problems.

Conditional diffusion models have shown remarkable success in visual content generation, producing high-quality samples across various domains, largely due to classifier-free guidance (CFG). Recent attempts to extend guidance to unconditional models have relied on heuristic techniques, resulting in suboptimal generation quality and unintended effects. In this work, we propose Smoothed Energy Guidance (SEG), a novel training-and condition-free approach that leverages the energy-based perspective of the self-attention mechanism to enhance image generation. By defining the energy of self-attention, we introduce a method to reduce the curvature of the energy landscape of attention and use the output as the unconditional prediction. Practically, we control the curvature of the energy landscape by adjusting the Gaussian kernel parameter while keeping the guidance scale parameter fixed. Additionally, we present a query blurring method that is equivalent to blurring the entire attention weights without incurring quadratic complexity in the number of tokens. In our experiments, SEG achieves a Pareto improvement in both quality and the reduction of side effects.