arXiv subjects

Karsten Kreis

Publications and source records attributed to Karsten Kreis.

At least 19 recordsLinked to original sources

arXiv2026

DiLaDiff: Distilled Latent-Augmented Diffusion for Language Modeling

Diffusion language models intrinsically fail to capture correlations between decoded tokens, which leads to a harsh trade-off between sampling quality and throughput. To solve this issue, we propose DiLaDiff, a variant of masked diffusion language models with three components: (1) a continuous latent space with semantic capabilities, learned by an auto-encoder fine-tuned from an existing masked diffusion language model; (2) a latent diffusion model learning the prior over the encoder distribution; (3) a consistency model distilling the learned prior into a few-step latent generative model. We show that, even without distillation, our latent-guided diffusion model outperforms the masked diffusion baseline while significantly accelerating inference. Consistency distillation further lowers the computational overhead of continuous diffusion, such that the latent is generated in negligible time compared to discrete decoding.

cs.LG↗

arXiv2026

Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute

Protein interaction modeling is central to protein design, which has been transformed by machine learning with applications in drug discovery and beyond. In this landscape, structure-based de novo binder design is cast as either conditional generative modeling or sequence optimization via structure predictors ("hallucination"). We argue that this is a false dichotomy and propose Proteina-Complexa, a novel fully atomistic binder generation method unifying both paradigms. We extend recent flow-based latent protein generation architectures and leverage the domain-domain interactions of monomeric computationally predicted protein structures to construct Teddymer, a new large-scale dataset of synthetic binder-target pairs for pretraining. Combined with high-quality experimental multimers, this enables training a strong base model. We then perform inference-time optimization with this generative prior, unifying the strengths of previously distinct generative and hallucination methods. Proteina-Complexa sets a new state of the art in computational binder design benchmarks: it delivers markedly higher in-silico success rates than existing generative approaches, and our novel test-time optimization strategies greatly outperform previous hallucination methods under normalized compute budgets. We also demonstrate interface hydrogen bond optimization, fold class-guided binder generation, and extensions to small molecule targets and enzyme design tasks, again surpassing prior methods. Code, models and new data will be publicly released.

cs.LG↗

arXiv2026

Demystifying Data-Driven Probabilistic Medium-Range Weather Forecasting

The recent revolution in data-driven methods for weather forecasting has lead to a fragmented landscape of complex, bespoke architectures and training strategies, obscuring the fundamental drivers of forecast accuracy. Here, we demonstrate that state-of-the-art probabilistic skill requires neither intricate architectural constraints nor specialized training heuristics. We introduce a scalable framework for learning multi-scale atmospheric dynamics by combining a directly downsampled latent space with a history-conditioned local projector that resolves high-resolution physics. We find that our framework design is robust to the choice of probabilistic estimator, seamlessly supporting stochastic interpolants, diffusion models, and CRPS-based ensemble training. Validated against the Integrated Forecasting System and the deep learning probabilistic model GenCast, our framework achieves statistically significant improvements on most of the variables. These results suggest scaling a general-purpose model is sufficient for state-of-the-art medium-range prediction, eliminating the need for tailored training recipes and proving effective across the full spectrum of probabilistic frameworks.

cs.LG↗

arXiv2026

Exploring Synthesizable Chemical Space with Iterative Pathway Refinements

A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effectively navigate exponentially large combinatorial space of synthesizable molecules and suffer from poor coverage. To address this problem, we introduce ReaSyn, an iterative generative pathway refinement framework that obtains synthesizable analogs to input molecules by projecting them onto synthesizable space. Specifically, we propose a simple synthetic pathway representation that allows for generating pathways in both bottom-up and top-down traversal of synthetic trees. We design ReaSyn so that both bottom-up and top-down pathways can be sampled with a single unified autoregressive model. ReaSyn can thus iteratively refine subtrees of generated synthetic trees in a bidirectional manner. Further, we introduce a discrete flow model that refines the generated pathway at the entire pathway level with edit operations: insertion, deletion, and substitution. The iterative refinement cycle of (1) bottom-up decoding, (2) top-down decoding, and (3) holistic editing constitutes a powerful pathway reasoning strategy, allowing the model to explore the vast space of synthesizable molecules. Experimentally, ReaSyn achieves the highest reconstruction rate and pathway diversity in synthesizable molecule reconstruction and the highest optimization performance in synthesizable goal-directed molecular optimization, and significantly outperforms previous synthesizable projection methods in synthesizable hit expansion. These results highlight ReaSyn's superior ability to navigate combinatorially-large synthesizable chemical space.

