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Dec 12

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

  • 3 authors
·
Dec 23, 2024 2

Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

  • 5 authors
·
Sep 29, 2023

Agentic End-to-End De Novo Protein Design for Tailored Dynamics Using a Language Diffusion Model

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

  • 2 authors
·
Feb 14 2

Generative augmentations for improved cardiac ultrasound segmentation using diffusion models

One of the main challenges in current research on segmentation in cardiac ultrasound is the lack of large and varied labeled datasets and the differences in annotation conventions between datasets. This makes it difficult to design robust segmentation models that generalize well to external datasets. This work utilizes diffusion models to create generative augmentations that can significantly improve diversity of the dataset and thus the generalisability of segmentation models without the need for more annotated data. The augmentations are applied in addition to regular augmentations. A visual test survey showed that experts cannot clearly distinguish between real and fully generated images. Using the proposed generative augmentations, segmentation robustness was increased when training on an internal dataset and testing on an external dataset with an improvement of over 20 millimeters in Hausdorff distance. Additionally, the limits of agreement for automatic ejection fraction estimation improved by up to 20% of absolute ejection fraction value on out of distribution cases. These improvements come exclusively from the increased variation of the training data using the generative augmentations, without modifying the underlying machine learning model. The augmentation tool is available as an open source Python library at https://github.com/GillesVanDeVyver/EchoGAINS.

  • 8 authors
·
Feb 27

Unifying Diffusion Models' Latent Space, with Applications to CycleDiffusion and Guidance

Diffusion models have achieved unprecedented performance in generative modeling. The commonly-adopted formulation of the latent code of diffusion models is a sequence of gradually denoised samples, as opposed to the simpler (e.g., Gaussian) latent space of GANs, VAEs, and normalizing flows. This paper provides an alternative, Gaussian formulation of the latent space of various diffusion models, as well as an invertible DPM-Encoder that maps images into the latent space. While our formulation is purely based on the definition of diffusion models, we demonstrate several intriguing consequences. (1) Empirically, we observe that a common latent space emerges from two diffusion models trained independently on related domains. In light of this finding, we propose CycleDiffusion, which uses DPM-Encoder for unpaired image-to-image translation. Furthermore, applying CycleDiffusion to text-to-image diffusion models, we show that large-scale text-to-image diffusion models can be used as zero-shot image-to-image editors. (2) One can guide pre-trained diffusion models and GANs by controlling the latent codes in a unified, plug-and-play formulation based on energy-based models. Using the CLIP model and a face recognition model as guidance, we demonstrate that diffusion models have better coverage of low-density sub-populations and individuals than GANs. The code is publicly available at https://github.com/ChenWu98/cycle-diffusion.

  • 2 authors
·
Oct 11, 2022 1

Efficient Video Diffusion Models via Content-Frame Motion-Latent Decomposition

Video diffusion models have recently made great progress in generation quality, but are still limited by the high memory and computational requirements. This is because current video diffusion models often attempt to process high-dimensional videos directly. To tackle this issue, we propose content-motion latent diffusion model (CMD), a novel efficient extension of pretrained image diffusion models for video generation. Specifically, we propose an autoencoder that succinctly encodes a video as a combination of a content frame (like an image) and a low-dimensional motion latent representation. The former represents the common content, and the latter represents the underlying motion in the video, respectively. We generate the content frame by fine-tuning a pretrained image diffusion model, and we generate the motion latent representation by training a new lightweight diffusion model. A key innovation here is the design of a compact latent space that can directly utilizes a pretrained image diffusion model, which has not been done in previous latent video diffusion models. This leads to considerably better quality generation and reduced computational costs. For instance, CMD can sample a video 7.7times faster than prior approaches by generating a video of 512times1024 resolution and length 16 in 3.1 seconds. Moreover, CMD achieves an FVD score of 212.7 on WebVid-10M, 27.3% better than the previous state-of-the-art of 292.4.

  • 6 authors
·
Mar 21, 2024 1

T-Stitch: Accelerating Sampling in Pre-Trained Diffusion Models with Trajectory Stitching

Sampling from diffusion probabilistic models (DPMs) is often expensive for high-quality image generation and typically requires many steps with a large model. In this paper, we introduce sampling Trajectory Stitching T-Stitch, a simple yet efficient technique to improve the sampling efficiency with little or no generation degradation. Instead of solely using a large DPM for the entire sampling trajectory, T-Stitch first leverages a smaller DPM in the initial steps as a cheap drop-in replacement of the larger DPM and switches to the larger DPM at a later stage. Our key insight is that different diffusion models learn similar encodings under the same training data distribution and smaller models are capable of generating good global structures in the early steps. Extensive experiments demonstrate that T-Stitch is training-free, generally applicable for different architectures, and complements most existing fast sampling techniques with flexible speed and quality trade-offs. On DiT-XL, for example, 40% of the early timesteps can be safely replaced with a 10x faster DiT-S without performance drop on class-conditional ImageNet generation. We further show that our method can also be used as a drop-in technique to not only accelerate the popular pretrained stable diffusion (SD) models but also improve the prompt alignment of stylized SD models from the public model zoo. Code is released at https://github.com/NVlabs/T-Stitch

  • 8 authors
·
Feb 21, 2024 1

Latent Diffusion Autoencoders: Toward Efficient and Meaningful Unsupervised Representation Learning in Medical Imaging

This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE

  • 6 authors
·
Apr 11 2

A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

  • 7 authors
·
May 30, 2023

MaterialFusion: Enhancing Inverse Rendering with Material Diffusion Priors

Recent works in inverse rendering have shown promise in using multi-view images of an object to recover shape, albedo, and materials. However, the recovered components often fail to render accurately under new lighting conditions due to the intrinsic challenge of disentangling albedo and material properties from input images. To address this challenge, we introduce MaterialFusion, an enhanced conventional 3D inverse rendering pipeline that incorporates a 2D prior on texture and material properties. We present StableMaterial, a 2D diffusion model prior that refines multi-lit data to estimate the most likely albedo and material from given input appearances. This model is trained on albedo, material, and relit image data derived from a curated dataset of approximately ~12K artist-designed synthetic Blender objects called BlenderVault. we incorporate this diffusion prior with an inverse rendering framework where we use score distillation sampling (SDS) to guide the optimization of the albedo and materials, improving relighting performance in comparison with previous work. We validate MaterialFusion's relighting performance on 4 datasets of synthetic and real objects under diverse illumination conditions, showing our diffusion-aided approach significantly improves the appearance of reconstructed objects under novel lighting conditions. We intend to publicly release our BlenderVault dataset to support further research in this field.

