TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model

Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue environments, enhances downstream tasks by augmenting training data, aligns more closely with pathologists' domain knowledge, and offers new opportunities for controlling and generalizing the tumor microenvironment. In this paper, we propose a novel approach that integrates topological constraints into a diffusion model to improve the generation of realistic, contextually accurate cell topologies. Our method refines the simulation of cell distributions and interactions, increasing the precision and interpretability of results in downstream tasks such as cell detection and classification. To assess the topological fidelity of generated layouts, we introduce a new metric, Topological Frechet Distance (TopoFD), which overcomes the limitations of traditional metrics like FID in evaluating topological structure. Experimental results demonstrate the effectiveness of our approach in generating multi-class cell layouts that capture intricate topological relationships.

Gen-SIS: Generative Self-augmentation Improves Self-supervised Learning

Self-supervised learning (SSL) methods have emerged as strong visual representation learners by training an image encoder to maximize similarity between features of different views of the same image. To perform this view-invariance task, current SSL algorithms rely on hand-crafted augmentations such as random cropping and color jittering to create multiple views of an image. Recently, generative diffusion models have been shown to improve SSL by providing a wider range of data augmentations. However, these diffusion models require pre-training on large-scale image-text datasets, which might not be available for many specialized domains like histopathology. In this work, we introduce Gen-SIS, a diffusion-based augmentation technique trained exclusively on unlabeled image data, eliminating any reliance on external sources of supervision such as text captions. We first train an initial SSL encoder on a dataset using only hand-crafted augmentations. We then train a diffusion model conditioned on embeddings from that SSL encoder. Following training, given an embedding of the source image, this diffusion model can synthesize its diverse views. We show that these `self-augmentations', i.e. generative augmentations based on the vanilla SSL encoder embeddings, facilitate the training of a stronger SSL encoder. Furthermore, based on the ability to interpolate between images in the encoder latent space, we introduce the novel pretext task of disentangling the two source images of an interpolated synthetic image. We validate Gen-SIS's effectiveness by demonstrating performance improvements across various downstream tasks in both natural images, which are generally object-centric, as well as digital histopathology images, which are typically context-based.

2DMamba: Efficient State Space Model for Image Representation with Applications on Giga-Pixel Whole Slide Image Classification

Efficiently modeling large 2D contexts is essential for various fields including Giga-Pixel Whole Slide Imaging (WSI) and remote sensing. Transformer-based models offer high parallelism but face challenges due to their quadratic complexity for handling long sequences. Recently, Mamba introduced a selective State Space Model (SSM) with linear complexity and high parallelism, enabling effective and efficient modeling of wide context in 1D sequences. However, extending Mamba to vision tasks, which inherently involve 2D structures, results in spatial discrepancies due to the limitations of 1D sequence processing. On the other hand, current 2D SSMs inherently model 2D structures but they suffer from prohibitively slow computation due to the lack of efficient parallel algorithms. In this work, we propose 2DMamba, a novel 2D selective SSM framework that incorporates the 2D spatial structure of images into Mamba, with a highly optimized hardware-aware operator, adopting both spatial continuity and computational efficiency. We validate the versatility of our approach on both WSIs and natural images. Extensive experiments on 10 public datasets for WSI classification and survival analysis show that 2DMamba~improves up to $2.48\%$ in AUC, $3.11\%$ in F1 score, $2.47\%$ in accuracy and $5.52\%$ in C-index. Additionally, integrating our method with VMamba for natural imaging yields $0.5$ to $0.7$ improvements in mIoU on the ADE20k semantic segmentation dataset, and $0.2\%$ accuracy improvement on ImageNet-1K classification dataset. Our code is available at https://github.com/AtlasAnalyticsLab/2DMamba.

MLI-NeRF: Multi-Light Intrinsic-Aware Neural Radiance Fields

Current methods for extracting intrinsic image components, such as reflectance and shading, primarily rely on statistical priors. These methods focus mainly on simple synthetic scenes and isolated objects and struggle to perform well on challenging real-world data. To address this issue, we propose MLI-NeRF, which integrates \textbf{M}ultiple \textbf{L}ight information in \textbf{I}ntrinsic-aware \textbf{Ne}ural \textbf{R}adiance \textbf{F}ields. By leveraging scene information provided by different light source positions complementing the multi-view information, we generate pseudo-label images for reflectance and shading to guide intrinsic image decomposition without the need for ground truth data. Our method introduces straightforward supervision for intrinsic component separation and ensures robustness across diverse scene types. We validate our approach on both synthetic and real-world datasets, outperforming existing state-of-the-art methods. Additionally, we demonstrate its applicability to various image editing tasks. The code and data are publicly available.

