Alexandros Graikos

Edward J. Hu, Nikolay Malkin, Moksh Jain et al. · mila

Latent variable models (LVMs) with discrete compositional latents are an important but challenging setting due to a combinatorially large number of possible configurations of the latents. A key tradeoff in modeling the posteriors over latents is between expressivity and tractable optimization. For algorithms based on expectation-maximization (EM), the E-step is often intractable without restrictive approximations to the posterior. We propose the use of GFlowNets, algorithms for sampling from an unnormalized density by learning a stochastic policy for sequential construction of samples, for this intractable E-step. By training GFlowNets to sample from the posterior over latents, we take advantage of their strengths as amortized variational inference algorithms for complex distributions over discrete structures. Our approach, GFlowNet-EM, enables the training of expressive LVMs with discrete compositional latents, as shown by experiments on non-context-free grammar induction and on images using discrete variational autoencoders (VAEs) without conditional independence enforced in the encoder.

Alexandros Graikos, Nikolay Malkin, Nebojsa Jojic et al.

We consider the problem of inferring high-dimensional data $\mathbf{x}$ in a model that consists of a prior $p(\mathbf{x})$ and an auxiliary differentiable constraint $c(\mathbf{x},\mathbf{y})$ on $x$ given some additional information $\mathbf{y}$. In this paper, the prior is an independently trained denoising diffusion generative model. The auxiliary constraint is expected to have a differentiable form, but can come from diverse sources. The possibility of such inference turns diffusion models into plug-and-play modules, thereby allowing a range of potential applications in adapting models to new domains and tasks, such as conditional generation or image segmentation. The structure of diffusion models allows us to perform approximate inference by iterating differentiation through the fixed denoising network enriched with different amounts of noise at each step. Considering many noised versions of $\mathbf{x}$ in evaluation of its fitness is a novel search mechanism that may lead to new algorithms for solving combinatorial optimization problems.

Minh-Quan Le, Alexandros Graikos, Srikar Yellapragada et al.

Synthesizing high-resolution images from intricate, domain-specific information remains a significant challenge in generative modeling, particularly for applications in large-image domains such as digital histopathology and remote sensing. Existing methods face critical limitations: conditional diffusion models in pixel or latent space cannot exceed the resolution on which they were trained without losing fidelity, and computational demands increase significantly for larger image sizes. Patch-based methods offer computational efficiency but fail to capture long-range spatial relationships due to their overreliance on local information. In this paper, we introduce a novel conditional diffusion model in infinite dimensions, $\infty$-Brush for controllable large image synthesis. We propose a cross-attention neural operator to enable conditioning in function space. Our model overcomes the constraints of traditional finite-dimensional diffusion models and patch-based methods, offering scalability and superior capability in preserving global image structures while maintaining fine details. To our best knowledge, $\infty$-Brush is the first conditional diffusion model in function space, that can controllably synthesize images at arbitrary resolutions of up to $4096\times4096$ pixels. The code is available at https://github.com/cvlab-stonybrook/infinity-brush.

Haoyu Wu, Alexandros Graikos, Dimitris Samaras

Neural rendering of implicit surfaces performs well in 3D vision applications. However, it requires dense input views as supervision. When only sparse input images are available, output quality drops significantly due to the shape-radiance ambiguity problem. We note that this ambiguity can be constrained when a 3D point is visible in multiple views, as is the case in multi-view stereo (MVS). We thus propose to regularize neural rendering optimization with an MVS solution. The use of an MVS probability volume and a generalized cross entropy loss leads to a noise-tolerant optimization process. In addition, neural rendering provides global consistency constraints that guide the MVS depth hypothesis sampling and thus improves MVS performance. Given only three sparse input views, experiments show that our method not only outperforms generic neural rendering models by a large margin but also significantly increases the reconstruction quality of MVS models. Project page: https://hao-yu-wu.github.io/s-volsdf/.

Alexandros Graikos, Srikar Yellapragada, Dimitris Samaras

Denoising diffusion models have gained popularity as a generative modeling technique for producing high-quality and diverse images. Applying these models to downstream tasks requires conditioning, which can take the form of text, class labels, or other forms of guidance. However, providing conditioning information to these models can be challenging, particularly when annotations are scarce or imprecise. In this paper, we propose adapting pre-trained unconditional diffusion models to new conditions using the learned internal representations of the denoiser network. We demonstrate the effectiveness of our approach on various conditional generation tasks, including attribute-conditioned generation and mask-conditioned generation. Additionally, we show that augmenting the Tiny ImageNet training set with synthetic images generated by our approach improves the classification accuracy of ResNet baselines by up to 8%. Our approach provides a powerful and flexible way to adapt diffusion models to new conditions and generate high-quality augmented data for various conditional generation tasks.