  • 7 authors
·
Sep 23, 2024 2

One-Way Ticket:Time-Independent Unified Encoder for Distilling Text-to-Image Diffusion Models

Text-to-Image (T2I) diffusion models have made remarkable advancements in generative modeling; however, they face a trade-off between inference speed and image quality, posing challenges for efficient deployment. Existing distilled T2I models can generate high-fidelity images with fewer sampling steps, but often struggle with diversity and quality, especially in one-step models. From our analysis, we observe redundant computations in the UNet encoders. Our findings suggest that, for T2I diffusion models, decoders are more adept at capturing richer and more explicit semantic information, while encoders can be effectively shared across decoders from diverse time steps. Based on these observations, we introduce the first Time-independent Unified Encoder TiUE for the student model UNet architecture, which is a loop-free image generation approach for distilling T2I diffusion models. Using a one-pass scheme, TiUE shares encoder features across multiple decoder time steps, enabling parallel sampling and significantly reducing inference time complexity. In addition, we incorporate a KL divergence term to regularize noise prediction, which enhances the perceptual realism and diversity of the generated images. Experimental results demonstrate that TiUE outperforms state-of-the-art methods, including LCM, SD-Turbo, and SwiftBrushv2, producing more diverse and realistic results while maintaining the computational efficiency.

  • 10 authors
·
May 28 2

Euclid Quick Data Release (Q1). Active galactic nuclei identification using diffusion-based inpainting of Euclid VIS images

Light emission from galaxies exhibit diverse brightness profiles, influenced by factors such as galaxy type, structural features and interactions with other galaxies. Elliptical galaxies feature more uniform light distributions, while spiral and irregular galaxies have complex, varied light profiles due to their structural heterogeneity and star-forming activity. In addition, galaxies with an active galactic nucleus (AGN) feature intense, concentrated emission from gas accretion around supermassive black holes, superimposed on regular galactic light, while quasi-stellar objects (QSO) are the extreme case of the AGN emission dominating the galaxy. The challenge of identifying AGN and QSO has been discussed many times in the literature, often requiring multi-wavelength observations. This paper introduces a novel approach to identify AGN and QSO from a single image. Diffusion models have been recently developed in the machine-learning literature to generate realistic-looking images of everyday objects. Utilising the spatial resolving power of the Euclid VIS images, we created a diffusion model trained on one million sources, without using any source pre-selection or labels. The model learns to reconstruct light distributions of normal galaxies, since the population is dominated by them. We condition the prediction of the central light distribution by masking the central few pixels of each source and reconstruct the light according to the diffusion model. We further use this prediction to identify sources that deviate from this profile by examining the reconstruction error of the few central pixels regenerated in each source's core. Our approach, solely using VIS imaging, features high completeness compared to traditional methods of AGN and QSO selection, including optical, near-infrared, mid-infrared, and X-rays.

  • 274 authors
·
Mar 19

Personalized Face Inpainting with Diffusion Models by Parallel Visual Attention

Face inpainting is important in various applications, such as photo restoration, image editing, and virtual reality. Despite the significant advances in face generative models, ensuring that a person's unique facial identity is maintained during the inpainting process is still an elusive goal. Current state-of-the-art techniques, exemplified by MyStyle, necessitate resource-intensive fine-tuning and a substantial number of images for each new identity. Furthermore, existing methods often fall short in accommodating user-specified semantic attributes, such as beard or expression. To improve inpainting results, and reduce the computational complexity during inference, this paper proposes the use of Parallel Visual Attention (PVA) in conjunction with diffusion models. Specifically, we insert parallel attention matrices to each cross-attention module in the denoising network, which attends to features extracted from reference images by an identity encoder. We train the added attention modules and identity encoder on CelebAHQ-IDI, a dataset proposed for identity-preserving face inpainting. Experiments demonstrate that PVA attains unparalleled identity resemblance in both face inpainting and face inpainting with language guidance tasks, in comparison to various benchmarks, including MyStyle, Paint by Example, and Custom Diffusion. Our findings reveal that PVA ensures good identity preservation while offering effective language-controllability. Additionally, in contrast to Custom Diffusion, PVA requires just 40 fine-tuning steps for each new identity, which translates to a significant speed increase of over 20 times.

  • 7 authors
·
Dec 6, 2023 2

EchoDistill: Bidirectional Concept Distillation for One-Step Diffusion Personalization

Recent advances in accelerating text-to-image (T2I) diffusion models have enabled the synthesis of high-fidelity images even in a single step. However, personalizing these models to incorporate novel concepts remains a challenge due to the limited capacity of one-step models to capture new concept distributions effectively. We propose a bidirectional concept distillation framework, EchoDistill, to enable one-step diffusion personalization (1-SDP). Our approach involves an end-to-end training process where a multi-step diffusion model (teacher) and a one-step diffusion model (student) are trained simultaneously. The concept is first distilled from the teacher model to the student, and then echoed back from the student to the teacher. During the EchoDistill, we share the text encoder between the two models to ensure consistent semantic understanding. Following this, the student model is optimized with adversarial losses to align with the real image distribution and with alignment losses to maintain consistency with the teacher's output. Furthermore, we introduce the bidirectional echoing refinement strategy, wherein the student model leverages its faster generation capability to feedback to the teacher model. This bidirectional concept distillation mechanism not only enhances the student ability to personalize novel concepts but also improves the generative quality of the teacher model. Our experiments demonstrate that this collaborative framework significantly outperforms existing personalization methods over the 1-SDP setup, establishing a novel paradigm for rapid and effective personalization in T2I diffusion models.

