Dimitris Samaras

Jingyi Xu, Hieu Le, Vu Nguyen et al.

Class-agnostic object counting aims to count object instances of an arbitrary class at test time. It is challenging but also enables many potential applications. Current methods require human-annotated exemplars as inputs which are often unavailable for novel categories, especially for autonomous systems. Thus, we propose zero-shot object counting (ZSC), a new setting where only the class name is available during test time. Such a counting system does not require human annotators in the loop and can operate automatically. Starting from a class name, we propose a method that can accurately identify the optimal patches which can then be used as counting exemplars. Specifically, we first construct a class prototype to select the patches that are likely to contain the objects of interest, namely class-relevant patches. Furthermore, we introduce a model that can quantitatively measure how suitable an arbitrary patch is as a counting exemplar. By applying this model to all the candidate patches, we can select the most suitable patches as exemplars for counting. Experimental results on a recent class-agnostic counting dataset, FSC-147, validate the effectiveness of our method. Code is available at https://github.com/cvlab-stonybrook/zero-shot-counting

Mahdi S. Hosseini, Babak Ehteshami Bejnordi, Vincent Quoc-Huy Trinh et al.

Computational Pathology CPath is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath (https://github.com/AtlasAnalyticsLab/CPath_Survey).

Zhibo Yang, Sounak Mondal, Seoyoung Ahn et al.

Most models of visual attention aim at predicting either top-down or bottom-up control, as studied using different visual search and free-viewing tasks. In this paper we propose the Human Attention Transformer (HAT), a single model that predicts both forms of attention control. HAT uses a novel transformer-based architecture and a simplified foveated retina that collectively create a spatio-temporal awareness akin to the dynamic visual working memory of humans. HAT not only establishes a new state-of-the-art in predicting the scanpath of fixations made during target-present and target-absent visual search and ``taskless'' free viewing, but also makes human gaze behavior interpretable. Unlike previous methods that rely on a coarse grid of fixation cells and experience information loss due to fixation discretization, HAT features a sequential dense prediction architecture and outputs a dense heatmap for each fixation, thus avoiding discretizing fixations. HAT sets a new standard in computational attention, which emphasizes effectiveness, generality, and interpretability. HAT's demonstrated scope and applicability will likely inspire the development of new attention models that can better predict human behavior in various attention-demanding scenarios. Code is available at https://github.com/cvlab-stonybrook/HAT.

Jingwei Zhang, Saarthak Kapse, Ke Ma et al.

Whole slide image (WSI) classification is a critical task in computational pathology, requiring the processing of gigapixel-sized images, which is challenging for current deep-learning methods. Current state of the art methods are based on multi-instance learning schemes (MIL), which usually rely on pretrained features to represent the instances. Due to the lack of task-specific annotated data, these features are either obtained from well-established backbones on natural images, or, more recently from self-supervised models pretrained on histopathology. However, both approaches yield task-agnostic features, resulting in performance loss compared to the appropriate task-related supervision, if available. In this paper, we show that when task-specific annotations are limited, we can inject such supervision into downstream task training, to reduce the gap between fully task-tuned and task agnostic features. We propose Prompt-MIL, an MIL framework that integrates prompts into WSI classification. Prompt-MIL adopts a prompt tuning mechanism, where only a small fraction of parameters calibrates the pretrained features to encode task-specific information, rather than the conventional full fine-tuning approaches. Extensive experiments on three WSI datasets, TCGA-BRCA, TCGA-CRC, and BRIGHT, demonstrate the superiority of Prompt-MIL over conventional MIL methods, achieving a relative improvement of 1.49%-4.03% in accuracy and 0.25%-8.97% in AUROC while using fewer than 0.3% additional parameters. Compared to conventional full fine-tuning approaches, we fine-tune less than 1.3% of the parameters, yet achieve a relative improvement of 1.29%-13.61% in accuracy and 3.22%-27.18% in AUROC and reduce GPU memory consumption by 38%-45% while training 21%-27% faster. Our code is available at https://github.com/cvlab-stonybrook/PromptMIL.

Lei Zhou, Huidong Liu, Joseph Bae et al.

Masked Autoencoder (MAE) has recently been shown to be effective in pre-training Vision Transformers (ViT) for natural image analysis. By reconstructing full images from partially masked inputs, a ViT encoder aggregates contextual information to infer masked image regions. We believe that this context aggregation ability is particularly essential to the medical image domain where each anatomical structure is functionally and mechanically connected to other structures and regions. Because there is no ImageNet-scale medical image dataset for pre-training, we investigate a self pre-training paradigm with MAE for medical image analysis tasks. Our method pre-trains a ViT on the training set of the target data instead of another dataset. Thus, self pre-training can benefit more scenarios where pre-training data is hard to acquire. Our experimental results show that MAE self pre-training markedly improves diverse medical image tasks including chest X-ray disease classification, abdominal CT multi-organ segmentation, and MRI brain tumor segmentation. Code is available at https://github.com/cvlab-stonybrook/SelfMedMAE

Jingwei Zhang, Xin Zhang, Ke Ma et al.