cs.LG↗

arXiv2025

Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design

High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage ProteinMPNN, whose sequences are experimentally favorable as well as amenable to folding, together with structure prediction models to align high-quality synthetic structures with recoverable synthetic sequences. In that way, we create a new dataset designed specifically for training expressive, fully atomistic protein generators. By retraining La-Proteina, which models discrete residue type and side chain structure in a continuous latent space, on this dataset, we achieve new state-of-the-art results, with improvements of +54% in structural diversity and +27% in co-designability. To validate the broad utility of our approach, we further introduce Proteina Atomistica, a unified flow-based framework that jointly learns the distribution of protein backbone structure, discrete sequences, and atomistic side chains without latent variables. We again find that training on our new sequence-structure data dramatically boosts benchmark performance, improving \method's structural diversity by +73% and co-designability by +5%. Our work highlights the critical importance of aligned sequence-structure data for training high-performance de novo protein design models. Our new dataset https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/resources/proteina-atomistica_data/files?version=release , the Consistency Distilled Synthetic Protein Database, is made available as an open-source resource.

q-bio.BM↗

arXiv2025

Elucidated Rolling Diffusion Models for Probabilistic Forecasting of Complex Dynamics

Diffusion models are a powerful tool for probabilistic forecasting, yet most applications in high-dimensional complex systems predict future states individually. This approach struggles to model complex temporal dependencies and fails to explicitly account for the progressive growth of uncertainty inherent to the systems. While rolling diffusion frameworks, which apply increasing noise to forecasts at longer lead times, have been proposed to address this, their integration with state-of-the-art, high-fidelity diffusion techniques remains a significant challenge. We tackle this problem by introducing Elucidated Rolling Diffusion Models (ERDM), the first framework to successfully unify a rolling forecast structure with the principled, performant design of Elucidated Diffusion Models (EDM). To do this, we adapt the core EDM components-its noise schedule, network preconditioning, and Heun sampler-to the rolling forecast setting. The success of this integration is driven by three key contributions: (i) a novel loss weighting scheme that focuses model capacity on the mid-range forecast horizons where determinism gives way to stochasticity; (ii) an efficient initialization strategy using a pre-trained EDM for the initial window; and (iii) a bespoke hybrid sequence architecture for robust spatiotemporal feature extraction under progressive denoising. On 2D Navier-Stokes simulations and ERA5 global weather forecasting at 1.5-degree resolution, ERDM consistently outperforms key diffusion-based baselines, including conditional autoregressive EDM. ERDM offers a flexible and powerful general framework for tackling diffusion-based dynamics forecasting problems where modeling uncertainty propagation is paramount.

cs.LG↗

arXiv2025

Test-time scaling of diffusions with flow maps

A common recipe to improve diffusion models at test-time so that samples score highly against a user-specified reward is to introduce the gradient of the reward into the dynamics of the diffusion itself. This procedure is often ill posed, as user-specified rewards are usually only well defined on the data distribution at the end of generation. While common workarounds to this problem are to use a denoiser to estimate what a sample would have been at the end of generation, we propose a simple solution to this problem by working directly with a flow map. By exploiting a relationship between the flow map and velocity field governing the instantaneous transport, we construct an algorithm, Flow Map Trajectory Tilting (FMTT), which provably performs better ascent on the reward than standard test-time methods involving the gradient of the reward. The approach can be used to either perform exact sampling via importance weighting or principled search that identifies local maximizers of the reward-tilted distribution. We demonstrate the efficacy of our approach against other look-ahead techniques, and show how the flow map enables engagement with complicated reward functions that make possible new forms of image editing, e.g. by interfacing with vision language models.

cs.LG↗

arXiv2025

GenMol: A Drug Discovery Generalist with Discrete Diffusion

Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present Generalist Molecular generative model (GenMol), a versatile framework that uses only a single discrete diffusion model to handle diverse drug discovery scenarios. GenMol generates Sequential Attachment-based Fragment Embedding (SAFE) sequences through non-autoregressive bidirectional parallel decoding, thereby allowing the utilization of a molecular context that does not rely on the specific token ordering while having better sampling efficiency. GenMol uses fragments as basic building blocks for molecules and introduces fragment remasking, a strategy that optimizes molecules by regenerating masked fragments, enabling effective exploration of chemical space. We further propose molecular context guidance (MCG), a guidance method tailored for masked discrete diffusion of GenMol. GenMol significantly outperforms the previous GPT-based model in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design. Our code is available at https://github.com/NVIDIA-Digital-Bio/genmol.