  • 7 authors
·
Oct 23 1

PSyDUCK: Training-Free Steganography for Latent Diffusion

Recent advances in generative AI have opened promising avenues for steganography, which can securely protect sensitive information for individuals operating in hostile environments, such as journalists, activists, and whistleblowers. However, existing methods for generative steganography have significant limitations, particularly in scalability and their dependence on retraining diffusion models. We introduce PSyDUCK, a training-free, model-agnostic steganography framework specifically designed for latent diffusion models. PSyDUCK leverages controlled divergence and local mixing within the latent denoising process, enabling high-capacity, secure message embedding without compromising visual fidelity. Our method dynamically adapts embedding strength to balance accuracy and detectability, significantly improving upon existing pixel-space approaches. Crucially, PSyDUCK extends generative steganography to latent-space video diffusion models, surpassing previous methods in both encoding capacity and robustness. Extensive experiments demonstrate PSyDUCK's superiority over state-of-the-art techniques, achieving higher transmission accuracy and lower detectability rates across diverse image and video datasets. By overcoming the key challenges associated with latent diffusion model architectures, PSyDUCK sets a new standard for generative steganography, paving the way for scalable, real-world steganographic applications.

  • 6 authors
·
Jan 31

DiffusionEngine: Diffusion Model is Scalable Data Engine for Object Detection

Data is the cornerstone of deep learning. This paper reveals that the recently developed Diffusion Model is a scalable data engine for object detection. Existing methods for scaling up detection-oriented data often require manual collection or generative models to obtain target images, followed by data augmentation and labeling to produce training pairs, which are costly, complex, or lacking diversity. To address these issues, we presentDiffusionEngine (DE), a data scaling-up engine that provides high-quality detection-oriented training pairs in a single stage. DE consists of a pre-trained diffusion model and an effective Detection-Adapter, contributing to generating scalable, diverse and generalizable detection data in a plug-and-play manner. Detection-Adapter is learned to align the implicit semantic and location knowledge in off-the-shelf diffusion models with detection-aware signals to make better bounding-box predictions. Additionally, we contribute two datasets, i.e., COCO-DE and VOC-DE, to scale up existing detection benchmarks for facilitating follow-up research. Extensive experiments demonstrate that data scaling-up via DE can achieve significant improvements in diverse scenarios, such as various detection algorithms, self-supervised pre-training, data-sparse, label-scarce, cross-domain, and semi-supervised learning. For example, when using DE with a DINO-based adapter to scale up data, mAP is improved by 3.1% on COCO, 7.6% on VOC, and 11.5% on Clipart.

  • 10 authors
·
Sep 7, 2023

De novo protein design using geometric vector field networks

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

  • 7 authors
·
Oct 18, 2023

Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow connections to multiple atoms through single bonds, solely using pair-wise distance to model molecule geometries is insufficient. Therefore, the first one involves proposing an effective neural network as the denoising kernel that is capable to capture complex multi-body interatomic relationships and learn high-quality features. Due to the discrete nature of graphs, mainstream diffusion-based methods for molecules heavily rely on predefined rules and generate edges in an indirect manner. The second challenge involves accommodating molecule generation to diffusion and accurately predicting the existence of bonds. In our research, we view the iterative way of updating molecule conformations in diffusion process is consistent with molecular dynamics and introduce a novel molecule generation method named Geometric-Facilitated Molecular Diffusion (GFMDiff). For the first challenge, we introduce a Dual-Track Transformer Network (DTN) to fully excevate global spatial relationships and learn high quality representations which contribute to accurate predictions of features and geometries. As for the second challenge, we design Geometric-Facilitated Loss (GFLoss) which intervenes the formation of bonds during the training period, instead of directly embedding edges into the latent space. Comprehensive experiments on current benchmarks demonstrate the superiority of GFMDiff.

  • 5 authors
·
Jan 5, 2024

InstructVideo: Instructing Video Diffusion Models with Human Feedback

Diffusion models have emerged as the de facto paradigm for video generation. However, their reliance on web-scale data of varied quality often yields results that are visually unappealing and misaligned with the textual prompts. To tackle this problem, we propose InstructVideo to instruct text-to-video diffusion models with human feedback by reward fine-tuning. InstructVideo has two key ingredients: 1) To ameliorate the cost of reward fine-tuning induced by generating through the full DDIM sampling chain, we recast reward fine-tuning as editing. By leveraging the diffusion process to corrupt a sampled video, InstructVideo requires only partial inference of the DDIM sampling chain, reducing fine-tuning cost while improving fine-tuning efficiency. 2) To mitigate the absence of a dedicated video reward model for human preferences, we repurpose established image reward models, e.g., HPSv2. To this end, we propose Segmental Video Reward, a mechanism to provide reward signals based on segmental sparse sampling, and Temporally Attenuated Reward, a method that mitigates temporal modeling degradation during fine-tuning. Extensive experiments, both qualitative and quantitative, validate the practicality and efficacy of using image reward models in InstructVideo, significantly enhancing the visual quality of generated videos without compromising generalization capabilities. Code and models will be made publicly available.