Histopathology whole slide images (WSIs) play a very important role in clinical studies and serve as the gold standard for many cancer diagnoses. However, generating automatic tools for processing WSIs is challenging due to their enormous sizes. Currently, to deal with this issue, conventional methods rely on a multiple instance learning (MIL) strategy to process a WSI at patch level. Although effective, such methods are computationally expensive, because tiling a WSI into patches takes time and does not explore the spatial relations between these tiles. To tackle these limitations, we propose a locally supervised learning framework which processes the entire slide by exploring the entire local and global information that it contains. This framework divides a pre-trained network into several modules and optimizes each module locally using an auxiliary model. We also introduce a random feature reconstruction unit (RFR) to preserve distinguishing features during training and improve the performance of our method by 1% to 3%. Extensive experiments on three publicly available WSI datasets: TCGA-NSCLC, TCGA-RCC and LKS, highlight the superiority of our method on different classification tasks. Our method outperforms the state-of-the-art MIL methods by 2% to 5% in accuracy, while being 7 to 10 times faster. Additionally, when dividing it into eight modules, our method requires as little as 20% of the total gpu memory required by end-to-end training. Our code is available at https://github.com/cvlab-stonybrook/local_learning_wsi.

Jingwei Zhang, Saarthak Kapse, Ke Ma et al.

Dense prediction tasks such as segmentation and detection of pathological entities hold crucial clinical value in computational pathology workflows. However, obtaining dense annotations on large cohorts is usually tedious and expensive. Contrastive learning (CL) is thus often employed to leverage large volumes of unlabeled data to pre-train the backbone network. To boost CL for dense prediction, some studies have proposed variations of dense matching objectives in pre-training. However, our analysis shows that employing existing dense matching strategies on histopathology images enforces invariance among incorrect pairs of dense features and, thus, is imprecise. To address this, we propose a precise location-based matching mechanism that utilizes the overlapping information between geometric transformations to precisely match regions in two augmentations. Extensive experiments on two pretraining datasets (TCGA-BRCA, NCT-CRC-HE) and three downstream datasets (GlaS, CRAG, BCSS) highlight the superiority of our method in semantic and instance segmentation tasks. Our method outperforms previous dense matching methods by up to 7.2% in average precision for detection and 5.6% in average precision for instance segmentation tasks. Additionally, by using our matching mechanism in the three popular contrastive learning frameworks, MoCo-v2, VICRegL, and ConCL, the average precision in detection is improved by 0.7% to 5.2%, and the average precision in segmentation is improved by 0.7% to 4.0%, demonstrating generalizability. Our code is available at https://github.com/cvlab-stonybrook/PLM_SSL.

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.

Sounak Mondal, Zhibo Yang, Seoyoung Ahn et al.

Predicting human gaze is important in Human-Computer Interaction (HCI). However, to practically serve HCI applications, gaze prediction models must be scalable, fast, and accurate in their spatial and temporal gaze predictions. Recent scanpath prediction models focus on goal-directed attention (search). Such models are limited in their application due to a common approach relying on trained target detectors for all possible objects, and the availability of human gaze data for their training (both not scalable). In response, we pose a new task called ZeroGaze, a new variant of zero-shot learning where gaze is predicted for never-before-searched objects, and we develop a novel model, Gazeformer, to solve the ZeroGaze problem. In contrast to existing methods using object detector modules, Gazeformer encodes the target using a natural language model, thus leveraging semantic similarities in scanpath prediction. We use a transformer-based encoder-decoder architecture because transformers are particularly useful for generating contextual representations. Gazeformer surpasses other models by a large margin on the ZeroGaze setting. It also outperforms existing target-detection models on standard gaze prediction for both target-present and target-absent search tasks. In addition to its improved performance, Gazeformer is more than five times faster than the state-of-the-art target-present visual search model.

Jingyi Xu, Hieu Le, Dimitris Samaras

Two-stage object detectors generate object proposals and classify them to detect objects in images. These proposals often do not contain the objects perfectly but overlap with them in many possible ways, exhibiting great variability in the difficulty levels of the proposals. Training a robust classifier against this crop-related variability requires abundant training data, which is not available in few-shot settings. To mitigate this issue, we propose a novel variational autoencoder (VAE) based data generation model, which is capable of generating data with increased crop-related diversity. The main idea is to transform the latent space such latent codes with different norms represent different crop-related variations. This allows us to generate features with increased crop-related diversity in difficulty levels by simply varying the latent norm. In particular, each latent code is rescaled such that its norm linearly correlates with the IoU score of the input crop w.r.t. the ground-truth box. Here the IoU score is a proxy that represents the difficulty level of the crop. We train this VAE model on base classes conditioned on the semantic code of each class and then use the trained model to generate features for novel classes. In our experiments our generated features consistently improve state-of-the-art few-shot object detection methods on the PASCAL VOC and MS COCO datasets.

Jingwei Zhang, Ke Ma, Saarthak Kapse et al.

