ScoreNet: Learning Non-Uniform Attention and Augmentation for Transformer-Based Histopathological Image Classification

Progress in digital pathology is hindered by high-resolution images and the prohibitive cost of exhaustive localized annotations. The commonly used paradigm to categorize pathology images is patch-based processing, which often incorporates multiple instance learning (MIL) to aggregate local patch-level representations yielding image-level prediction. Nonetheless, diagnostically relevant regions may only take a small fraction of the whole tissue, and current MIL-based approaches often process images uniformly, discarding the inter-patches interactions. To alleviate these issues, we propose ScoreNet, a new efficient transformer that exploits a differentiable recommendation stage to extract discriminative image regions and dedicate computational resources accordingly. The proposed transformer leverages the local and global attention of a few dynamically recommended high-resolution regions at an efficient computational cost. We further introduce a novel Mixup-based data-augmentation, namely ScoreMix, by leveraging the image's semantic distribution to guide the data mixing and produce coherent sample-label pairs. ScoreMix is embarrassingly simple and mitigates the pitfalls of previous augmentations, which assume a uniform semantic distribution and risk mislabeling the samples. Thorough experiments and ablation studies on three breast cancer histology datasets of Haematoxylin & Eosin (H&E) have validated the superiority of our approach over prior arts, including transformer-based models on tumour regions-of-interest (TRoIs) classification. ScoreNet equipped with proposed ScoreMix augmentation demonstrates better generalization capabilities and achieves new state-of-the-art (SOTA) results with only 50% of the data compared to other Mixup augmentation variants. Finally, ScoreNet yields high efficacy and outperforms SOTA efficient transformers, namely TransPath and SwinTransformer.

Self-Supervised Generative Style Transfer for One-Shot Medical Image Segmentation

In medical image segmentation, supervised deep networks' success comes at the cost of requiring abundant labeled data. While asking domain experts to annotate only one or a few of the cohort's images is feasible, annotating all available images is impractical. This issue is further exacerbated when pre-trained deep networks are exposed to a new image dataset from an unfamiliar distribution. Using available open-source data for ad-hoc transfer learning or hand-tuned techniques for data augmentation only provides suboptimal solutions. Motivated by atlas-based segmentation, we propose a novel volumetric self-supervised learning for data augmentation capable of synthesizing volumetric image-segmentation pairs via learning transformations from a single labeled atlas to the unlabeled data. Our work's central tenet benefits from a combined view of one-shot generative learning and the proposed self-supervised training strategy that cluster unlabeled volumetric images with similar styles together. Unlike previous methods, our method does not require input volumes at inference time to synthesize new images. Instead, it can generate diversified volumetric image-segmentation pairs from a prior distribution given a single or multi-site dataset. Augmented data generated by our method used to train the segmentation network provide significant improvements over state-of-the-art deep one-shot learning methods on the task of brain MRI segmentation. Ablation studies further exemplified that the proposed appearance model and joint training are crucial to synthesize realistic examples compared to existing medical registration methods. The code, data, and models are available at https://github.com/devavratTomar/SST.

Self-Rule to Adapt: Generalized Multi-source Feature Learning Using Unsupervised Domain Adaptation for Colorectal Cancer Tissue Detection

Supervised learning is constrained by the availability of labeled data, which are especially expensive to acquire in the field of digital pathology. Making use of open-source data for pre-training or using domain adaptation can be a way to overcome this issue. However, pre-trained networks often fail to generalize to new test domains that are not distributed identically due to variations in tissue stainings, types, and textures. Additionally, current domain adaptation methods mainly rely on fully-labeled source datasets. In this work, we propose SRA, which takes advantage of self-supervised learning to perform domain adaptation and removes the necessity of a fully-labeled source dataset. SRA can effectively transfer the discriminative knowledge obtained from a few labeled source domain's data to a new target domain without requiring additional tissue annotations. Our method harnesses both domains' structures by capturing visual similarity with intra-domain and cross-domain self-supervision. Moreover, we present a generalized formulation of our approach that allows the architecture to learn from multi-source domains. We show that our proposed method outperforms baselines for domain adaptation of colorectal tissue type classification and further validate our approach on our in-house clinical cohort. The code and models are available open-source: https://github.com/christianabbet/SRA.

Test-Time Adaptation for Super-Resolution: You Only Need to Overfit on a Few More Images

Existing reference (RF)-based super-resolution (SR) models try to improve perceptual quality in SR under the assumption of the availability of high-resolution RF images paired with low-resolution (LR) inputs at testing. As the RF images should be similar in terms of content, colors, contrast, etc. to the test image, this hinders the applicability in a real scenario. Other approaches to increase the perceptual quality of images, including perceptual loss and adversarial losses, tend to dramatically decrease fidelity to the ground-truth through significant decreases in PSNR/SSIM. Addressing both issues, we propose a simple yet universal approach to improve the perceptual quality of the HR prediction from a pre-trained SR network on a given LR input by further fine-tuning the SR network on a subset of images from the training dataset with similar patterns of activation as the initial HR prediction, with respect to the filters of a feature extractor. In particular, we show the effects of fine-tuning on these images in terms of the perceptual quality and PSNR/SSIM values. Contrary to perceptually driven approaches, we demonstrate that the fine-tuned network produces a HR prediction with both greater perceptual quality and minimal changes to the PSNR/SSIM with respect to the initial HR prediction. Further, we present novel numerical experiments concerning the filters of SR networks, where we show through filter correlation, that the filters of the fine-tuned network from our method are closer to "ideal" filters, than those of the baseline network or a network fine-tuned on random images.