  • 10 authors
·
Dec 19, 2023 1

Divot: Diffusion Powers Video Tokenizer for Comprehension and Generation

In recent years, there has been a significant surge of interest in unifying image comprehension and generation within Large Language Models (LLMs). This growing interest has prompted us to explore extending this unification to videos. The core challenge lies in developing a versatile video tokenizer that captures both the spatial characteristics and temporal dynamics of videos to obtain representations for LLMs, and the representations can be further decoded into realistic video clips to enable video generation. In this work, we introduce Divot, a Diffusion-Powered Video Tokenizer, which leverages the diffusion process for self-supervised video representation learning. We posit that if a video diffusion model can effectively de-noise video clips by taking the features of a video tokenizer as the condition, then the tokenizer has successfully captured robust spatial and temporal information. Additionally, the video diffusion model inherently functions as a de-tokenizer, decoding videos from their representations. Building upon the Divot tokenizer, we present Divot-Vicuna through video-to-text autoregression and text-to-video generation by modeling the distributions of continuous-valued Divot features with a Gaussian Mixture Model. Experimental results demonstrate that our diffusion-based video tokenizer, when integrated with a pre-trained LLM, achieves competitive performance across various video comprehension and generation benchmarks. The instruction tuned Divot-Vicuna also excels in video storytelling, generating interleaved narratives and corresponding videos.

  • 4 authors
·
Dec 5, 2024 2

InstructCV: Instruction-Tuned Text-to-Image Diffusion Models as Vision Generalists

Recent advances in generative diffusion models have enabled text-controlled synthesis of realistic and diverse images with impressive quality. Despite these remarkable advances, the application of text-to-image generative models in computer vision for standard visual recognition tasks remains limited. The current de facto approach for these tasks is to design model architectures and loss functions that are tailored to the task at hand. In this paper, we develop a unified language interface for computer vision tasks that abstracts away task-specific design choices and enables task execution by following natural language instructions. Our approach involves casting multiple computer vision tasks as text-to-image generation problems. Here, the text represents an instruction describing the task, and the resulting image is a visually-encoded task output. To train our model, we pool commonly-used computer vision datasets covering a range of tasks, including segmentation, object detection, depth estimation, and classification. We then use a large language model to paraphrase prompt templates that convey the specific tasks to be conducted on each image, and through this process, we create a multi-modal and multi-task training dataset comprising input and output images along with annotated instructions. Following the InstructPix2Pix architecture, we apply instruction-tuning to a text-to-image diffusion model using our constructed dataset, steering its functionality from a generative model to an instruction-guided multi-task vision learner. Experiments demonstrate that our model, dubbed InstructCV, performs competitively compared to other generalist and task-specific vision models. Moreover, it exhibits compelling generalization capabilities to unseen data, categories, and user instructions.

  • 5 authors
·
Sep 30, 2023 2

DiffusionRet: Generative Text-Video Retrieval with Diffusion Model

Existing text-video retrieval solutions are, in essence, discriminant models focused on maximizing the conditional likelihood, i.e., p(candidates|query). While straightforward, this de facto paradigm overlooks the underlying data distribution p(query), which makes it challenging to identify out-of-distribution data. To address this limitation, we creatively tackle this task from a generative viewpoint and model the correlation between the text and the video as their joint probability p(candidates,query). This is accomplished through a diffusion-based text-video retrieval framework (DiffusionRet), which models the retrieval task as a process of gradually generating joint distribution from noise. During training, DiffusionRet is optimized from both the generation and discrimination perspectives, with the generator being optimized by generation loss and the feature extractor trained with contrastive loss. In this way, DiffusionRet cleverly leverages the strengths of both generative and discriminative methods. Extensive experiments on five commonly used text-video retrieval benchmarks, including MSRVTT, LSMDC, MSVD, ActivityNet Captions, and DiDeMo, with superior performances, justify the efficacy of our method. More encouragingly, without any modification, DiffusionRet even performs well in out-domain retrieval settings. We believe this work brings fundamental insights into the related fields. Code is available at https://github.com/jpthu17/DiffusionRet.

  • 8 authors
·
Mar 17, 2023

DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the main goals in drug discovery -- designing novel ligands with desired properties, e.g., high binding affinity, easily synthesizable, etc. This challenge becomes particularly pronounced when the target-ligand pairs used for training do not align with these desired properties. Moreover, most existing methods aim at solving de novo design task, while many generative scenarios requiring flexible controllability, such as R-group optimization and scaffold hopping, have received little attention. In this work, we propose DecompOpt, a structure-based molecular optimization method based on a controllable and decomposed diffusion model. DecompOpt presents a new generation paradigm which combines optimization with conditional diffusion models to achieve desired properties while adhering to the molecular grammar. Additionally, DecompOpt offers a unified framework covering both de novo design and controllable generation. To achieve so, ligands are decomposed into substructures which allows fine-grained control and local optimization. Experiments show that DecompOpt can efficiently generate molecules with improved properties than strong de novo baselines, and demonstrate great potential in controllable generation tasks.

  • 6 authors
·
Mar 6, 2024

Text-to-Image Diffusion Models Cannot Count, and Prompt Refinement Cannot Help

Generative modeling is widely regarded as one of the most essential problems in today's AI community, with text-to-image generation having gained unprecedented real-world impacts. Among various approaches, diffusion models have achieved remarkable success and have become the de facto solution for text-to-image generation. However, despite their impressive performance, these models exhibit fundamental limitations in adhering to numerical constraints in user instructions, frequently generating images with an incorrect number of objects. While several prior works have mentioned this issue, a comprehensive and rigorous evaluation of this limitation remains lacking. To address this gap, we introduce T2ICountBench, a novel benchmark designed to rigorously evaluate the counting ability of state-of-the-art text-to-image diffusion models. Our benchmark encompasses a diverse set of generative models, including both open-source and private systems. It explicitly isolates counting performance from other capabilities, provides structured difficulty levels, and incorporates human evaluations to ensure high reliability. Extensive evaluations with T2ICountBench reveal that all state-of-the-art diffusion models fail to generate the correct number of objects, with accuracy dropping significantly as the number of objects increases. Additionally, an exploratory study on prompt refinement demonstrates that such simple interventions generally do not improve counting accuracy. Our findings highlight the inherent challenges in numerical understanding within diffusion models and point to promising directions for future improvements.