Semantic segmentations of pathological entities have crucial clinical value in computational pathology workflows. Foundation models, such as the Segment Anything Model (SAM), have been recently proposed for universal use in segmentation tasks. SAM shows remarkable promise in instance segmentation on natural images. However, the applicability of SAM to computational pathology tasks is limited due to the following factors: (1) lack of comprehensive pathology datasets used in SAM training and (2) the design of SAM is not inherently optimized for semantic segmentation tasks. In this work, we adapt SAM for semantic segmentation by introducing trainable class prompts, followed by further enhancements through the incorporation of a pathology encoder, specifically a pathology foundation model. Our framework, SAM-Path enhances SAM's ability to conduct semantic segmentation in digital pathology without human input prompts. Through experiments on two public pathology datasets, the BCSS and the CRAG datasets, we demonstrate that the fine-tuning with trainable class prompts outperforms vanilla SAM with manual prompts and post-processing by 27.52% in Dice score and 71.63% in IOU. On these two datasets, the proposed additional pathology foundation model further achieves a relative improvement of 5.07% to 5.12% in Dice score and 4.50% to 8.48% in IOU.

Zhibo Yang, Sounak Mondal, Seoyoung Ahn et al.

The prediction of human gaze behavior is important for building human-computer interactive systems that can anticipate a user's attention. Computer vision models have been developed to predict the fixations made by people as they search for target objects. But what about when the image has no target? Equally important is to know how people search when they cannot find a target, and when they would stop searching. In this paper, we propose the first data-driven computational model that addresses the search-termination problem and predicts the scanpath of search fixations made by people searching for targets that do not appear in images. We model visual search as an imitation learning problem and represent the internal knowledge that the viewer acquires through fixations using a novel state representation that we call Foveated Feature Maps (FFMs). FFMs integrate a simulated foveated retina into a pretrained ConvNet that produces an in-network feature pyramid, all with minimal computational overhead. Our method integrates FFMs as the state representation in inverse reinforcement learning. Experimentally, we improve the state of the art in predicting human target-absent search behavior on the COCO-Search18 dataset

Qiaomu Miao, Minh Hoai, Dimitris Samaras

Gaze following aims to predict where a person is looking in a scene, by predicting the target location, or indicating that the target is located outside the image. Recent works detect the gaze target by training a heatmap regression task with a pixel-wise mean-square error (MSE) loss, while formulating the in/out prediction task as a binary classification task. This training formulation puts a strict, pixel-level constraint in higher resolution on the single annotation available in training, and does not consider annotation variance and the correlation between the two subtasks. To address these issues, we introduce the patch distribution prediction (PDP) method. We replace the in/out prediction branch in previous models with the PDP branch, by predicting a patch-level gaze distribution that also considers the outside cases. Experiments show that our model regularizes the MSE loss by predicting better heatmap distributions on images with larger annotation variances, meanwhile bridging the gap between the target prediction and in/out prediction subtasks, showing a significant improvement in performance on both subtasks on public gaze following datasets.

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/.

Xiaoling Hu, Dimitris Samaras, Chao Chen

Accurate delineation of fine-scale structures is a very important yet challenging problem. Existing methods use topological information as an additional training loss, but are ultimately making pixel-wise predictions. In this paper, we propose the first deep learning based method to learn topological/structural representations. We use discrete Morse theory and persistent homology to construct an one-parameter family of structures as the topological/structural representation space. Furthermore, we learn a probabilistic model that can perform inference tasks in such a topological/structural representation space. Our method generates true structures rather than pixel-maps, leading to better topological integrity in automatic segmentation tasks. It also facilitates semi-automatic interactive annotation/proofreading via the sampling of structures and structure-aware uncertainty.

Jingyi Xu, Hieu Le, Dimitris Samaras

Advances in generative models increase the need for sample quality assessment. To do so, previous methods rely on a pre-trained feature extractor to embed the generated samples and real samples into a common space for comparison. However, different feature extractors might lead to inconsistent assessment outcomes. Moreover, these methods are not applicable for domains where a robust, universal feature extractor does not yet exist, such as medical images or 3D assets. In this paper, we propose to directly examine the latent space of the trained generative model to infer generated sample quality. This is feasible because the quality a generated sample directly relates to the amount of training data resembling it, and we can infer this information by examining the density of the latent space. Accordingly, we use a latent density score function to quantify sample quality. We show that the proposed score correlates highly with the sample quality for various generative models including VAEs, GANs and Latent Diffusion Models. Compared with previous quality assessment methods, our method has the following advantages: 1) pre-generation quality estimation with reduced computational cost, 2) generalizability to various domains and modalities, and 3) applicability to latent-based image editing and generation methods. Extensive experiments demonstrate that our proposed methods can benefit downstream tasks such as few-shot image classification and latent face image editing. Code is available at https://github.com/cvlab-stonybrook/LS-sample-quality.

Souradeep Chakraborty, Zijun Wei, Conor Kelton et al.

We present a model for predicting visual attention during the free viewing of graphic design documents. While existing works on this topic have aimed at predicting static saliency of graphic designs, our work is the first attempt to predict both spatial attention and dynamic temporal order in which the document regions are fixated by gaze using a deep learning based model. We propose a two-stage model for predicting dynamic attention on such documents, with webpages being our primary choice of document design for demonstration. In the first stage, we predict the saliency maps for each of the document components (e.g. logos, banners, texts, etc. for webpages) conditioned on the type of document layout. These component saliency maps are then jointly used to predict the overall document saliency. In the second stage, we use these layout-specific component saliency maps as the state representation for an inverse reinforcement learning model of fixation scanpath prediction during document viewing. To test our model, we collected a new dataset consisting of eye movements from 41 people freely viewing 450 webpages (the largest dataset of its kind). Experimental results show that our model outperforms existing models in both saliency and scanpath prediction for webpages, and also generalizes very well to other graphic design documents such as comics, posters, mobile UIs, etc. and natural images.

