arXiv subjects

Nicholas Matthew Boffi

Publications and source records attributed to Nicholas Matthew Boffi.

4 recordsLinked to original sources

arXiv2026

Few-step Cofolding with All-Atom Flow Maps

All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems. Generating structures at the atomic level of fidelity, however, typically requires expensive iterative diffusion rollouts, making both conventional deployment and inference-time search techniques computationally costly. In this paper, we introduce the Denoiser Cofolding All-Atom Flowmap (DeCAF) framework for distilling state-of-the-art all-atom cofolding models into all-atom flow maps that produce high-quality samples in only a few inference steps. We build DeCAF on a denoiser-based formulation of flow maps with endpoint losses that naturally support SE(3) rigid alignment, which we show is critical for training accurate models. We further derive a simple change of variables that lets DeCAF operate in the σ-space noise schedule of EDM-style architectures, enabling direct distillation from pretrained cofolding diffusion models. Equipped with DeCAF's flowmap lookahead, we introduce a purpose-built inference-time framework that improves sampling through reward-guided search. Empirically, DeCAF-Boltz statistically improves over Boltz-1x in both accuracy (RMSD) and physical validity scores of protein-ligand poses at strict NFE budgets on the challenging Runs N' Poses, while also showing a more optimal Pareto frontier across all inference compute budgets on PoseBusters. Distilling the state-of-the-art Pearl cofolding model, DeCAF-Pearl outperforms diffusion-based cofolding models and matches its teacher on success rate while using 5x fewer NFEs. We release our code at https://github.com/genesistherapeutics/decaf.

cs.LG↗

arXiv2026

Diamond Maps: Efficient Reward Alignment via Stochastic Flow Maps

Flow and diffusion models produce high-quality samples, but adapting them to user preferences or constraints post-training remains costly and brittle, a challenge commonly called reward alignment. We argue that efficient reward alignment should be a property of the generative model itself, not an afterthought, and redesign the model for adaptability. We propose "Diamond Maps", stochastic flow map models that enable efficient and accurate alignment to arbitrary rewards at inference time. Diamond Maps amortize many simulation steps into a single-step sampler, like flow maps, while preserving the stochasticity required for optimal reward alignment. This design makes search, Sequential Monte Carlo, and guidance scalable by enabling efficient and consistent estimation of the value function. Our experiments show that Diamond Maps can be learned efficiently via distillation from GLASS Flows, achieve stronger reward alignment performance, and scale better than existing methods. Our results point toward a practical route to generative models that can be rapidly adapted to arbitrary preferences and constraints at inference time.

cs.LG↗

arXiv2026

Joint Distillation for Fast Likelihood Evaluation and Sampling in Flow-based Models

Log-likelihood evaluation enables important capabilities in generative models, including model comparison, certain fine-tuning objectives, and many downstream applications. Yet paradoxically, some of today's best generative models -- diffusion and flow-based models -- still require hundreds to thousands of neural function evaluations (NFEs) to compute a single likelihood. While recent distillation methods have successfully accelerated sampling to just a few steps, they achieve this at the cost of likelihood tractability: existing approaches either abandon likelihood computation entirely or still require expensive integration over full trajectories. We present fast flow joint distillation (F2D2), a framework that simultaneously reduces the number of NFEs required for both sampling and likelihood evaluation by two orders of magnitude. Our key insight is that in continuous normalizing flows, the coupled ODEs for sampling and likelihood are computed from a shared underlying velocity field, allowing us to jointly distill both the sampling trajectory and cumulative divergence using a single flow map. F2D2 is modular, compatible with existing flow-based few-step sampling models, and requires only an additional divergence prediction head. Experiments demonstrate F2D2's capability of achieving accurate log-likelihood with few-step evaluations while maintaining high sample quality, solving a long-standing computational bottleneck in flow-based generative models. As an application of our approach, we propose a lightweight self-guidance method that enables a 2-step MeanFlow to outperform a 1024 step flow matching model with only a single additional backward NFE.

cs.LG↗

arXiv2026

Pre-Generating Multi-Difficulty PDE Data for Few-Shot Neural PDE Solvers

A key aspect of learned partial differential equation (PDE) solvers is that the main cost often comes from generating training data with classical solvers rather than learning the model itself. Another is that there are clear axes of difficulty--e.g., more complex geometries and higher Reynolds numbers--along which problems become (1) harder for classical solvers and thus (2) more likely to benefit from neural speedups. Towards addressing this chicken-and-egg challenge, we study difficulty transfer on 2D incompressible Navier-Stokes, systematically varying task complexity along geometry (number and placement of obstacles), physics (Reynolds number), and their combination. Similar to how it is possible to spend compute to pre-train foundation models and improve their performance on downstream tasks, we find that by classically solving (analogously pre-generating) many low and medium difficulty examples and including them in the training set, it is possible to learn high-difficulty physics from far fewer samples. Furthermore, we show that by combining low and high difficulty data, we can spend 8.9x less compute on pre-generating a dataset to achieve the same error as using only high difficulty examples. Our results highlight that how we allocate classical-solver compute across difficulty levels is as important as how much we allocate overall, and suggest substantial gains from principled curation of pre-generated PDE data for neural solvers. Our code is available at https://github.com/Naman-Choudhary-AI-ML/pregenerating-pde

cs.LG↗