  • 8 authors
·
Mar 9

GenMol: A Drug Discovery Generalist with Discrete Diffusion

Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

  • 9 authors
·
Jan 10

The Superposition of Diffusion Models Using the Itô Density Estimator

The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable It\^o density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, and improved unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion

  • 5 authors
·
Dec 23, 2024 2

Unified Auto-Encoding with Masked Diffusion

At the core of both successful generative and self-supervised representation learning models there is a reconstruction objective that incorporates some form of image corruption. Diffusion models implement this approach through a scheduled Gaussian corruption process, while masked auto-encoder models do so by masking patches of the image. Despite their different approaches, the underlying similarity in their methodologies suggests a promising avenue for an auto-encoder capable of both de-noising tasks. We propose a unified self-supervised objective, dubbed Unified Masked Diffusion (UMD), that combines patch-based and noise-based corruption techniques within a single auto-encoding framework. Specifically, UMD modifies the diffusion transformer (DiT) training process by introducing an additional noise-free, high masking representation step in the diffusion noising schedule, and utilizes a mixed masked and noised image for subsequent timesteps. By integrating features useful for diffusion modeling and for predicting masked patch tokens, UMD achieves strong performance in downstream generative and representation learning tasks, including linear probing and class-conditional generation. This is achieved without the need for heavy data augmentations, multiple views, or additional encoders. Furthermore, UMD improves over the computational efficiency of prior diffusion based methods in total training time. We release our code at https://github.com/philippe-eecs/small-vision.

  • 4 authors
·
Jun 25, 2024

DiffSpectra: Molecular Structure Elucidation from Spectra using Diffusion Models

Molecular structure elucidation from spectra is a foundational problem in chemistry, with profound implications for compound identification, synthesis, and drug development. Traditional methods rely heavily on expert interpretation and lack scalability. Pioneering machine learning methods have introduced retrieval-based strategies, but their reliance on finite libraries limits generalization to novel molecules. Generative models offer a promising alternative, yet most adopt autoregressive SMILES-based architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that directly infers both 2D and 3D molecular structures from multi-modal spectral data using diffusion models. DiffSpectra formulates structure elucidation as a conditional generation process. Its denoising network is parameterized by Diffusion Molecule Transformer, an SE(3)-equivariant architecture that integrates topological and geometric information. Conditioning is provided by SpecFormer, a transformer-based spectral encoder that captures intra- and inter-spectral dependencies from multi-modal spectra. Extensive experiments demonstrate that DiffSpectra achieves high accuracy in structure elucidation, recovering exact structures with 16.01% top-1 accuracy and 96.86% top-20 accuracy through sampling. The model benefits significantly from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. These results highlight the effectiveness of spectrum-conditioned diffusion modeling in addressing the challenge of molecular structure elucidation. To our knowledge, DiffSpectra is the first framework to unify multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

  • 25 authors
·
Mar 9

A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

  • 58 authors
·
Mar 28, 2024

Local Graph Clustering with Noisy Labels

The growing interest in machine learning problems over graphs with additional node information such as texts, images, or labels has popularized methods that require the costly operation of processing the entire graph. Yet, little effort has been made to the development of fast local methods (i.e. without accessing the entire graph) that extract useful information from such data. To that end, we propose a study of local graph clustering using noisy node labels as a proxy for additional node information. In this setting, nodes receive initial binary labels based on cluster affiliation: 1 if they belong to the target cluster and 0 otherwise. Subsequently, a fraction of these labels is flipped. We investigate the benefits of incorporating noisy labels for local graph clustering. By constructing a weighted graph with such labels, we study the performance of graph diffusion-based local clustering method on both the original and the weighted graphs. From a theoretical perspective, we consider recovering an unknown target cluster with a single seed node in a random graph with independent noisy node labels. We provide sufficient conditions on the label noise under which, with high probability, using diffusion in the weighted graph yields a more accurate recovery of the target cluster. This approach proves more effective than using the given labels alone or using diffusion in the label-free original graph. Empirically, we show that reliable node labels can be obtained with just a few samples from an attributed graph. Moreover, utilizing these labels via diffusion in the weighted graph leads to significantly better local clustering performance across several real-world datasets, improving F1 scores by up to 13%.

  • 3 authors
·
Oct 12, 2023

InterLCM: Low-Quality Images as Intermediate States of Latent Consistency Models for Effective Blind Face Restoration

Diffusion priors have been used for blind face restoration (BFR) by fine-tuning diffusion models (DMs) on restoration datasets to recover low-quality images. However, the naive application of DMs presents several key limitations. (i) The diffusion prior has inferior semantic consistency (e.g., ID, structure and color.), increasing the difficulty of optimizing the BFR model; (ii) reliance on hundreds of denoising iterations, preventing the effective cooperation with perceptual losses, which is crucial for faithful restoration. Observing that the latent consistency model (LCM) learns consistency noise-to-data mappings on the ODE-trajectory and therefore shows more semantic consistency in the subject identity, structural information and color preservation, we propose InterLCM to leverage the LCM for its superior semantic consistency and efficiency to counter the above issues. Treating low-quality images as the intermediate state of LCM, InterLCM achieves a balance between fidelity and quality by starting from earlier LCM steps. LCM also allows the integration of perceptual loss during training, leading to improved restoration quality, particularly in real-world scenarios. To mitigate structural and semantic uncertainties, InterLCM incorporates a Visual Module to extract visual features and a Spatial Encoder to capture spatial details, enhancing the fidelity of restored images. Extensive experiments demonstrate that InterLCM outperforms existing approaches in both synthetic and real-world datasets while also achieving faster inference speed.