Jingyi Xu, Hieu Le, Dimitris Samaras

Class-agnostic object counting aims to count object instances of an arbitrary class at test time. It is challenging but also enables many potential applications. Current methods require human-annotated exemplars as inputs which are often unavailable for novel categories, especially for autonomous systems. Thus, we propose zero-shot object counting (ZSC), a new setting where only the class name is available during test time. This obviates the need for human annotators and enables automated operation. To perform ZSC, we propose finding a few object crops from the input image and use them as counting exemplars. The goal is to identify patches containing the objects of interest while also being visually representative for all instances in the image. To do this, we first construct class prototypes using large language-vision models, including CLIP and Stable Diffusion, to select the patches containing the target objects. Furthermore, we propose a ranking model that estimates the counting error of each patch to select the most suitable exemplars for counting. Experimental results on a recent class-agnostic counting dataset, FSC-147, validate the effectiveness of our method.

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.

Priyank Pathak, Jingwei Zhang, Dimitris Samaras

Transformers are becoming increasingly popular due to their superior performance over conventional convolutional neural networks(CNNs). However, transformers usually require a much larger amount of memory to train than CNNs, which prevents their application in many low resource settings. Local learning, which divides the network into several distinct modules and trains them individually, is a promising alternative to the end-to-end (E2E) training approach to reduce the amount of memory for training and to increase parallelism. This paper is the first to apply Local Learning on transformers for this purpose. The standard CNN-based local learning method, InfoPro [32], reconstructs the input images for each module in a CNN. However, reconstructing the entire image does not generalize well. In this paper, we propose a new mechanism for each local module, where instead of reconstructing the entire image, we reconstruct its input features, generated from previous modules. We evaluate our approach on 4 commonly used datasets and 3 commonly used decoder structures on Swin-Tiny. The experiments show that our approach outperforms InfoPro-Transformer, the InfoPro with Transfomer backbone we introduced, by at up to 0.58% on CIFAR-10, CIFAR-100, STL-10 and SVHN datasets, while using up to 12% less memory. Compared to the E2E approach, we require 36% less GPU memory when the network is divided into 2 modules and 45% less GPU memory when the network is divided into 4 modules.

Shahira Abousamra, Rajarsi Gupta, Tahsin Kurc et al.

In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and holes. To model such structural patterns in a learnable fashion, we introduce several mathematical tools from spatial statistics and topological data analysis. We incorporate such structural descriptors into a deep generative model as both conditional inputs and a differentiable loss. This way, we are able to generate high quality multi-class cell layouts for the first time. We show that the topology-rich cell layouts can be used for data augmentation and improve the performance of downstream tasks such as cell classification.

Aggelina Chatziagapi, Dimitris Samaras

In this work, we present a multimodal solution to the problem of 4D face reconstruction from monocular videos. 3D face reconstruction from 2D images is an under-constrained problem due to the ambiguity of depth. State-of-the-art methods try to solve this problem by leveraging visual information from a single image or video, whereas 3D mesh animation approaches rely more on audio. However, in most cases (e.g. AR/VR applications), videos include both visual and speech information. We propose AVFace that incorporates both modalities and accurately reconstructs the 4D facial and lip motion of any speaker, without requiring any 3D ground truth for training. A coarse stage estimates the per-frame parameters of a 3D morphable model, followed by a lip refinement, and then a fine stage recovers facial geometric details. Due to the temporal audio and video information captured by transformer-based modules, our method is robust in cases when either modality is insufficient (e.g. face occlusions). Extensive qualitative and quantitative evaluation demonstrates the superiority of our method over the current state-of-the-art.

Lei Zhou, Huidong Liu, Joseph Bae et al.

Can we use sparse tokens for dense prediction, e.g., segmentation? Although token sparsification has been applied to Vision Transformers (ViT) to accelerate classification, it is still unknown how to perform segmentation from sparse tokens. To this end, we reformulate segmentation as a sparse encoding -> token completion -> dense decoding (SCD) pipeline. We first empirically show that naively applying existing approaches from classification token pruning and masked image modeling (MIM) leads to failure and inefficient training caused by inappropriate sampling algorithms and the low quality of the restored dense features. In this paper, we propose Soft-topK Token Pruning (STP) and Multi-layer Token Assembly (MTA) to address these problems. In sparse encoding, STP predicts token importance scores with a lightweight sub-network and samples the topK tokens. The intractable topK gradients are approximated through a continuous perturbed score distribution. In token completion, MTA restores a full token sequence by assembling both sparse output tokens and pruned multi-layer intermediate ones. The last dense decoding stage is compatible with existing segmentation decoders, e.g., UNETR. Experiments show SCD pipelines equipped with STP and MTA are much faster than baselines without token pruning in both training (up to 120% higher throughput and inference up to 60.6% higher throughput) while maintaining segmentation quality.