ZoomLDM: Latent Diffusion Model for multi-scale image generation

Diffusion models have revolutionized image generation, yet several challenges restrict their application to large-image domains, such as digital pathology and satellite imagery. Given that it is infeasible to directly train a model on 'whole' images from domains with potential gigapixel sizes, diffusion-based generative methods have focused on synthesizing small, fixed-size patches extracted from these images. However, generating small patches has limited applicability since patch-based models fail to capture the global structures and wider context of large images, which can be crucial for synthesizing (semantically) accurate samples. In this paper, to overcome this limitation, we present ZoomLDM, a diffusion model tailored for generating images across multiple scales. Central to our approach is a novel magnification-aware conditioning mechanism that utilizes self-supervised learning (SSL) embeddings and allows the diffusion model to synthesize images at different 'zoom' levels, i.e., fixed-size patches extracted from large images at varying scales. ZoomLDM achieves state-of-the-art image generation quality across all scales, excelling particularly in the data-scarce setting of generating thumbnails of entire large images. The multi-scale nature of ZoomLDM unlocks additional capabilities in large image generation, enabling computationally tractable and globally coherent image synthesis up to $4096 \times 4096$ pixels and $4\times$ super-resolution. Additionally, multi-scale features extracted from ZoomLDM are highly effective in multiple instance learning experiments. We provide high-resolution examples of the generated images on our website https://histodiffusion.github.io/docs/publications/zoomldm/.

Importance-based Token Merging for Diffusion Models

Diffusion models excel at high-quality image and video generation. However, a major drawback is their high latency. A simple yet powerful way to speed them up is by merging similar tokens for faster computation, though this can result in some quality loss. In this paper, we demonstrate that preserving important tokens during merging significantly improves sample quality. Notably, the importance of each token can be reliably determined using the classifier-free guidance magnitude, as this measure is strongly correlated with the conditioning input and corresponds to output fidelity. Since classifier-free guidance incurs no additional computational cost or requires extra modules, our method can be easily integrated into most diffusion-based frameworks. Experiments show that our approach significantly outperforms the baseline across various applications, including text-to-image synthesis, multi-view image generation, and video generation.

Instance-Aware Generalized Referring Expression Segmentation

Recent works on Generalized Referring Expression Segmentation (GRES) struggle with handling complex expressions referring to multiple distinct objects. This is because these methods typically employ an end-to-end foreground-background segmentation and lack a mechanism to explicitly differentiate and associate different object instances to the text query. To this end, we propose InstAlign, a method that incorporates object-level reasoning into the segmentation process. Our model leverages both text and image inputs to extract a set of object-level tokens that capture both the semantic information in the input prompt and the objects within the image. By modeling the text-object alignment via instance-level supervision, each token uniquely represents an object segment in the image, while also aligning with relevant semantic information from the text. Extensive experiments on the gRefCOCO and Ref-ZOM benchmarks demonstrate that our method significantly advances state-of-the-art performance, setting a new standard for precise and flexible GRES.

Direct and Explicit 3D Generation from a Single Image

Current image-to-3D approaches suffer from high computational costs and lack scalability for high-resolution outputs. In contrast, we introduce a novel framework to directly generate explicit surface geometry and texture using multi-view 2D depth and RGB images along with 3D Gaussian features using a repurposed Stable Diffusion model. We introduce a depth branch into U-Net for efficient and high quality multi-view, cross-domain generation and incorporate epipolar attention into the latent-to-pixel decoder for pixel-level multi-view consistency. By back-projecting the generated depth pixels into 3D space, we create a structured 3D representation that can be either rendered via Gaussian splatting or extracted to high-quality meshes, thereby leveraging additional novel view synthesis loss to further improve our performance. Extensive experiments demonstrate that our method surpasses existing baselines in geometry and texture quality while achieving significantly faster generation time.

Fast constrained sampling in pre-trained diffusion models

Diffusion models have dominated the field of large, generative image models, with the prime examples of Stable Diffusion and DALL-E 3 being widely adopted. These models have been trained to perform text-conditioned generation on vast numbers of image-caption pairs and as a byproduct, have acquired general knowledge about natural image statistics. However, when confronted with the task of constrained sampling, e.g. generating the right half of an image conditioned on the known left half, applying these models is a delicate and slow process, with previously proposed algorithms relying on expensive iterative operations that are usually orders of magnitude slower than text-based inference. This is counter-intuitive, as image-conditioned generation should rely less on the difficult-to-learn semantic knowledge that links captions and imagery, and should instead be achievable by lower-level correlations among image pixels. In practice, inverse models are trained or tuned separately for each inverse problem, e.g. by providing parts of images during training as an additional condition, to allow their application in realistic settings. However, we argue that this is not necessary and propose an algorithm for fast-constrained sampling in large pre-trained diffusion models (Stable Diffusion) that requires no expensive backpropagation operations through the model and produces results comparable even to the state-of-the-art \emph{tuned} models. Our method is based on a novel optimization perspective to sampling under constraints and employs a numerical approximation to the expensive gradients, previously computed using backpropagation, incurring significant speed-ups.

TopoDiffusionNet: A Topology-aware Diffusion Model

Diffusion models excel at creating visually impressive images but often struggle to generate images with a specified topology. The Betti number, which represents the number of structures in an image, is a fundamental measure in topology. Yet, diffusion models fail to satisfy even this basic constraint. This limitation restricts their utility in applications requiring exact control, like robotics and environmental modeling. To address this, we propose TopoDiffusionNet (TDN), a novel approach that enforces diffusion models to maintain the desired topology. We leverage tools from topological data analysis, particularly persistent homology, to extract the topological structures within an image. We then design a topology-based objective function to guide the denoising process, preserving intended structures while suppressing noisy ones. Our experiments across four datasets demonstrate significant improvements in topological accuracy. TDN is the first to integrate topology with diffusion models, opening new avenues of research in this area.