cs.LG↗

arXiv2025

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

cs.LG↗

arXiv2025

Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow

Fast and accurate generation of molecular conformers is desired for downstream computational chemistry and drug discovery tasks. Currently, training and sampling state-of-the-art diffusion or flow-based models for conformer generation require significant computational resources. In this work, we build upon flow-matching and propose two mechanisms for accelerating training and inference of generative models for 3D molecular conformer generation. For fast training, we introduce the SO(3)-Averaged Flow training objective, which leads to faster convergence to better generation quality compared to conditional optimal transport flow or Kabsch-aligned flow. We demonstrate that models trained using SO(3)-Averaged Flow can reach state-of-the-art conformer generation quality. For fast inference, we show that the reflow and distillation methods of flow-based models enable few-steps or even one-step molecular conformer generation with high quality. The training techniques proposed in this work show a path towards highly efficient molecular conformer generation with flow-based models.

cs.LG↗

arXiv2025

Align Your Flow: Scaling Continuous-Time Flow Map Distillation

Diffusion- and flow-based models have emerged as state-of-the-art generative modeling approaches, but they require many sampling steps. Consistency models can distill these models into efficient one-step generators; however, unlike flow- and diffusion-based methods, their performance inevitably degrades when increasing the number of steps, which we show both analytically and empirically. Flow maps generalize these approaches by connecting any two noise levels in a single step and remain effective across all step counts. In this paper, we introduce two new continuous-time objectives for training flow maps, along with additional novel training techniques, generalizing existing consistency and flow matching objectives. We further demonstrate that autoguidance can improve performance, using a low-quality model for guidance during distillation, and an additional boost can be achieved by adversarial finetuning, with minimal loss in sample diversity. We extensively validate our flow map models, called Align Your Flow, on challenging image generation benchmarks and achieve state-of-the-art few-step generation performance on both ImageNet 64x64 and 512x512, using small and efficient neural networks. Finally, we show text-to-image flow map models that outperform all existing non-adversarially trained few-step samplers in text-conditioned synthesis.

cs.CV↗

arXiv2025

Hierarchical protein backbone generation with latent and structure diffusion

We propose a hierarchical protein backbone generative model that separates coarse and fine-grained details. Our approach called LSD consists of two stages: sampling latents which are decoded into a contact map then sampling atomic coordinates conditioned on the contact map. LSD allows new ways to control protein generation towards desirable properties while scaling to large datasets. In particular, the AlphaFold DataBase (AFDB) is appealing due as its diverse structure topologies but suffers from poor designability. We train LSD on AFDB and show latent diffusion guidance towards AlphaFold2 Predicted Alignment Error and long range contacts can explicitly balance designability, diversity, and noveltys in the generated samples. Our results are competitive with structure diffusion models and outperforms prior latent diffusion models.

q-bio.QM↗

arXiv2025

Energy-Based Diffusion Language Models for Text Generation

Despite remarkable progress in autoregressive language models, alternative generative paradigms beyond left-to-right generation are still being actively explored. Discrete diffusion models, with the capacity for parallel generation, have recently emerged as a promising alternative. Unfortunately, these models still underperform the autoregressive counterparts, with the performance gap increasing when reducing the number of sampling steps. Our analysis reveals that this degradation is a consequence of an imperfect approximation used by diffusion models. In this work, we propose Energy-based Diffusion Language Model (EDLM), an energy-based model operating at the full sequence level for each diffusion step, introduced to improve the underlying approximation used by diffusion models. More specifically, we introduce an EBM in a residual form, and show that its parameters can be obtained by leveraging a pretrained autoregressive model or by finetuning a bidirectional transformer via noise contrastive estimation. We also propose an efficient generation algorithm via parallel important sampling. Comprehensive experiments on language modeling benchmarks show that our model can consistently outperform state-of-the-art diffusion models by a significant margin, and approaches autoregressive models' perplexity. We further show that, without any generation performance drop, our framework offers a 1.3$\times$ sampling speedup over existing diffusion models. Reproduced code is available at https://github.com/MinkaiXu/Energy-Diffusion-LLM.

