arXiv subjects

Arash Vahdat

Publications and source records attributed to Arash Vahdat.

At least 37 records · Page 2Linked to original sources

arXiv2025

Climate in a Bottle: Towards a Generative Foundation Model for the Kilometer-Scale Global Atmosphere

Climate modeling is reaching unprecedented resolution, producing petabytes of data. AI climate model emulators offer a path to computationally cheap analysis, enabling new scientific insight and scenario planning. Recent advances show promise in faithfully emulating climate data. However, prevailing auto-regressive paradigms are difficult to train on climate time horizons due to drifts, instabilities, and component-coupling challenges. They are hard to scale to high resolution and require sifting through troves of output to identify rare extremes of interest. We present Climate in a Bottle (cBottle), a generative diffusion-based framework emulating global 5 km climate simulations and reanalysis on the HEALPix grid. cBottle samples directly from the full distribution of atmospheric states, avoiding auto-regressive rollout, and is the first to reach this 12.5M-pixel global resolution. It consists of two stages: a coarse-resolution generator conditioned on sea surface temperatures and solar position, followed by a patch-based 16x super-resolution stage. cBottle passes a battery of tests, including diurnal-to-seasonal variability, large-scale modes of variability, tropical cyclone statistics, and trends of climate change and weather extremes. It is a step toward a foundation model: bridging data modalities (reanalysis and simulation), enabling zero-shot bias correction, downscaling, and data infilling. It also enables new interactivity via guided diffusion. For example, we train a tropical cyclone (TC) classifier alongside the generator, guide towards TC states, and obtain physically credible samples. This opens the door to guidance methods for a wide array of user queries and new ways of interacting with climate data.

physics.ao-ph↗

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

One-step Diffusion Models with $f$-Divergence Distribution Matching

Sampling from diffusion models involves a slow iterative process that hinders their practical deployment, especially for interactive applications. To accelerate generation speed, recent approaches distill a multi-step diffusion model into a single-step student generator via variational score distillation, which matches the distribution of samples generated by the student to the teacher's distribution. However, these approaches use the reverse Kullback-Leibler (KL) divergence for distribution matching which is known to be mode seeking. In this paper, we generalize the distribution matching approach using a novel $f$-divergence minimization framework, termed $f$-distill, that covers different divergences with different trade-offs in terms of mode coverage and training variance. We derive the gradient of the $f$-divergence between the teacher and student distributions and show that it is expressed as the product of their score differences and a weighting function determined by their density ratio. This weighting function naturally emphasizes samples with higher density in the teacher distribution, when using a less mode-seeking divergence. We observe that the popular variational score distillation approach using the reverse-KL divergence is a special case within our framework. Empirically, we demonstrate that alternative $f$-divergences, such as forward-KL and Jensen-Shannon divergences, outperform the current best variational score distillation methods across image generation tasks. In particular, when using Jensen-Shannon divergence, $f$-distill achieves current state-of-the-art one-step generation performance on ImageNet64 and zero-shot text-to-image generation on MS-COCO. Project page: https://research.nvidia.com/labs/genair/f-distill

cs.LG↗

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

Not-So-Optimal Transport Flows for 3D Point Cloud Generation

Learning generative models of 3D point clouds is one of the fundamental problems in 3D generative learning. One of the key properties of point clouds is their permutation invariance, i.e., changing the order of points in a point cloud does not change the shape they represent. In this paper, we analyze the recently proposed equivariant OT flows that learn permutation invariant generative models for point-based molecular data and we show that these models scale poorly on large point clouds. Also, we observe learning (equivariant) OT flows is generally challenging since straightening flow trajectories makes the learned flow model complex at the beginning of the trajectory. To remedy these, we propose not-so-optimal transport flow models that obtain an approximate OT by an offline OT precomputation, enabling an efficient construction of OT pairs for training. During training, we can additionally construct a hybrid coupling by combining our approximate OT and independent coupling to make the target flow models easier to learn. In an extensive empirical study, we show that our proposed model outperforms prior diffusion- and flow-based approaches on a wide range of unconditional generation and shape completion on the ShapeNet benchmark.

cs.CV↗

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↗

arXiv2025

BlobGEN-Vid: Compositional Text-to-Video Generation with Blob Video Representations

Existing video generation models struggle to follow complex text prompts and synthesize multiple objects, raising the need for additional grounding input for improved controllability. In this work, we propose to decompose videos into visual primitives - blob video representation, a general representation for controllable video generation. Based on blob conditions, we develop a blob-grounded video diffusion model named BlobGEN-Vid that allows users to control object motions and fine-grained object appearance. In particular, we introduce a masked 3D attention module that effectively improves regional consistency across frames. In addition, we introduce a learnable module to interpolate text embeddings so that users can control semantics in specific frames and obtain smooth object transitions. We show that our framework is model-agnostic and build BlobGEN-Vid based on both U-Net and DiT-based video diffusion models. Extensive experimental results show that BlobGEN-Vid achieves superior zero-shot video generation ability and state-of-the-art layout controllability on multiple benchmarks. When combined with an LLM for layout planning, our framework even outperforms proprietary text-to-video generators in terms of compositional accuracy.