Ritik Raina, Abe Leite, Alexandros Graikos et al.

Human vision combines low-resolution "gist" information from the visual periphery with sparse but high-resolution information from fixated locations to construct a coherent understanding of a visual scene. In this paper, we introduce MetamerGen, a tool for generating scenes that are aligned with latent human scene representations. MetamerGen is a latent diffusion model that combines peripherally obtained scene gist information with information obtained from scene-viewing fixations to generate image metamers for what humans understand after viewing a scene. Generating images from both high and low resolution (i.e. "foveated") inputs constitutes a novel image-to-image synthesis problem, which we tackle by introducing a dual-stream representation of the foveated scenes consisting of DINOv2 tokens that fuse detailed features from fixated areas with peripherally degraded features capturing scene context. To evaluate the perceptual alignment of MetamerGen generated images to latent human scene representations, we conducted a same-different behavioral experiment where participants were asked for a "same" or "different" response between the generated and the original image. With that, we identify scene generations that are indeed metamers for the latent scene representations formed by the viewers. MetamerGen is a powerful tool for understanding scene understanding. Our proof-of-concept analyses uncovered specific features at multiple levels of visual processing that contributed to human judgments. While it can generate metamers even conditioned on random fixations, we find that high-level semantic alignment most strongly predicts metamerism when the generated scenes are conditioned on viewers' own fixated regions.

Irene Kim, Sai Tanmay Reddy Chakkera, Alexandros Graikos et al.

Monocular surface normal estimators trained on large-scale RGB-normal data often perform poorly in the edge cases of reflective, textureless, and dark surfaces. Polarization encodes surface orientation independently of texture and albedo, offering a physics-based complement for these cases. Existing polarization methods, however, require multi-view capture or specialized training data, limiting generalization. We introduce Poppy, a training-free framework that refines normals from any frozen RGB backbone using single-shot polarization measurements at test time. Keeping backbone weights frozen, Poppy optimizes per-pixel offsets to the input RGB and output normal along with a learned reflectance decomposition. A differentiable rendering layer converts the refined normals into polarization predictions and penalizes mismatches with the observed signal. Across seven benchmarks and three backbone architectures (diffusion, flow, and feed-forward), Poppy reduces mean angular error by 23-26% on synthetic data and 6-16% on real data. These results show that guiding learned RGB-based normal estimators with polarization cues at test time refines normals on challenging surfaces without retraining.

Snehal Singh Tomar, Alexandros Graikos, Arjun Krishna et al.

Modern deep learning methods typically treat image sequences as large tensors of sequentially stacked frames. However, is this straightforward representation ideal given the current state-of-the-art (SoTA)? In this work, we address this question in the context of generative models and aim to devise a more effective way of modeling image sequence data. Observing the inefficiencies and bottlenecks of current SoTA image sequence generation methods, we showcase that rather than working with large tensors, we can improve the generation process by factorizing it into first generating the coarse sequence at low resolution and then refining the individual frames at high resolution. We train a generative model solely on grid images comprising subsampled frames. Yet, we learn to generate image sequences, using the strong self-attention mechanism of the Diffusion Transformer (DiT) to capture correlations between frames. In effect, our formulation extends a 2D image generator to operate as a low-resolution 3D image-sequence generator without introducing any architectural modifications. Subsequently, we super-resolve each frame individually to add the sequence-independent high-resolution details. This approach offers several advantages and can overcome key limitations of the SoTA in this domain. Compared to existing image sequence generation models, our method achieves superior synthesis quality and improved coherence across sequences. It also delivers high-fidelity generation of arbitrary-length sequences and increased efficiency in inference time and training data usage. Furthermore, our straightforward formulation enables our method to generalize effectively across diverse data domains, which typically require additional priors and supervision to model in a generative context. Our method consistently outperforms SoTA in quality and inference speed (at least twice-as-fast) across datasets.