Self-Attentive Spatial Adaptive Normalization for Cross-Modality Domain Adaptation

Despite the successes of deep neural networks on many challenging vision tasks, they often fail to generalize to new test domains that are not distributed identically to the training data. The domain adaptation becomes more challenging for cross-modality medical data with a notable domain shift. Given that specific annotated imaging modalities may not be accessible nor complete. Our proposed solution is based on the cross-modality synthesis of medical images to reduce the costly annotation burden by radiologists and bridge the domain gap in radiological images. We present a novel approach for image-to-image translation in medical images, capable of supervised or unsupervised (unpaired image data) setups. Built upon adversarial training, we propose a learnable self-attentive spatial normalization of the deep convolutional generator network's intermediate activations. Unlike previous attention-based image-to-image translation approaches, which are either domain-specific or require distortion of the source domain's structures, we unearth the importance of the auxiliary semantic information to handle the geometric changes and preserve anatomical structures during image translation. We achieve superior results for cross-modality segmentation between unpaired MRI and CT data for multi-modality whole heart and multi-modal brain tumor MRI (T1/T2) datasets compared to the state-of-the-art methods. We also observe encouraging results in cross-modality conversion for paired MRI and CT images on a brain dataset. Furthermore, a detailed analysis of the cross-modality image translation, thorough ablation studies confirm our proposed method's efficacy.

Learning Whole-Slide Segmentation from Inexact and Incomplete Labels using Tissue Graphs

Segmenting histology images into diagnostically relevant regions is imperative to support timely and reliable decisions by pathologists. To this end, computer-aided techniques have been proposed to delineate relevant regions in scanned histology slides. However, the techniques necessitate task-specific large datasets of annotated pixels, which is tedious, time-consuming, expensive, and infeasible to acquire for many histology tasks. Thus, weakly-supervised semantic segmentation techniques are proposed to utilize weak supervision that is cheaper and quicker to acquire. In this paper, we propose SegGini, a weakly supervised segmentation method using graphs, that can utilize weak multiplex annotations, i.e. inexact and incomplete annotations, to segment arbitrary and large images, scaling from tissue microarray (TMA) to whole slide image (WSI). Formally, SegGini constructs a tissue-graph representation for an input histology image, where the graph nodes depict tissue regions. Then, it performs weakly-supervised segmentation via node classification by using inexact image-level labels, incomplete scribbles, or both. We evaluated SegGini on two public prostate cancer datasets containing TMAs and WSIs. Our method achieved state-of-the-art segmentation performance on both datasets for various annotation settings while being comparable to a pathologist baseline.

Self-Taught Semi-Supervised Anomaly Detection on Upper Limb X-rays

Detecting anomalies in musculoskeletal radiographs is of paramount importance for large-scale screening in the radiology workflow. Supervised deep networks take for granted a large number of annotations by radiologists, which is often prohibitively very time-consuming to acquire. Moreover, supervised systems are tailored to closed set scenarios, e.g., trained models suffer from overfitting to previously seen rare anomalies at training. Instead, our approach's rationale is to use task agnostic pretext tasks to leverage unlabeled data based on a cross-sample similarity measure. Besides, we formulate a complex distribution of data from normal class within our framework to avoid a potential bias on the side of anomalies. Through extensive experiments, we show that our method outperforms baselines across unsupervised and self-supervised anomaly detection settings on a real-world medical dataset, the MURA dataset. We also provide rich ablation studies to analyze each training stage's effect and loss terms on the final performance.

Quantifying Explainers of Graph Neural Networks in Computational Pathology

Explainability of deep learning methods is imperative to facilitate their clinical adoption in digital pathology. However, popular deep learning methods and explainability techniques (explainers) based on pixel-wise processing disregard biological entities' notion, thus complicating comprehension by pathologists. In this work, we address this by adopting biological entity-based graph processing and graph explainers enabling explanations accessible to pathologists. In this context, a major challenge becomes to discern meaningful explainers, particularly in a standardized and quantifiable fashion. To this end, we propose herein a set of novel quantitative metrics based on statistics of class separability using pathologically measurable concepts to characterize graph explainers. We employ the proposed metrics to evaluate three types of graph explainers, namely the layer-wise relevance propagation, gradient-based saliency, and graph pruning approaches, to explain Cell-Graph representations for Breast Cancer Subtyping. The proposed metrics are also applicable in other domains by using domain-specific intuitive concepts. We validate the qualitative and quantitative findings on the BRACS dataset, a large cohort of breast cancer RoIs, by expert pathologists.

Anomaly Detection on X-Rays Using Self-Supervised Aggregation Learning

Deep anomaly detection models using a supervised mode of learning usually work under a closed set assumption and suffer from overfitting to previously seen rare anomalies at training, which hinders their applicability in a real scenario. In addition, obtaining annotations for X-rays is very time consuming and requires extensive training of radiologists. Hence, training anomaly detection in a fully unsupervised or self-supervised fashion would be advantageous, allowing a significant reduction of time spent on the report by radiologists. In this paper, we present SALAD, an end-to-end deep self-supervised methodology for anomaly detection on X-Ray images. The proposed method is based on an optimization strategy in which a deep neural network is encouraged to represent prototypical local patterns of the normal data in the embedding space. During training, we record the prototypical patterns of normal training samples via a memory bank. Our anomaly score is then derived by measuring similarity to a weighted combination of normal prototypical patterns within a memory bank without using any anomalous patterns. We present extensive experiments on the challenging NIH Chest X-rays and MURA dataset, which indicate that our algorithm improves state-of-the-art methods by a wide margin.