Jingyi Xu, Hieu Le, Dimitris Samaras

Class-agnostic counting (CAC) has numerous potential applications across various domains. The goal is to count objects of an arbitrary category during testing, based on only a few annotated exemplars. In this paper, we point out that the task of counting objects of interest when there are multiple object classes in the image (namely, multi-class object counting) is particularly challenging for current object counting models. They often greedily count every object regardless of the exemplars. To address this issue, we propose localizing the area containing the objects of interest via an exemplar-based segmentation model before counting them. The key challenge here is the lack of segmentation supervision to train this model. To this end, we propose a method to obtain pseudo segmentation masks using only box exemplars and dot annotations. We show that the segmentation model trained on these pseudo-labeled masks can effectively localize objects of interest for an arbitrary multi-class image based on the exemplars. To evaluate the performance of different methods on multi-class counting, we introduce two new benchmarks, a synthetic multi-class dataset and a new test set of real images in which objects from multiple classes are present. Our proposed method shows a significant advantage over the previous CAC methods on these two benchmarks.

Saarthak Kapse, Srijan Das, Jingwei Zhang et al.

We propose DiRL, a Diversity-inducing Representation Learning technique for histopathology imaging. Self-supervised learning techniques, such as contrastive and non-contrastive approaches, have been shown to learn rich and effective representations of digitized tissue samples with limited pathologist supervision. Our analysis of vanilla SSL-pretrained models' attention distribution reveals an insightful observation: sparsity in attention, i.e, models tends to localize most of their attention to some prominent patterns in the image. Although attention sparsity can be beneficial in natural images due to these prominent patterns being the object of interest itself, this can be sub-optimal in digital pathology; this is because, unlike natural images, digital pathology scans are not object-centric, but rather a complex phenotype of various spatially intermixed biological components. Inadequate diversification of attention in these complex images could result in crucial information loss. To address this, we leverage cell segmentation to densely extract multiple histopathology-specific representations, and then propose a prior-guided dense pretext task for SSL, designed to match the multiple corresponding representations between the views. Through this, the model learns to attend to various components more closely and evenly, thus inducing adequate diversification in attention for capturing context rich representations. Through quantitative and qualitative analysis on multiple tasks across cancer types, we demonstrate the efficacy of our method and observe that the attention is more globally distributed.

Mahmudul Hasan, Jakub R. Kaczmarzyk, David Paredes et al.

Understanding the impact of tumor biology on the composition of nearby cells often requires characterizing the impact of biologically distinct tumor regions. Biomarkers have been developed to label biologically distinct tumor regions, but challenges arise because of differences in the spatial extent and distribution of differentially labeled regions. In this work, we present a framework for systematically investigating the impact of distinct tumor regions on cells near the tumor borders, accounting their cross spatial distributions. We apply the framework to multiplex immunohistochemistry (mIHC) studies of pancreatic cancer and show its efficacy in demonstrating how biologically different tumor regions impact the immune response in the tumor microenvironment. Furthermore, we show that the proposed framework can be extended to largescale whole slide image analysis.

Jianyuan Deng, Zhibo Yang, Hehe Wang et al.

Artificial intelligence (AI) has been widely applied in drug discovery with a major task as molecular property prediction. Despite booming techniques in molecular representation learning, key elements underlying molecular property prediction remain largely unexplored, which impedes further advancements in this field. Herein, we conduct an extensive evaluation of representative models using various representations on the MoleculeNet datasets, a suite of opioids-related datasets and two additional activity datasets from the literature. To investigate the predictive power in low-data and high-data space, a series of descriptors datasets of varying sizes are also assembled to evaluate the models. In total, we have trained 62,820 models, including 50,220 models on fixed representations, 4,200 models on SMILES sequences and 8,400 models on molecular graphs. Based on extensive experimentation and rigorous comparison, we show that representation learning models exhibit limited performance in molecular property prediction in most datasets. Besides, multiple key elements underlying molecular property prediction can affect the evaluation results. Furthermore, we show that activity cliffs can significantly impact model prediction. Finally, we explore into potential causes why representation learning models can fail and show that dataset size is essential for representation learning models to excel.

Sounak Mondal, Seoyoung Ahn, Zhibo Yang et al.

For computer systems to effectively interact with humans using spoken language, they need to understand how the words being generated affect the users' moment-by-moment attention. Our study focuses on the incremental prediction of attention as a person is seeing an image and hearing a referring expression defining the object in the scene that should be fixated by gaze. To predict the gaze scanpaths in this incremental object referral task, we developed the Attention in Referral Transformer model or ART, which predicts the human fixations spurred by each word in a referring expression. ART uses a multimodal transformer encoder to jointly learn gaze behavior and its underlying grounding tasks, and an autoregressive transformer decoder to predict, for each word, a variable number of fixations based on fixation history. To train ART, we created RefCOCO-Gaze, a large-scale dataset of 19,738 human gaze scanpaths, corresponding to 2,094 unique image-expression pairs, from 220 participants performing our referral task. In our quantitative and qualitative analyses, ART not only outperforms existing methods in scanpath prediction, but also appears to capture several human attention patterns, such as waiting, scanning, and verification.

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.

Panagiotis Kaliosis, Adithya V Ganesan, Oscar N. E. Kjell et al.