Alexandros Graikos, Nebojsa Jojic, Dimitris Samaras

Large denoising diffusion models, such as Stable Diffusion, have been trained on billions of image-caption pairs to perform text-conditioned image generation. As a byproduct of this training, these models have acquired general knowledge about image statistics, which can be useful for other inference tasks. However, when confronted with sampling an image under new constraints, e.g. generating the missing parts of an image, using large pre-trained text-to-image diffusion models is inefficient and often unreliable. Previous approaches either utilized backpropagation through the denoiser network, making them significantly slower and more memory-demanding than simple text-to-image generation, or only enforced the constraint locally, failing to capture critical long-range correlations in the sampled image. In this work, we propose an algorithm that enables fast, high-quality generation under arbitrary constraints. We show that in denoising diffusion models, we can employ an approximation to Newton's optimization method that allows us to speed up inference and avoid the expensive backpropagation operations. Our approach produces results that rival or surpass the state-of-the-art training-free inference methods while requiring a fraction of the time. We demonstrate the effectiveness of our algorithm under both linear (inpainting, super-resolution) and non-linear (style-guided generation) constraints. An implementation is provided at https://github.com/cvlab-stonybrook/fast-constrained-sampling.

Srikar Yellapragada, Alexandros Graikos, Kostas Triaridis et al.

The growing volume of high-resolution Whole Slide Images in digital histopathology poses significant storage, transmission, and computational efficiency challenges. Standard compression methods, such as JPEG, reduce file sizes but often fail to preserve fine-grained phenotypic details critical for downstream tasks. In this work, we repurpose autoencoders (AEs) designed for Latent Diffusion Models as an efficient learned compression framework for pathology images. We systematically benchmark three AE models with varying compression levels and evaluate their reconstruction ability using pathology foundation models. We introduce a fine-tuning strategy to further enhance reconstruction fidelity that optimizes a pathology-specific learned perceptual metric. We validate our approach on downstream tasks, including segmentation, patch classification, and multiple instance learning, showing that replacing images with AE-compressed reconstructions leads to minimal performance degradation. Additionally, we propose a K-means clustering-based quantization method for AE latents, improving storage efficiency while maintaining reconstruction quality. We provide the weights of the fine-tuned autoencoders at https://huggingface.co/collections/StonyBrook-CVLab/pathology-fine-tuned-aes-67d45f223a659ff2e3402dd0.

Alexandros Graikos, Srikar Yellapragada, Minh-Quan Le et al.

To synthesize high-fidelity samples, diffusion models typically require auxiliary data to guide the generation process. However, it is impractical to procure the painstaking patch-level annotation effort required in specialized domains like histopathology and satellite imagery; it is often performed by domain experts and involves hundreds of millions of patches. Modern-day self-supervised learning (SSL) representations encode rich semantic and visual information. In this paper, we posit that such representations are expressive enough to act as proxies to fine-grained human labels. We introduce a novel approach that trains diffusion models conditioned on embeddings from SSL. Our diffusion models successfully project these features back to high-quality histopathology and remote sensing images. In addition, we construct larger images by assembling spatially consistent patches inferred from SSL embeddings, preserving long-range dependencies. Augmenting real data by generating variations of real images improves downstream classifier accuracy for patch-level and larger, image-scale classification tasks. Our models are effective even on datasets not encountered during training, demonstrating their robustness and generalizability. Generating images from learned embeddings is agnostic to the source of the embeddings. The SSL embeddings used to generate a large image can either be extracted from a reference image, or sampled from an auxiliary model conditioned on any related modality (e.g. class labels, text, genomic data). As proof of concept, we introduce the text-to-large image synthesis paradigm where we successfully synthesize large pathology and satellite images out of text descriptions.

Srikar Yellapragada, Alexandros Graikos, Kostas Triaridis et al.

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. 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 synthesizes coherent histopathology images that remain contextually accurate and detailed at different zoom levels, achieving state-of-the-art image generation quality across all scales and excelling 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.

Varun Belagali, Srikar Yellapragada, Alexandros Graikos et al.

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.

Kostas Triaridis, Alexandros Graikos, Aggelina Chatziagapi et al.

Diffusion models, despite their impressive demos, often produce hallucinatory samples with structural inconsistencies that lie outside of the support of the true data distribution. Such hallucinations can be attributed to excessive smoothing between modes of the data distribution. However, semantic interpolations are often desirable and can lead to generation diversity, thus we believe a more nuanced solution is required. In this work, we introduce Dynamic Guidance, which tackles this issue. Dynamic Guidance mitigates hallucinations by selectively sharpening the score function only along the pre-determined directions known to cause artifacts, while preserving valid semantic variations. To our knowledge, this is the first approach that addresses hallucinations at generation time rather than through post-hoc filtering. Dynamic Guidance substantially reduces hallucinations on both controlled and natural image datasets, significantly outperforming baselines.