  • 9 authors
·
Feb 4 1

Deformable MRI Sequence Registration for AI-based Prostate Cancer Diagnosis

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

  • 8 authors
·
Apr 15, 2024

F-ViTA: Foundation Model Guided Visible to Thermal Translation

Thermal imaging is crucial for scene understanding, particularly in low-light and nighttime conditions. However, collecting large thermal datasets is costly and labor-intensive due to the specialized equipment required for infrared image capture. To address this challenge, researchers have explored visible-to-thermal image translation. Most existing methods rely on Generative Adversarial Networks (GANs) or Diffusion Models (DMs), treating the task as a style transfer problem. As a result, these approaches attempt to learn both the modality distribution shift and underlying physical principles from limited training data. In this paper, we propose F-ViTA, a novel approach that leverages the general world knowledge embedded in foundation models to guide the diffusion process for improved translation. Specifically, we condition an InstructPix2Pix Diffusion Model with zero-shot masks and labels from foundation models such as SAM and Grounded DINO. This allows the model to learn meaningful correlations between scene objects and their thermal signatures in infrared imagery. Extensive experiments on five public datasets demonstrate that F-ViTA outperforms state-of-the-art (SOTA) methods. Furthermore, our model generalizes well to out-of-distribution (OOD) scenarios and can generate Long-Wave Infrared (LWIR), Mid-Wave Infrared (MWIR), and Near-Infrared (NIR) translations from the same visible image. Code: https://github.com/JayParanjape/F-ViTA/tree/master.

  • 3 authors
·
Apr 3

Free-Lunch Color-Texture Disentanglement for Stylized Image Generation

Recent advances in Text-to-Image (T2I) diffusion models have transformed image generation, enabling significant progress in stylized generation using only a few style reference images. However, current diffusion-based methods struggle with fine-grained style customization due to challenges in controlling multiple style attributes, such as color and texture. This paper introduces the first tuning-free approach to achieve free-lunch color-texture disentanglement in stylized T2I generation, addressing the need for independently controlled style elements for the Disentangled Stylized Image Generation (DisIG) problem. Our approach leverages the Image-Prompt Additivity property in the CLIP image embedding space to develop techniques for separating and extracting Color-Texture Embeddings (CTE) from individual color and texture reference images. To ensure that the color palette of the generated image aligns closely with the color reference, we apply a whitening and coloring transformation to enhance color consistency. Additionally, to prevent texture loss due to the signal-leak bias inherent in diffusion training, we introduce a noise term that preserves textural fidelity during the Regularized Whitening and Coloring Transformation (RegWCT). Through these methods, our Style Attributes Disentanglement approach (SADis) delivers a more precise and customizable solution for stylized image generation. Experiments on images from the WikiArt and StyleDrop datasets demonstrate that, both qualitatively and quantitatively, SADis surpasses state-of-the-art stylization methods in the DisIG task.Code will be released at https://deepffff.github.io/sadis.github.io/.

  • 7 authors
·
Mar 18

One-Prompt-One-Story: Free-Lunch Consistent Text-to-Image Generation Using a Single Prompt

Text-to-image generation models can create high-quality images from input prompts. However, they struggle to support the consistent generation of identity-preserving requirements for storytelling. Existing approaches to this problem typically require extensive training in large datasets or additional modifications to the original model architectures. This limits their applicability across different domains and diverse diffusion model configurations. In this paper, we first observe the inherent capability of language models, coined context consistency, to comprehend identity through context with a single prompt. Drawing inspiration from the inherent context consistency, we propose a novel training-free method for consistent text-to-image (T2I) generation, termed "One-Prompt-One-Story" (1Prompt1Story). Our approach 1Prompt1Story concatenates all prompts into a single input for T2I diffusion models, initially preserving character identities. We then refine the generation process using two novel techniques: Singular-Value Reweighting and Identity-Preserving Cross-Attention, ensuring better alignment with the input description for each frame. In our experiments, we compare our method against various existing consistent T2I generation approaches to demonstrate its effectiveness through quantitative metrics and qualitative assessments. Code is available at https://github.com/byliutao/1Prompt1Story.

  • 9 authors
·
Jan 23 2

Generating Synthetic Fair Syntax-agnostic Data by Learning and Distilling Fair Representation

Data Fairness is a crucial topic due to the recent wide usage of AI powered applications. Most of the real-world data is filled with human or machine biases and when those data are being used to train AI models, there is a chance that the model will reflect the bias in the training data. Existing bias-mitigating generative methods based on GANs, Diffusion models need in-processing fairness objectives and fail to consider computational overhead while choosing computationally-heavy architectures, which may lead to high computational demands, instability and poor optimization performance. To mitigate this issue, in this work, we present a fair data generation technique based on knowledge distillation, where we use a small architecture to distill the fair representation in the latent space. The idea of fair latent space distillation enables more flexible and stable training of Fair Generative Models (FGMs). We first learn a syntax-agnostic (for any data type) fair representation of the data, followed by distillation in the latent space into a smaller model. After distillation, we use the distilled fair latent space to generate high-fidelity fair synthetic data. While distilling, we employ quality loss (for fair distillation) and utility loss (for data utility) to ensure that the fairness and data utility characteristics remain in the distilled latent space. Our approaches show a 5%, 5% and 10% rise in performance in fairness, synthetic sample quality and data utility, respectively, than the state-of-the-art fair generative model.

  • 4 authors
·
Aug 20, 2024

Predicting and generating antibiotics against future pathogens with ApexOracle

Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly identify effective molecules against novel pathogens or emerging drug-resistant strains. Here, we introduce ApexOracle, an artificial intelligence (AI) model that both predicts the antibacterial potency of existing compounds and designs de novo molecules active against strains it has never encountered. Departing from models that rely solely on molecular features, ApexOracle incorporates pathogen-specific context through the integration of molecular features captured via a foundational discrete diffusion language model and a dual-embedding framework that combines genomic- and literature-derived strain representations. Across diverse bacterial species and chemical modalities, ApexOracle consistently outperformed state-of-the-art approaches in activity prediction and demonstrated reliable transferability to novel pathogens with little or no antimicrobial data. Its unified representation-generation architecture further enables the in silico creation of "new-to-nature" molecules with high predicted efficacy against priority threats. By pairing rapid activity prediction with targeted molecular generation, ApexOracle offers a scalable strategy for countering AMR and preparing for future infectious-disease outbreaks.