cs.CL↗

arXiv2025

ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids

We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from a statistical model, with each option unlocking new capabilities. Hand-specifying ellipsoids enables users to control the location, size, orientation, secondary structure, and approximate shape of protein substructures. Conditioning on ellipsoids of existing proteins enables redesigning their substructure's connectivity or editing substructure properties. By conditioning on novel and diverse ellipsoid layouts from a simple statistical model, we improve protein generation with expanded Pareto frontiers between designability, novelty, and diversity. Further, this enables sampling designable proteins with a helix-fraction that matches PDB proteins, unlike existing generative models that commonly oversample conceptually simple helix bundles. Code is available at https://github.com/NVlabs/protcomposer.

q-bio.BM↗

arXiv2025

Proteina: Scaling Flow-based Protein Structure Generative Models

Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture with up to 5x as many parameters as previous models. To meaningfully quantify performance, we introduce a new set of metrics that directly measure the distributional similarity of generated proteins with reference sets, complementing existing metrics. We further explore scaling training data to millions of synthetic protein structures and explore improved training and sampling recipes adapted to protein backbone generation. This includes fine-tuning strategies like LoRA for protein backbones, new guidance methods like classifier-free guidance and autoguidance for protein backbones, and new adjusted training objectives. Proteina achieves state-of-the-art performance on de novo protein backbone design and produces diverse and designable proteins at unprecedented length, up to 800 residues. The hierarchical conditioning offers novel control, enabling high-level secondary-structure guidance as well as low-level fold-specific generation.

cs.LG↗

arXiv2025

Truncated Consistency Models

Consistency models have recently been introduced to accelerate sampling from diffusion models by directly predicting the solution (i.e., data) of the probability flow ODE (PF ODE) from initial noise. However, the training of consistency models requires learning to map all intermediate points along PF ODE trajectories to their corresponding endpoints. This task is much more challenging than the ultimate objective of one-step generation, which only concerns the PF ODE's noise-to-data mapping. We empirically find that this training paradigm limits the one-step generation performance of consistency models. To address this issue, we generalize consistency training to the truncated time range, which allows the model to ignore denoising tasks at earlier time steps and focus its capacity on generation. We propose a new parameterization of the consistency function and a two-stage training procedure that prevents the truncated-time training from collapsing to a trivial solution. Experiments on CIFAR-10 and ImageNet $64\times64$ datasets show that our method achieves better one-step and two-step FIDs than the state-of-the-art consistency models such as iCT-deep, using more than 2$\times$ smaller networks. Project page: https://truncated-cm.github.io/

cs.LG↗

arXiv2025

Score-based Diffusion Models in Function Space

Diffusion models have recently emerged as a powerful framework for generative modeling. They consist of a forward process that perturbs input data with Gaussian white noise and a reverse process that learns a score function to generate samples by denoising. Despite their tremendous success, they are mostly formulated on finite-dimensional spaces, e.g., Euclidean, limiting their applications to many domains where the data has a functional form, such as in scientific computing and 3D geometric data analysis. This work introduces a mathematically rigorous framework called Denoising Diffusion Operators (DDOs) for training diffusion models in function space. In DDOs, the forward process perturbs input functions gradually using a Gaussian process. The generative process is formulated by a function-valued annealed Langevin dynamic. Our approach requires an appropriate notion of the score for the perturbed data distribution, which we obtain by generalizing denoising score matching to function spaces that can be infinite-dimensional. We show that the corresponding discretized algorithm generates accurate samples at a fixed cost independent of the data resolution. We theoretically and numerically verify the applicability of our approach on a set of function-valued problems, including generating solutions to the Navier-Stokes equation viewed as the push-forward distribution of forcings from a Gaussian Random Field (GRF), as well as volcano InSAR and MNIST-SDF.

cs.LG↗

arXiv2024

EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants

Mapping the conformational dynamics of proteins is crucial for elucidating their functional mechanisms. While Molecular Dynamics (MD) simulation enables detailed time evolution of protein motion, its computational toll hinders its use in practice. To address this challenge, multiple deep learning models for reproducing and accelerating MD have been proposed drawing on transport-based generative methods. However, existing work focuses on generation through transport of samples from prior distributions, that can often be distant from the data manifold. The recently proposed framework of stochastic interpolants, instead, enables transport between arbitrary distribution endpoints. Building upon this work, we introduce EquiJump, a transferable SO(3)-equivariant model that bridges all-atom protein dynamics simulation time steps directly. Our approach unifies diverse sampling methods and is benchmarked against existing models on trajectory data of fast folding proteins. EquiJump achieves state-of-the-art results on dynamics simulation with a transferable model on all of the fast folding proteins.

cs.LG↗