Srikar Yellapragada, Alexandros Graikos, Zilinghan Li et al.

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

Sachin Kumar Danisetty, Alexandros Graikos, Srikar Yellapragada et al.

Image segmentation is crucial in many computational pathology pipelines, including accurate disease diagnosis, subtyping, outcome, and survivability prediction. The common approach for training a segmentation model relies on a pre-trained feature extractor and a dataset of paired image and mask annotations. These are used to train a lightweight prediction model that translates features into per-pixel classes. The choice of the feature extractor is central to the performance of the final segmentation model, and recent literature has focused on finding tasks to pre-train the feature extractor. In this paper, we propose PathSegDiff, a novel approach for histopathology image segmentation that leverages Latent Diffusion Models (LDMs) as pre-trained featured extractors. Our method utilizes a pathology-specific LDM, guided by a self-supervised encoder, to extract rich semantic information from H\&E stained histopathology images. We employ a simple, fully convolutional network to process the features extracted from the LDM and generate segmentation masks. Our experiments demonstrate significant improvements over traditional methods on the BCSS and GlaS datasets, highlighting the effectiveness of domain-specific diffusion pre-training in capturing intricate tissue structures and enhancing segmentation accuracy in histopathology images.

Qiaomu Miao, Alexandros Graikos, Jingwei Zhang et al.

Training gaze following models requires a large number of images with gaze target coordinates annotated by human annotators, which is a laborious and inherently ambiguous process. We propose the first semi-supervised method for gaze following by introducing two novel priors to the task. We obtain the first prior using a large pretrained Visual Question Answering (VQA) model, where we compute Grad-CAM heatmaps by `prompting' the VQA model with a gaze following question. These heatmaps can be noisy and not suited for use in training. The need to refine these noisy annotations leads us to incorporate a second prior. We utilize a diffusion model trained on limited human annotations and modify the reverse sampling process to refine the Grad-CAM heatmaps. By tuning the diffusion process we achieve a trade-off between the human annotation prior and the VQA heatmap prior, which retains the useful VQA prior information while exhibiting similar properties to the training data distribution. Our method outperforms simple pseudo-annotation generation baselines on the GazeFollow image dataset. More importantly, our pseudo-annotation strategy, applied to a widely used supervised gaze following model (VAT), reduces the annotation need by 50%. Our method also performs the best on the VideoAttentionTarget dataset.

Srikar Yellapragada, Alexandros Graikos, Prateek Prasanna et al.

To achieve high-quality results, diffusion models must be trained on large datasets. This can be notably prohibitive for models in specialized domains, such as computational pathology. Conditioning on labeled data is known to help in data-efficient model training. Therefore, histopathology reports, which are rich in valuable clinical information, are an ideal choice as guidance for a histopathology generative model. In this paper, we introduce PathLDM, the first text-conditioned Latent Diffusion Model tailored for generating high-quality histopathology images. Leveraging the rich contextual information provided by pathology text reports, our approach fuses image and textual data to enhance the generation process. By utilizing GPT's capabilities to distill and summarize complex text reports, we establish an effective conditioning mechanism. Through strategic conditioning and necessary architectural enhancements, we achieved a SoTA FID score of 7.64 for text-to-image generation on the TCGA-BRCA dataset, significantly outperforming the closest text-conditioned competitor with FID 30.1.

Esther Rolf, Nikolay Malkin, Alexandros Graikos et al.

We propose a method for jointly inferring labels across a collection of data samples, where each sample consists of an observation and a prior belief about the label. By implicitly assuming the existence of a generative model for which a differentiable predictor is the posterior, we derive a training objective that allows learning under weak beliefs. This formulation unifies various machine learning settings; the weak beliefs can come in the form of noisy or incomplete labels, likelihoods given by a different prediction mechanism on auxiliary input, or common-sense priors reflecting knowledge about the structure of the problem at hand. We demonstrate the proposed algorithms on diverse problems: classification with negative training examples, learning from rankings, weakly and self-supervised aerial imagery segmentation, co-segmentation of video frames, and coarsely supervised text classification.