  • 4 authors
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Jul 10

FabricDiffusion: High-Fidelity Texture Transfer for 3D Garments Generation from In-The-Wild Clothing Images

We introduce FabricDiffusion, a method for transferring fabric textures from a single clothing image to 3D garments of arbitrary shapes. Existing approaches typically synthesize textures on the garment surface through 2D-to-3D texture mapping or depth-aware inpainting via generative models. Unfortunately, these methods often struggle to capture and preserve texture details, particularly due to challenging occlusions, distortions, or poses in the input image. Inspired by the observation that in the fashion industry, most garments are constructed by stitching sewing patterns with flat, repeatable textures, we cast the task of clothing texture transfer as extracting distortion-free, tileable texture materials that are subsequently mapped onto the UV space of the garment. Building upon this insight, we train a denoising diffusion model with a large-scale synthetic dataset to rectify distortions in the input texture image. This process yields a flat texture map that enables a tight coupling with existing Physically-Based Rendering (PBR) material generation pipelines, allowing for realistic relighting of the garment under various lighting conditions. We show that FabricDiffusion can transfer various features from a single clothing image including texture patterns, material properties, and detailed prints and logos. Extensive experiments demonstrate that our model significantly outperforms state-to-the-art methods on both synthetic data and real-world, in-the-wild clothing images while generalizing to unseen textures and garment shapes.

  • 7 authors
·
Oct 2, 2024

Adapting Vehicle Detectors for Aerial Imagery to Unseen Domains with Weak Supervision

Detecting vehicles in aerial imagery is a critical task with applications in traffic monitoring, urban planning, and defense intelligence. Deep learning methods have provided state-of-the-art (SOTA) results for this application. However, a significant challenge arises when models trained on data from one geographic region fail to generalize effectively to other areas. Variability in factors such as environmental conditions, urban layouts, road networks, vehicle types, and image acquisition parameters (e.g., resolution, lighting, and angle) leads to domain shifts that degrade model performance. This paper proposes a novel method that uses generative AI to synthesize high-quality aerial images and their labels, improving detector training through data augmentation. Our key contribution is the development of a multi-stage, multi-modal knowledge transfer framework utilizing fine-tuned latent diffusion models (LDMs) to mitigate the distribution gap between the source and target environments. Extensive experiments across diverse aerial imagery domains show consistent performance improvements in AP50 over supervised learning on source domain data, weakly supervised adaptation methods, unsupervised domain adaptation methods, and open-set object detectors by 4-23%, 6-10%, 7-40%, and more than 50%, respectively. Furthermore, we introduce two newly annotated aerial datasets from New Zealand and Utah to support further research in this field. Project page is available at: https://humansensinglab.github.io/AGenDA

  • 8 authors
·
Jul 28 3

Consolidating Attention Features for Multi-view Image Editing

Large-scale text-to-image models enable a wide range of image editing techniques, using text prompts or even spatial controls. However, applying these editing methods to multi-view images depicting a single scene leads to 3D-inconsistent results. In this work, we focus on spatial control-based geometric manipulations and introduce a method to consolidate the editing process across various views. We build on two insights: (1) maintaining consistent features throughout the generative process helps attain consistency in multi-view editing, and (2) the queries in self-attention layers significantly influence the image structure. Hence, we propose to improve the geometric consistency of the edited images by enforcing the consistency of the queries. To do so, we introduce QNeRF, a neural radiance field trained on the internal query features of the edited images. Once trained, QNeRF can render 3D-consistent queries, which are then softly injected back into the self-attention layers during generation, greatly improving multi-view consistency. We refine the process through a progressive, iterative method that better consolidates queries across the diffusion timesteps. We compare our method to a range of existing techniques and demonstrate that it can achieve better multi-view consistency and higher fidelity to the input scene. These advantages allow us to train NeRFs with fewer visual artifacts, that are better aligned with the target geometry.

  • 5 authors
·
Feb 22, 2024 1

Dynamic Prompt Learning: Addressing Cross-Attention Leakage for Text-Based Image Editing

Large-scale text-to-image generative models have been a ground-breaking development in generative AI, with diffusion models showing their astounding ability to synthesize convincing images following an input text prompt. The goal of image editing research is to give users control over the generated images by modifying the text prompt. Current image editing techniques are susceptible to unintended modifications of regions outside the targeted area, such as on the background or on distractor objects which have some semantic or visual relationship with the targeted object. According to our experimental findings, inaccurate cross-attention maps are at the root of this problem. Based on this observation, we propose Dynamic Prompt Learning (DPL) to force cross-attention maps to focus on correct noun words in the text prompt. By updating the dynamic tokens for nouns in the textual input with the proposed leakage repairment losses, we achieve fine-grained image editing over particular objects while preventing undesired changes to other image regions. Our method DPL, based on the publicly available Stable Diffusion, is extensively evaluated on a wide range of images, and consistently obtains superior results both quantitatively (CLIP score, Structure-Dist) and qualitatively (on user-evaluation). We show improved prompt editing results for Word-Swap, Prompt Refinement, and Attention Re-weighting, especially for complex multi-object scenes.

  • 5 authors
·
Sep 27, 2023

PINN surrogate of Li-ion battery models for parameter inference. Part II: Regularization and application of the pseudo-2D model

Bayesian parameter inference is useful to improve Li-ion battery diagnostics and can help formulate battery aging models. However, it is computationally intensive and cannot be easily repeated for multiple cycles, multiple operating conditions, or multiple replicate cells. To reduce the computational cost of Bayesian calibration, numerical solvers for physics-based models can be replaced with faster surrogates. A physics-informed neural network (PINN) is developed as a surrogate for the pseudo-2D (P2D) battery model calibration. For the P2D surrogate, additional training regularization was needed as compared to the PINN single-particle model (SPM) developed in Part I. Both the PINN SPM and P2D surrogate models are exercised for parameter inference and compared to data obtained from a direct numerical solution of the governing equations. A parameter inference study highlights the ability to use these PINNs to calibrate scaling parameters for the cathode Li diffusion and the anode exchange current density. By realizing computational speed-ups of 2250x for the P2D model, as compared to using standard integrating methods, the PINN surrogates enable rapid state-of-health diagnostics. In the low-data availability scenario, the testing error was estimated to 2mV for the SPM surrogate and 10mV for the P2D surrogate which could be mitigated with additional data.

