Evaluating Computational Pathology Foundation Models for Prostate Cancer Grading under Distribution Shifts

Foundation models have recently become a popular research direction within computational pathology. They are intended to be general-purpose feature extractors, promising to achieve good performance on a range of downstream tasks. Real-world pathology image data does however exhibit considerable variability. Foundation models should be robust to these variations and other distribution shifts which might be encountered in practice. We evaluate two computational pathology foundation models: UNI (trained on more than 100,000 whole-slide images) and CONCH (trained on more than 1.1 million image-caption pairs), by utilizing them as feature extractors within prostate cancer grading models. We find that while UNI and CONCH perform well relative to baselines, the absolute performance can still be far from satisfactory in certain settings. The fact that foundation models have been trained on large and varied datasets does not guarantee that downstream models always will be robust to common distribution shifts.

Evaluating Deep Regression Models for WSI-Based Gene-Expression Prediction

Prediction of mRNA gene-expression profiles directly from routine whole-slide images (WSIs) using deep learning models could potentially offer cost-effective and widely accessible molecular phenotyping. While such WSI-based gene-expression prediction models have recently emerged within computational pathology, the high-dimensional nature of the corresponding regression problem offers numerous design choices which remain to be analyzed in detail. This study provides recommendations on how deep regression models should be trained for WSI-based gene-expression prediction. For example, we conclude that training a single model to simultaneously regress all 20530 genes is a computationally efficient yet very strong baseline.

Taming Diffusion Models for Image Restoration: A Review

Diffusion models have achieved remarkable progress in generative modelling, particularly in enhancing image quality to conform to human preferences. Recently, these models have also been applied to low-level computer vision for photo-realistic image restoration (IR) in tasks such as image denoising, deblurring, dehazing, etc. In this review paper, we introduce key constructions in diffusion models and survey contemporary techniques that make use of diffusion models in solving general IR tasks. Furthermore, we point out the main challenges and limitations of existing diffusion-based IR frameworks and provide potential directions for future work.

Photo-Realistic Image Restoration in the Wild with Controlled Vision-Language Models

Though diffusion models have been successfully applied to various image restoration (IR) tasks, their performance is sensitive to the choice of training datasets. Typically, diffusion models trained in specific datasets fail to recover images that have out-of-distribution degradations. To address this problem, this work leverages a capable vision-language model and a synthetic degradation pipeline to learn image restoration in the wild (wild IR). More specifically, all low-quality images are simulated with a synthetic degradation pipeline that contains multiple common degradations such as blur, resize, noise, and JPEG compression. Then we introduce robust training for a degradation-aware CLIP model to extract enriched image content features to assist high-quality image restoration. Our base diffusion model is the image restoration SDE (IR-SDE). Built upon it, we further present a posterior sampling strategy for fast noise-free image generation. We evaluate our model on both synthetic and real-world degradation datasets. Moreover, experiments on the unified image restoration task illustrate that the proposed posterior sampling improves image generation quality for various degradations.

Controlling Vision-Language Models for Universal Image Restoration

Vision-language models such as CLIP have shown great impact on diverse downstream tasks for zero-shot or label-free predictions. However, when it comes to low-level vision such as image restoration their performance deteriorates dramatically due to corrupted inputs. In this paper, we present a degradation-aware vision-language model (DA-CLIP) to better transfer pretrained vision-language models to low-level vision tasks as a universal framework for image restoration. More specifically, DA-CLIP trains an additional controller that adapts the fixed CLIP image encoder to predict high-quality feature embeddings. By integrating the embedding into an image restoration network via cross-attention, we are able to pilot the model to learn a high-fidelity image reconstruction. The controller itself will also output a degradation feature that matches the real corruptions of the input, yielding a natural classifier for different degradation types. In addition, we construct a mixed degradation dataset with synthetic captions for DA-CLIP training. Our approach advances state-of-the-art performance on both degradation-specific and unified image restoration tasks, showing a promising direction of prompting image restoration with large-scale pretrained vision-language models. Our code is available at https://github.com/Algolzw/daclip-uir.

Refusion: Enabling Large-Size Realistic Image Restoration with Latent-Space Diffusion Models

This work aims to improve the applicability of diffusion models in realistic image restoration. Specifically, we enhance the diffusion model in several aspects such as network architecture, noise level, denoising steps, training image size, and optimizer/scheduler. We show that tuning these hyperparameters allows us to achieve better performance on both distortion and perceptual scores. We also propose a U-Net based latent diffusion model which performs diffusion in a low-resolution latent space while preserving high-resolution information from the original input for the decoding process. Compared to the previous latent-diffusion model which trains a VAE-GAN to compress the image, our proposed U-Net compression strategy is significantly more stable and can recover highly accurate images without relying on adversarial optimization. Importantly, these modifications allow us to apply diffusion models to various image restoration tasks, including real-world shadow removal, HR non-homogeneous dehazing, stereo super-resolution, and bokeh effect transformation. By simply replacing the datasets and slightly changing the noise network, our model, named Refusion, is able to deal with large-size images (e.g., 6000 x 4000 x 3 in HR dehazing) and produces good results on all the above restoration problems. Our Refusion achieves the best perceptual performance in the NTIRE 2023 Image Shadow Removal Challenge and wins 2nd place overall.