cs.CV↗

arXiv2024

Molecule Generation with Fragment Retrieval Augmentation

Fragment-based drug discovery, in which molecular fragments are assembled into new molecules with desirable biochemical properties, has achieved great success. However, many fragment-based molecule generation methods show limited exploration beyond the existing fragments in the database as they only reassemble or slightly modify the given ones. To tackle this problem, we propose a new fragment-based molecule generation framework with retrieval augmentation, namely Fragment Retrieval-Augmented Generation (f-RAG). f-RAG is based on a pre-trained molecular generative model that proposes additional fragments from input fragments to complete and generate a new molecule. Given a fragment vocabulary, f-RAG retrieves two types of fragments: (1) hard fragments, which serve as building blocks that will be explicitly included in the newly generated molecule, and (2) soft fragments, which serve as reference to guide the generation of new fragments through a trainable fragment injection module. To extrapolate beyond the existing fragments, f-RAG updates the fragment vocabulary with generated fragments via an iterative refinement process which is further enhanced with post-hoc genetic fragment modification. f-RAG can achieve an improved exploration-exploitation trade-off by maintaining a pool of fragments and expanding it with novel and high-quality fragments through a strong generative prior.

cs.LG↗

arXiv2024

Heavy-Tailed Diffusion Models

Diffusion models achieve state-of-the-art generation quality across many applications, but their ability to capture rare or extreme events in heavy-tailed distributions remains unclear. In this work, we show that traditional diffusion and flow-matching models with standard Gaussian priors fail to capture heavy-tailed behavior. We address this by repurposing the diffusion framework for heavy-tail estimation using multivariate Student-t distributions. We develop a tailored perturbation kernel and derive the denoising posterior based on the conditional Student-t distribution for the backward process. Inspired by $γ$-divergence for heavy-tailed distributions, we derive a training objective for heavy-tailed denoisers. The resulting framework introduces controllable tail generation using only a single scalar hyperparameter, making it easily tunable for diverse real-world distributions. As specific instantiations of our framework, we introduce t-EDM and t-Flow, extensions of existing diffusion and flow models that employ a Student-t prior. Remarkably, our approach is readily compatible with standard Gaussian diffusion models and requires only minimal code changes. Empirically, we show that our t-EDM and t-Flow outperform standard diffusion models in heavy-tail estimation on high-resolution weather datasets in which generating rare and extreme events is crucial.

cs.LG↗

arXiv2024

Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization

Generating ligand molecules for specific protein targets, known as structure-based drug design, is a fundamental problem in therapeutics development and biological discovery. Recently, target-aware generative models, especially diffusion models, have shown great promise in modeling protein-ligand interactions and generating candidate drugs. However, existing models primarily focus on learning the chemical distribution of all drug candidates, which lacks effective steerability on the chemical quality of model generations. In this paper, we propose a novel and general alignment framework to align pretrained target diffusion models with preferred functional properties, named AliDiff. AliDiff shifts the target-conditioned chemical distribution towards regions with higher binding affinity and structural rationality, specified by user-defined reward functions, via the preference optimization approach. To avoid the overfitting problem in common preference optimization objectives, we further develop an improved Exact Energy Preference Optimization method to yield an exact and efficient alignment of the diffusion models, and provide the closed-form expression for the converged distribution. Empirical studies on the CrossDocked2020 benchmark show that AliDiff can generate molecules with state-of-the-art binding energies with up to -7.07 Avg. Vina Score, while maintaining strong molecular properties. Code is available at https://github.com/MinkaiXu/AliDiff.

q-bio.BM↗

arXiv2024

Warped Diffusion: Solving Video Inverse Problems with Image Diffusion Models

Using image models naively for solving inverse video problems often suffers from flickering, texture-sticking, and temporal inconsistency in generated videos. To tackle these problems, in this paper, we view frames as continuous functions in the 2D space, and videos as a sequence of continuous warping transformations between different frames. This perspective allows us to train function space diffusion models only on images and utilize them to solve temporally correlated inverse problems. The function space diffusion models need to be equivariant with respect to the underlying spatial transformations. To ensure temporal consistency, we introduce a simple post-hoc test-time guidance towards (self)-equivariant solutions. Our method allows us to deploy state-of-the-art latent diffusion models such as Stable Diffusion XL to solve video inverse problems. We demonstrate the effectiveness of our method for video inpainting and $8\times$ video super-resolution, outperforming existing techniques based on noise transformations. We provide generated video results: https://giannisdaras.github.io/warped_diffusion.github.io/.