Large language models (LLMs) are increasingly being used in a zero-shot fashion to assess mental health conditions, yet we have limited knowledge on what factors affect their accuracy. In this study, we utilize a clinical dataset of natural language narratives and self-reported PTSD severity scores from 1,437 individuals to comprehensively evaluate the performance of 11 state-of-the-art LLMs. To understand the factors affecting accuracy, we systematically varied (i) contextual knowledge like subscale definitions, distribution summary, and interview questions, and (ii) modeling strategies including zero-shot vs few shot, amount of reasoning effort, model sizes, structured subscales vs direct scalar prediction, output rescaling and nine ensemble methods. Our findings indicate that (a) LLMs are most accurate when provided with detailed construct definitions and context of the narrative; (b) increased reasoning effort leads to better estimation accuracy; (c) performance of open-weight models (Llama, Deepseek), plateau beyond 70B parameters while closed-weight (o3-mini, gpt-5) models improve with newer generations; and (d) best performance is achieved when ensembling a supervised model with the zero-shot LLMs. Taken together, the results suggest choice of contextual knowledge and modeling strategies is important for deploying LLMs to accurately assess mental health.

ShahRukh Athar, Zhixin Shu, Zexiang Xu et al.

Recent advances in Neural Radiance Fields (NeRFs) have made it possible to reconstruct and reanimate dynamic portrait scenes with control over head-pose, facial expressions and viewing direction. However, training such models assumes photometric consistency over the deformed region e.g. the face must be evenly lit as it deforms with changing head-pose and facial expression. Such photometric consistency across frames of a video is hard to maintain, even in studio environments, thus making the created reanimatable neural portraits prone to artifacts during reanimation. In this work, we propose CoDyNeRF, a system that enables the creation of fully controllable 3D portraits in real-world capture conditions. CoDyNeRF learns to approximate illumination dependent effects via a dynamic appearance model in the canonical space that is conditioned on predicted surface normals and the facial expressions and head-pose deformations. The surface normals prediction is guided using 3DMM normals that act as a coarse prior for the normals of the human head, where direct prediction of normals is hard due to rigid and non-rigid deformations induced by head-pose and facial expression changes. Using only a smartphone-captured short video of a subject for training, we demonstrate the effectiveness of our method on free view synthesis of a portrait scene with explicit head pose and expression controls, and realistic lighting effects. The project page can be found here: http://shahrukhathar.github.io/2023/08/22/CoDyNeRF.html

Souradeep Chakraborty, Shujon Naha, Muhammet Bastan et al.

In this paper, we address the detection of co-occurring salient objects (CoSOD) in an image group using frequency statistics in an unsupervised manner, which further enable us to develop a semi-supervised method. While previous works have mostly focused on fully supervised CoSOD, less attention has been allocated to detecting co-salient objects when limited segmentation annotations are available for training. Our simple yet effective unsupervised method US-CoSOD combines the object co-occurrence frequency statistics of unsupervised single-image semantic segmentations with salient foreground detections using self-supervised feature learning. For the first time, we show that a large unlabeled dataset e.g. ImageNet-1k can be effectively leveraged to significantly improve unsupervised CoSOD performance. Our unsupervised model is a great pre-training initialization for our semi-supervised model SS-CoSOD, especially when very limited labeled data is available for training. To avoid propagating erroneous signals from predictions on unlabeled data, we propose a confidence estimation module to guide our semi-supervised training. Extensive experiments on three CoSOD benchmark datasets show that both of our unsupervised and semi-supervised models outperform the corresponding state-of-the-art models by a significant margin (e.g., on the Cosal2015 dataset, our US-CoSOD model has an 8.8% F-measure gain over a SOTA unsupervised co-segmentation model and our SS-CoSOD model has an 11.81% F-measure gain over a SOTA semi-supervised CoSOD model).

Jingyi Xu, Hieu Le, Zhixin Shu et al.

Human emotional expression is inherently dynamic, complex, and fluid, characterized by smooth transitions in intensity throughout verbal communication. However, the modeling of such intensity fluctuations has been largely overlooked by previous audio-driven talking-head generation methods, which often results in static emotional outputs. In this paper, we explore how emotion intensity fluctuates during speech, proposing a method for capturing and generating these subtle shifts for talking-head generation. Specifically, we develop a talking-head framework that is capable of generating a variety of emotions with precise control over intensity levels. This is achieved by learning a continuous emotion latent space, where emotion types are encoded within latent orientations and emotion intensity is reflected in latent norms. In addition, to capture the dynamic intensity fluctuations, we adopt an audio-to-intensity predictor by considering the speaking tone that reflects the intensity. The training signals for this predictor are obtained through our emotion-agnostic intensity pseudo-labeling method without the need of frame-wise intensity labeling. Extensive experiments and analyses validate the effectiveness of our proposed method in accurately capturing and reproducing emotion intensity fluctuations in talking-head generation, thereby significantly enhancing the expressiveness and realism of the generated outputs.

Shilin Hu, Hieu Le, ShahRukh Athar et al.