How Reliable is Your Regression Model's Uncertainty Under Real-World Distribution Shifts?

Many important computer vision applications are naturally formulated as regression problems. Within medical imaging, accurate regression models have the potential to automate various tasks, helping to lower costs and improve patient outcomes. Such safety-critical deployment does however require reliable estimation of model uncertainty, also under the wide variety of distribution shifts that might be encountered in practice. Motivated by this, we set out to investigate the reliability of regression uncertainty estimation methods under various real-world distribution shifts. To that end, we propose an extensive benchmark of 8 image-based regression datasets with different types of challenging distribution shifts. We then employ our benchmark to evaluate many of the most common uncertainty estimation methods, as well as two state-of-the-art uncertainty scores from the task of out-of-distribution detection. We find that while methods are well calibrated when there is no distribution shift, they all become highly overconfident on many of the benchmark datasets. This uncovers important limitations of current uncertainty estimation methods, and the proposed benchmark therefore serves as a challenge to the research community. We hope that our benchmark will spur more work on how to develop truly reliable regression uncertainty estimation methods. Code is available at https://github.com/fregu856/regression_uncertainty.

Image Restoration with Mean-Reverting Stochastic Differential Equations

This paper presents a stochastic differential equation (SDE) approach for general-purpose image restoration. The key construction consists in a mean-reverting SDE that transforms a high-quality image into a degraded counterpart as a mean state with fixed Gaussian noise. Then, by simulating the corresponding reverse-time SDE, we are able to restore the origin of the low-quality image without relying on any task-specific prior knowledge. Crucially, the proposed mean-reverting SDE has a closed-form solution, allowing us to compute the ground truth time-dependent score and learn it with a neural network. Moreover, we propose a maximum likelihood objective to learn an optimal reverse trajectory which stabilizes the training and improves the restoration results. In the experiments, we show that our proposed method achieves highly competitive performance in quantitative comparisons on image deraining, deblurring, and denoising, setting a new state-of-the-art on two deraining datasets. Finally, the general applicability of our approach is further demonstrated via qualitative results on image super-resolution, inpainting, and dehazing. Code is available at https://github.com/Algolzw/image-restoration-sde.

ECG-Based Electrolyte Prediction: Evaluating Regression and Probabilistic Methods

Objective: Imbalances of the electrolyte concentration levels in the body can lead to catastrophic consequences, but accurate and accessible measurements could improve patient outcomes. While blood tests provide accurate measurements, they are invasive and the laboratory analysis can be slow or inaccessible. In contrast, an electrocardiogram (ECG) is a widely adopted tool which is quick and simple to acquire. However, the problem of estimating continuous electrolyte concentrations directly from ECGs is not well-studied. We therefore investigate if regression methods can be used for accurate ECG-based prediction of electrolyte concentrations. Methods: We explore the use of deep neural networks (DNNs) for this task. We analyze the regression performance across four electrolytes, utilizing a novel dataset containing over 290000 ECGs. For improved understanding, we also study the full spectrum from continuous predictions to binary classification of extreme concentration levels. To enhance clinical usefulness, we finally extend to a probabilistic regression approach and evaluate different uncertainty estimates. Results: We find that the performance varies significantly between different electrolytes, which is clinically justified in the interplay of electrolytes and their manifestation in the ECG. We also compare the regression accuracy with that of traditional machine learning models, demonstrating superior performance of DNNs. Conclusion: Discretization can lead to good classification performance, but does not help solve the original problem of predicting continuous concentration levels. While probabilistic regression demonstrates potential practical usefulness, the uncertainty estimates are not particularly well-calibrated. Significance: Our study is a first step towards accurate and reliable ECG-based prediction of electrolyte concentration levels.

Learning Proposals for Practical Energy-Based Regression

Energy-based models (EBMs) have experienced a resurgence within machine learning in recent years, including as a promising alternative for probabilistic regression. However, energy-based regression requires a proposal distribution to be manually designed for training, and an initial estimate has to be provided at test-time. We address both of these issues by introducing a conceptually simple method to automatically learn an effective proposal distribution, which is parameterized by a separate network head. To this end, we derive a surprising result, leading to a unified training objective that jointly minimizes the KL divergence from the proposal to the EBM, and the negative log-likelihood of the EBM. At test-time, we can then employ importance sampling with the trained proposal to efficiently evaluate the learned EBM and produce stand-alone predictions. Furthermore, we utilize our derived training objective to learn mixture density networks (MDNs) with a jointly trained energy-based teacher, consistently outperforming conventional MDN training on four real-world regression tasks within computer vision. Code is available at https://github.com/fregu856/ebms_proposals.