cs.CV↗

arXiv2024

Stochastic Flow Matching for Resolving Small-Scale Physics

Conditioning diffusion and flow models have proven effective for super-resolving small-scale details in natural images.However, in physical sciences such as weather, super-resolving small-scale details poses significant challenges due to: (i) misalignment between input and output distributions (i.e., solutions to distinct partial differential equations (PDEs) follow different trajectories), (ii) multi-scale dynamics, deterministic dynamics at large scales vs. stochastic at small scales, and (iii) limited data, increasing the risk of overfitting. To address these challenges, we propose encoding the inputs to a latent base distribution that is closer to the target distribution, followed by flow matching to generate small-scale physics. The encoder captures the deterministic components, while flow matching adds stochastic small-scale details. To account for uncertainty in the deterministic part, we inject noise into the encoder output using an adaptive noise scaling mechanism, which is dynamically adjusted based on maximum-likelihood estimates of the encoder predictions. We conduct extensive experiments on both the real-world CWA weather dataset and the PDE-based Kolmogorov dataset, with the CWA task involving super-resolving the weather variables for the region of Taiwan from 25 km to 2 km scales. Our results show that the proposed stochastic flow matching (SFM) framework significantly outperforms existing methods such as conditional diffusion and flows.

cs.CV↗

arXiv2024

Elucidating Optimal Reward-Diversity Tradeoffs in Text-to-Image Diffusion Models

Text-to-image (T2I) diffusion models have become prominent tools for generating high-fidelity images from text prompts. However, when trained on unfiltered internet data, these models can produce unsafe, incorrect, or stylistically undesirable images that are not aligned with human preferences. To address this, recent approaches have incorporated human preference datasets to fine-tune T2I models or to optimize reward functions that capture these preferences. Although effective, these methods are vulnerable to reward hacking, where the model overfits to the reward function, leading to a loss of diversity in the generated images. In this paper, we prove the inevitability of reward hacking and study natural regularization techniques like KL divergence and LoRA scaling, and their limitations for diffusion models. We also introduce Annealed Importance Guidance (AIG), an inference-time regularization inspired by Annealed Importance Sampling, which retains the diversity of the base model while achieving Pareto-Optimal reward-diversity tradeoffs. Our experiments demonstrate the benefits of AIG for Stable Diffusion models, striking the optimal balance between reward optimization and image diversity. Furthermore, a user study confirms that AIG improves diversity and quality of generated images across different model architectures and reward functions.

cs.CV↗

arXiv2024

DiffUHaul: A Training-Free Method for Object Dragging in Images

Text-to-image diffusion models have proven effective for solving many image editing tasks. However, the seemingly straightforward task of seamlessly relocating objects within a scene remains surprisingly challenging. Existing methods addressing this problem often struggle to function reliably in real-world scenarios due to lacking spatial reasoning. In this work, we propose a training-free method, dubbed DiffUHaul, that harnesses the spatial understanding of a localized text-to-image model, for the object dragging task. Blindly manipulating layout inputs of the localized model tends to cause low editing performance due to the intrinsic entanglement of object representation in the model. To this end, we first apply attention masking in each denoising step to make the generation more disentangled across different objects and adopt the self-attention sharing mechanism to preserve the high-level object appearance. Furthermore, we propose a new diffusion anchoring technique: in the early denoising steps, we interpolate the attention features between source and target images to smoothly fuse new layouts with the original appearance; in the later denoising steps, we pass the localized features from the source images to the interpolated images to retain fine-grained object details. To adapt DiffUHaul to real-image editing, we apply a DDPM self-attention bucketing that can better reconstruct real images with the localized model. Finally, we introduce an automated evaluation pipeline for this task and showcase the efficacy of our method. Our results are reinforced through a user preference study.

cs.CV↗

arXiv2024

DiffiT: Diffusion Vision Transformers for Image Generation

Diffusion models with their powerful expressivity and high sample quality have achieved State-Of-The-Art (SOTA) performance in the generative domain. The pioneering Vision Transformer (ViT) has also demonstrated strong modeling capabilities and scalability, especially for recognition tasks. In this paper, we study the effectiveness of ViTs in diffusion-based generative learning and propose a new model denoted as Diffusion Vision Transformers (DiffiT). Specifically, we propose a methodology for finegrained control of the denoising process and introduce the Time-dependant Multihead Self Attention (TMSA) mechanism. DiffiT is surprisingly effective in generating high-fidelity images with significantly better parameter efficiency. We also propose latent and image space DiffiT models and show SOTA performance on a variety of class-conditional and unconditional synthesis tasks at different resolutions. The Latent DiffiT model achieves a new SOTA FID score of 1.73 on ImageNet256 dataset while having 19.85%, 16.88% less parameters than other Transformer-based diffusion models such as MDT and DiT,respectively. Code: https://github.com/NVlabs/DiffiT

cs.CV↗