Shadow boundaries can be confused with material boundaries as both exhibit sharp changes in luminance or contrast within a scene. However, shadows do not modify the intrinsic color or texture of surfaces. Therefore, on both sides of shadow edges traversing regions with the same material, the original color and textures should be the same if the shadow is removed properly. These shadow/shadow-free pairs are very useful but hard-to-collect supervision signals. The crucial contribution of this paper is to learn how to identify those shadow edges that traverse material-consistent regions and how to use them as self-supervision for shadow removal refinement during test time. To achieve this, we fine-tune SAM, an image segmentation foundation model, to produce a shadow-invariant segmentation and then extract material-consistent shadow edges by comparing the SAM segmentation with the shadow mask. Utilizing these shadow edges, we introduce color and texture-consistency losses to enhance the shadow removal process. We demonstrate the effectiveness of our method in improving shadow removal results on more challenging, in-the-wild images, outperforming the state-of-the-art shadow removal methods. Additionally, we propose a new metric and an annotated dataset for evaluating the performance of shadow removal methods without the need for paired shadow/shadow-free data.

Aggelina Chatziagapi, Grigorios G. Chrysos, Dimitris Samaras

We introduce MIGS (Multi-Identity Gaussian Splatting), a novel method that learns a single neural representation for multiple identities, using only monocular videos. Recent 3D Gaussian Splatting (3DGS) approaches for human avatars require per-identity optimization. However, learning a multi-identity representation presents advantages in robustly animating humans under arbitrary poses. We propose to construct a high-order tensor that combines all the learnable 3DGS parameters for all the training identities. By assuming a low-rank structure and factorizing the tensor, we model the complex rigid and non-rigid deformations of multiple subjects in a unified network, significantly reducing the total number of parameters. Our proposed approach leverages information from all the training identities and enables robust animation under challenging unseen poses, outperforming existing approaches. It can also be extended to learn unseen identities.

Jingwei Zhang, Anh Tien Nguyen, Xi Han et al.

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.

Meilong Xu, Saumya Gupta, Xiaoling Hu et al.

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. Code is available at https://github.com/Melon-Xu/TopoCellGen.

Saumya Gupta, Dimitris Samaras, Chao Chen

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. Code available at https://github.com/Saumya-Gupta-26/TopoDiffusionNet

Saarthak Kapse, Pushpak Pati, Srikar Yellapragada et al.

Pretraining a Multiple Instance Learning (MIL) aggregator enables the derivation of Whole Slide Image (WSI)-level embeddings from patch-level representations without supervision. While recent multimodal MIL pretraining approaches leveraging auxiliary modalities have demonstrated performance gains over unimodal WSI pretraining, the acquisition of these additional modalities necessitates extensive clinical profiling. This requirement increases costs and limits scalability in existing WSI datasets lacking such paired modalities. To address this, we propose Gigapixel Vision-Concept Knowledge Contrastive pretraining (GECKO), which aligns WSIs with a Concept Prior derived from the available WSIs. First, we derive an inherently interpretable concept prior by computing the similarity between each WSI patch and textual descriptions of predefined pathology concepts. GECKO then employs a dual-branch MIL network: one branch aggregates patch embeddings into a WSI-level deep embedding, while the other aggregates the concept prior into a corresponding WSI-level concept embedding. Both aggregated embeddings are aligned using a contrastive objective, thereby pretraining the entire dual-branch MIL model. Moreover, when auxiliary modalities such as transcriptomics data are available, GECKO seamlessly integrates them. Across five diverse tasks, GECKO consistently outperforms prior unimodal and multimodal pretraining approaches while also delivering clinically meaningful interpretability that bridges the gap between computational models and pathology expertise. Code is made available at https://github.com/bmi-imaginelab/GECKO

Sai Tanmay Reddy Chakkera, Aggelina Chatziagapi, Dimitris Samaras

We introduce a novel method for joint expression and audio-guided talking face generation. Recent approaches either struggle to preserve the speaker identity or fail to produce faithful facial expressions. To address these challenges, we propose a NeRF-based network. Since we train our network on monocular videos without any ground truth, it is essential to learn disentangled representations for audio and expression. We first learn audio features in a self-supervised manner, given utterances from multiple subjects. By incorporating a contrastive learning technique, we ensure that the learned audio features are aligned to the lip motion and disentangled from the muscle motion of the rest of the face. We then devise a transformer-based architecture that learns expression features, capturing long-range facial expressions and disentangling them from the speech-specific mouth movements. Through quantitative and qualitative evaluation, we demonstrate that our method can synthesize high-fidelity talking face videos, achieving state-of-the-art facial expression transfer along with lip synchronization to unseen audio.

Ruoyu Xue, Jingyi Xu, Sounak Mondal et al.

A personalized model for scanpath prediction provides insights into the visual preferences and attention patterns of individual subjects. However, existing methods for training scanpath prediction models are data-intensive and cannot be effectively personalized to new individuals with only a few available examples. In this paper, we propose few-shot personalized scanpath prediction task (FS-PSP) and a novel method to address it, which aims to predict scanpaths for an unseen subject using minimal support data of that subject's scanpath behavior. The key to our method's adaptability is the Subject-Embedding Network (SE-Net), specifically designed to capture unique, individualized representations for each subject's scanpaths. SE-Net generates subject embeddings that effectively distinguish between subjects while minimizing variability among scanpaths from the same individual. The personalized scanpath prediction model is then conditioned on these subject embeddings to produce accurate, personalized results. Experiments on multiple eye-tracking datasets demonstrate that our method excels in FS-PSP settings and does not require any fine-tuning steps at test time. Code is available at: https://github.com/cvlab-stonybrook/few-shot-scanpath

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.

