Jacob K. Christopher

Jingyi Cui, Jacob K. Christopher, Ankita Biswas et al.

Point defects affect material properties by altering electronic states and modifying local bonding environments. However, high-throughput first-principles simulations of point defects are costly due to large simulation cells and complex energy landscapes. To this end, we propose a generative framework for simulating point defects, overcoming the limits of costly first-principles simulators. By leveraging a primal-dual algorithm, we introduce a constraint-aware diffusion model which outperforms existing constrained diffusion approaches in this domain. Across six defect configuration settings for Bi2Te3, the proposed approach provides state-of-the-art performance generating physically grounded structures.

Jameson Sandler, Jacob K. Christopher, Thomas Hartvigsen et al.

Speculative decoding has become the standard approach for accelerating Large Language Model (LLM) inference. It exploits a lossless draft-then-verify procedure to circumvent the latency of autoregressive decoding, achieving impressive speed-ups. Yet, current speculative decoding approaches remain limited by two fundamental bottlenecks: (1) the autoregressive dependency during drafting which limits parallelism, and (2) frequent rejections of draft tokens caused by misalignment between the draft and verify models. This paper proposes SpecDiff-2, a novel framework to jointly address these two bottlenecks. It leverages discrete diffusion as a non-autoregressive drafter to address bottleneck (1) and develops novel techniques to calibrate discrete diffusion drafters with autoregressive verifiers, addressing bottleneck (2). Experimental results across a comprehensive benchmark suite show that SpecDiff-2 achieves a new state-of-the-art across reasoning, coding, and mathematical benchmarks, improving tokens-per-second by up to an average of +55% over previous baselines and obtaining up to 5.5x average speed-up over standard decoding, without any loss of accuracy.

Stefano Zampini, Jacob K. Christopher, Luca Oneto et al.

Stable diffusion models represent the state-of-the-art in data synthesis across diverse domains and hold transformative potential for applications in science and engineering, e.g., by facilitating the discovery of novel solutions and simulating systems that are computationally intractable to model explicitly. While there is increasing effort to incorporate physics-based constraints into generative models, existing techniques are either limited in their applicability to latent diffusion frameworks or lack the capability to strictly enforce domain-specific constraints. To address this limitation this paper proposes a novel integration of stable diffusion models with constrained optimization frameworks, enabling the generation of outputs satisfying stringent physical and functional requirements. The effectiveness of this approach is demonstrated through material design experiments requiring adherence to precise morphometric properties, challenging inverse design tasks involving the generation of materials inducing specific stress-strain responses, and copyright-constrained content generation tasks. All code has been released at https://github.com/RAISELab-atUVA/Constrained-Stable-Diffusion.

Jacob K. Christopher, James E. Warner, Ferdinando Fioretto

Deep generative models provide state-of-the-art performance across a wide array of applications, with recent studies showing increasing applicability for science and engineering. Despite a growing corpus of literature focused on the integration of physics-based constraints into the generation process, existing approaches fail to enforce strict constraint satisfaction while maintaining sample quality. In particular, training-free constrained sampling methods, while providing per-sample feasibility guarantees, introduce a fundamental mismatch between the training objective and the constrained sampling procedure, often leading to performance degradation. Identifying this training-sampling misalignment as a central limitation of current constrained generative modeling approaches, this paper proposes Constraint-Aware Flow Matching, a novel end-to-end framework that explicitly incorporates constraint projections into the training objective. By aligning the model's learned dynamics with the constrained sampling process, the proposed method mitigates distributional shift induced by projection-based corrections, enabling high-quality constrained generation. The proposed approach is evaluated on three challenging real-world benchmarks, illustrating the generality and efficacy of the method.

Jacob K. Christopher, Michael Cardei, Jinhao Liang et al.

Despite the remarkable generative capabilities of diffusion models, their integration into safety-critical or scientifically rigorous applications remains hindered by the need to ensure compliance with stringent physical, structural, and operational constraints. To address this challenge, this paper introduces Neuro-Symbolic Diffusion (NSD), a novel framework that interleaves diffusion steps with symbolic optimization, enabling the generation of certifiably consistent samples under user-defined functional and logic constraints. This key feature is provided for both standard and discrete diffusion models, enabling, for the first time, the generation of both continuous (e.g., images and trajectories) and discrete (e.g., molecular structures and natural language) outputs that comply with constraints. This ability is demonstrated on tasks spanning three key challenges: (1) Safety, in the context of non-toxic molecular generation and collision-free trajectory optimization; (2) Data scarcity, in domains such as drug discovery and materials engineering; and (3) Out-of-domain generalization, where enforcing symbolic constraints allows adaptation beyond the training distribution.

Jinhao Liang, Jacob K. Christopher, Sven Koenig et al.

Multi-Agent Path Finding (MAPF) is a fundamental problem in robotics, requiring the computation of collision-free paths for multiple agents moving from their respective start to goal positions. Coordinating multiple agents in a shared environment poses significant challenges, especially in continuous spaces where traditional optimization algorithms struggle with scalability. Moreover, these algorithms often depend on discretized representations of the environment, which can be impractical in image-based or high-dimensional settings. Recently, diffusion models have shown promise in single-agent path planning, capturing complex trajectory distributions and generating smooth paths that navigate continuous, high-dimensional spaces. However, directly extending diffusion models to MAPF introduces new challenges since these models struggle to ensure constraint feasibility, such as inter-agent collision avoidance. To overcome this limitation, this work proposes a novel approach that integrates constrained optimization with diffusion models for MAPF in continuous spaces. This unique combination directly produces feasible multi-agent trajectories that respect collision avoidance and kinematic constraints. The effectiveness of our approach is demonstrated across various challenging simulated scenarios of varying dimensionality.

Jacob K. Christopher, Austin Seamann, Jingyi Cui et al.

Diffusion models offer a powerful means of capturing the manifold of realistic protein structures, enabling rapid design for protein engineering tasks. However, existing approaches observe critical failure modes when precise constraints are necessary for functional design. To this end, we present a constrained diffusion framework for structure-guided protein design, ensuring strict adherence to functional requirements while maintaining precise stereochemical and geometric feasibility. The approach integrates proximal feasibility updates with ADMM decomposition into the generative process, scaling effectively to the complex constraint sets of this domain. We evaluate on challenging protein design tasks, including motif scaffolding and vacancy-constrained pocket design, while introducing a novel curated benchmark dataset for motif scaffolding in the PDZ domain. Our approach achieves state-of-the-art, providing perfect satisfaction of bonding and geometric constraints with no degradation in structural diversity.