  • 9 authors
·
Dec 28, 2023

MedShift: Implicit Conditional Transport for X-Ray Domain Adaptation

Synthetic medical data offers a scalable solution for training robust models, but significant domain gaps limit its generalizability to real-world clinical settings. This paper addresses the challenge of cross-domain translation between synthetic and real X-ray images of the head, focusing on bridging discrepancies in attenuation behavior, noise characteristics, and soft tissue representation. We propose MedShift, a unified class-conditional generative model based on Flow Matching and Schrodinger Bridges, which enables high-fidelity, unpaired image translation across multiple domains. Unlike prior approaches that require domain-specific training or rely on paired data, MedShift learns a shared domain-agnostic latent space and supports seamless translation between any pair of domains seen during training. We introduce X-DigiSkull, a new dataset comprising aligned synthetic and real skull X-rays under varying radiation doses, to benchmark domain translation models. Experimental results demonstrate that, despite its smaller model size compared to diffusion-based approaches, MedShift offers strong performance and remains flexible at inference time, as it can be tuned to prioritize either perceptual fidelity or structural consistency, making it a scalable and generalizable solution for domain adaptation in medical imaging. The code and dataset are available at https://caetas.github.io/medshift.html

  • 4 authors
·
Aug 29

Generative Visual Prompt: Unifying Distributional Control of Pre-Trained Generative Models

Generative models (e.g., GANs, diffusion models) learn the underlying data distribution in an unsupervised manner. However, many applications of interest require sampling from a particular region of the output space or sampling evenly over a range of characteristics. For efficient sampling in these scenarios, we propose Generative Visual Prompt (PromptGen), a framework for distributional control over pre-trained generative models by incorporating knowledge of other off-the-shelf models. PromptGen defines control as energy-based models (EBMs) and samples images in a feed-forward manner by approximating the EBM with invertible neural networks, avoiding optimization at inference. Our experiments demonstrate how PromptGen can efficiently sample from several unconditional generative models (e.g., StyleGAN2, StyleNeRF, diffusion autoencoder, NVAE) in a controlled or/and de-biased manner using various off-the-shelf models: (1) with the CLIP model as control, PromptGen can sample images guided by text, (2) with image classifiers as control, PromptGen can de-bias generative models across a set of attributes or attribute combinations, and (3) with inverse graphics models as control, PromptGen can sample images of the same identity in different poses. (4) Finally, PromptGen reveals that the CLIP model shows a "reporting bias" when used as control, and PromptGen can further de-bias this controlled distribution in an iterative manner. The code is available at https://github.com/ChenWu98/Generative-Visual-Prompt.

  • 4 authors
·
Sep 14, 2022

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

  • 96 authors
·
Feb 9, 2020

Re-ttention: Ultra Sparse Visual Generation via Attention Statistical Reshape

Diffusion Transformers (DiT) have become the de-facto model for generating high-quality visual content like videos and images. A huge bottleneck is the attention mechanism where complexity scales quadratically with resolution and video length. One logical way to lessen this burden is sparse attention, where only a subset of tokens or patches are included in the calculation. However, existing techniques fail to preserve visual quality at extremely high sparsity levels and might even incur non-negligible compute overheads. % To address this concern, we propose Re-ttention, which implements very high sparse attention for visual generation models by leveraging the temporal redundancy of Diffusion Models to overcome the probabilistic normalization shift within the attention mechanism. Specifically, Re-ttention reshapes attention scores based on the prior softmax distribution history in order to preserve the visual quality of the full quadratic attention at very high sparsity levels. % Experimental results on T2V/T2I models such as CogVideoX and the PixArt DiTs demonstrate that Re-ttention requires as few as 3.1\% of the tokens during inference, outperforming contemporary methods like FastDiTAttn, Sparse VideoGen and MInference. Further, we measure latency to show that our method can attain over 45\% end-to-end % and over 92\% self-attention latency reduction on an H100 GPU at negligible overhead cost. Code available online here: https://github.com/cccrrrccc/Re-ttention{https://github.com/cccrrrccc/Re-ttention}

  • 5 authors
·
May 28 2

Distilled Protein Backbone Generation

Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unprecedented capabilities for de novo protein design. However, while achieving notable performance in generation quality, these models are limited by their generating speed, often requiring hundreds of iterative steps in the reverse-diffusion process. This computational bottleneck limits their practical utility in large-scale protein discovery, where thousands to millions of candidate structures are needed. To address this challenge, we explore the techniques of score distillation, which has shown great success in reducing the number of sampling steps in the vision domain while maintaining high generation quality. However, a straightforward adaptation of these methods results in unacceptably low designability. Through extensive study, we have identified how to appropriately adapt Score identity Distillation (SiD), a state-of-the-art score distillation strategy, to train few-step protein backbone generators which significantly reduce sampling time, while maintaining comparable performance to their pretrained teacher model. In particular, multistep generation combined with inference time noise modulation is key to the success. We demonstrate that our distilled few-step generators achieve more than a 20-fold improvement in sampling speed, while achieving similar levels of designability, diversity, and novelty as the Proteina teacher model. This reduction in inference cost enables large-scale in silico protein design, thereby bringing diffusion-based models closer to real-world protein engineering applications. The PyTorch implementation is available at https://github.com/LY-Xie/SiD_Protein

  • 5 authors
·
Oct 3