Jianyuan Deng, Zhibo Yang, Iwao Ojima et al.

Artificial intelligence (AI) has been transforming the practice of drug discovery in the past decade. Various AI techniques have been used in a wide range of applications, such as virtual screening and drug design. In this survey, we first give an overview on drug discovery and discuss related applications, which can be reduced to two major tasks, i.e., molecular property prediction and molecule generation. We then discuss common data resources, molecule representations and benchmark platforms. Furthermore, to summarize the progress of AI in drug discovery, we present the relevant AI techniques including model architectures and learning paradigms in the papers surveyed. We expect that this survey will serve as a guide for researchers who are interested in working at the interface of artificial intelligence and drug discovery. We also provide a GitHub repository (https://github.com/dengjianyuan/Survey_AI_Drug_Discovery) with the collection of papers and codes, if applicable, as a learning resource, which is regularly updated.

Boyu Wang, Huidong Liu, Dimitris Samaras et al.

In crowd counting, each training image contains multiple people, where each person is annotated by a dot. Existing crowd counting methods need to use a Gaussian to smooth each annotated dot or to estimate the likelihood of every pixel given the annotated point. In this paper, we show that imposing Gaussians to annotations hurts generalization performance. Instead, we propose to use Distribution Matching for crowd COUNTing (DM-Count). In DM-Count, we use Optimal Transport (OT) to measure the similarity between the normalized predicted density map and the normalized ground truth density map. To stabilize OT computation, we include a Total Variation loss in our model. We show that the generalization error bound of DM-Count is tighter than that of the Gaussian smoothed methods. In terms of Mean Absolute Error, DM-Count outperforms the previous state-of-the-art methods by a large margin on two large-scale counting datasets, UCF-QNRF and NWPU, and achieves the state-of-the-art results on the ShanghaiTech and UCF-CC50 datasets. DM-Count reduced the error of the state-of-the-art published result by approximately 16%. Code is available at https://github.com/cvlab-stonybrook/DM-Count.

Han Le, Rajarsi Gupta, Le Hou et al.

Quantitative assessment of Tumor-TIL spatial relationships is increasingly important in both basic science and clinical aspects of breast cancer research. We have developed and evaluated convolutional neural network (CNN) analysis pipelines to generate combined maps of cancer regions and tumor infiltrating lymphocytes (TILs) in routine diagnostic breast cancer whole slide tissue images (WSIs). We produce interactive whole slide maps that provide 1) insight about the structural patterns and spatial distribution of lymphocytic infiltrates and 2) facilitate improved quantification of TILs. We evaluated both tumor and TIL analyses using three CNN networks - Resnet-34, VGG16 and Inception v4, and demonstrated that the results compared favorably to those obtained by what believe are the best published methods. We have produced open-source tools and generated a public dataset consisting of tumor/TIL maps for 1,015 TCGA breast cancer images. We also present a customized web-based interface that enables easy visualization and interactive exploration of high-resolution combined Tumor-TIL maps for 1,015TCGA invasive breast cancer cases that can be downloaded for further downstream analyses.

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.

Saarthak Kapse, Pushpak Pati, Srijan Das et al.

Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging, given the complexity of gigapixel slides. Traditionally, MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks, offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this, we propose Self-Interpretable MIL (SI-MIL), a method intrinsically designed for interpretability from the very outset. SI-MIL employs a deep MIL framework to guide an interpretable branch grounded on handcrafted pathological features, facilitating linear predictions. Beyond identifying salient regions, SI-MIL uniquely provides feature-level interpretations rooted in pathological insights for WSIs. Notably, SI-MIL, with its linear prediction constraints, challenges the prevalent myth of an inevitable trade-off between model interpretability and performance, demonstrating competitive results compared to state-of-the-art methods on WSI-level prediction tasks across three cancer types. In addition, we thoroughly benchmark the local and global-interpretability of SI-MIL in terms of statistical analysis, a domain expert study, and desiderata of interpretability, namely, user-friendliness and faithfulness.

Alfredo Rivero, ShahRukh Athar, Zhixin Shu et al.

Creating controllable 3D human portraits from casual smartphone videos is highly desirable due to their immense value in AR/VR applications. The recent development of 3D Gaussian Splatting (3DGS) has shown improvements in rendering quality and training efficiency. However, it still remains a challenge to accurately model and disentangle head movements and facial expressions from a single-view capture to achieve high-quality renderings. In this paper, we introduce Rig3DGS to address this challenge. We represent the entire scene, including the dynamic subject, using a set of 3D Gaussians in a canonical space. Using a set of control signals, such as head pose and expressions, we transform them to the 3D space with learned deformations to generate the desired rendering. Our key innovation is a carefully designed deformation method which is guided by a learnable prior derived from a 3D morphable model. This approach is highly efficient in training and effective in controlling facial expressions, head positions, and view synthesis across various captures. We demonstrate the effectiveness of our learned deformation through extensive quantitative and qualitative experiments. The project page can be found at http://shahrukhathar.github.io/2024/02/05/Rig3DGS.html