Abhir Bhalerao

Yiping Jiao, Jeroen van der Laak, Shadi Albarqouni et al. · eth-zurich

We introduce LYSTO, the Lymphocyte Assessment Hackathon, which was held in conjunction with the MICCAI 2019 Conference in Shenzen (China). The competition required participants to automatically assess the number of lymphocytes, in particular T-cells, in histopathological images of colon, breast, and prostate cancer stained with CD3 and CD8 immunohistochemistry. Differently from other challenges setup in medical image analysis, LYSTO participants were solely given a few hours to address this problem. In this paper, we describe the goal and the multi-phase organization of the hackathon; we describe the proposed methods and the on-site results. Additionally, we present post-competition results where we show how the presented methods perform on an independent set of lung cancer slides, which was not part of the initial competition, as well as a comparison on lymphocyte assessment between presented methods and a panel of pathologists. We show that some of the participants were capable to achieve pathologist-level performance at lymphocyte assessment. After the hackathon, LYSTO was left as a lightweight plug-and-play benchmark dataset on grand-challenge website, together with an automatic evaluation platform. LYSTO has supported a number of research in lymphocyte assessment in oncology. LYSTO will be a long-lasting educational challenge for deep learning and digital pathology, it is available at https://lysto.grand-challenge.org/.

Jun Wang, Abhir Bhalerao, Yulan He

Radiology report generation (RRG) aims to describe automatically a radiology image with human-like language and could potentially support the work of radiologists, reducing the burden of manual reporting. Previous approaches often adopt an encoder-decoder architecture and focus on single-modal feature learning, while few studies explore cross-modal feature interaction. Here we propose a Cross-modal PROtotype driven NETwork (XPRONET) to promote cross-modal pattern learning and exploit it to improve the task of radiology report generation. This is achieved by three well-designed, fully differentiable and complementary modules: a shared cross-modal prototype matrix to record the cross-modal prototypes; a cross-modal prototype network to learn the cross-modal prototypes and embed the cross-modal information into the visual and textual features; and an improved multi-label contrastive loss to enable and enhance multi-label prototype learning. XPRONET obtains substantial improvements on the IU-Xray and MIMIC-CXR benchmarks, where its performance exceeds recent state-of-the-art approaches by a large margin on IU-Xray and comparable performance on MIMIC-CXR.

Jun Wang, Abhir Bhalerao, Terry Yin et al.

Radiology report generation (RRG) has gained increasing research attention because of its huge potential to mitigate medical resource shortages and aid the process of disease decision making by radiologists. Recent advancements in RRG are largely driven by improving a model's capabilities in encoding single-modal feature representations, while few studies explicitly explore the cross-modal alignment between image regions and words. Radiologists typically focus first on abnormal image regions before composing the corresponding text descriptions, thus cross-modal alignment is of great importance to learn a RRG model which is aware of abnormalities in the image. Motivated by this, we propose a Class Activation Map guided Attention Network (CAMANet) which explicitly promotes crossmodal alignment by employing aggregated class activation maps to supervise cross-modal attention learning, and simultaneously enrich the discriminative information. CAMANet contains three complementary modules: a Visual Discriminative Map Generation module to generate the importance/contribution of each visual token; Visual Discriminative Map Assisted Encoder to learn the discriminative representation and enrich the discriminative information; and a Visual Textual Attention Consistency module to ensure the attention consistency between the visual and textual tokens, to achieve the cross-modal alignment. Experimental results demonstrate that CAMANet outperforms previous SOTA methods on two commonly used RRG benchmarks.

Quoc Dang Vu, Robert Jewsbury, Simon Graham et al.

Since the introduction of digital and computational pathology as a field, one of the major problems in the clinical application of algorithms has been the struggle to generalize well to examples outside the distribution of the training data. Existing work to address this in both pathology and natural images has focused almost exclusively on classification tasks. We explore and evaluate the robustness of the 7 best performing nuclear segmentation and classification models from the largest computational pathology challenge for this problem to date, the CoNIC challenge. We demonstrate that existing state-of-the-art (SoTA) models are robust towards compression artifacts but suffer substantial performance reduction when subjected to shifts in the color domain. We find that using stain normalization to address the domain shift problem can be detrimental to the model performance. On the other hand, neural style transfer is more consistent in improving test performance when presented with large color variations in the wild.

Kai Liang, Jun Wang, Abhir Bhalerao

Anticipating lane change intentions of surrounding vehicles is crucial for efficient and safe driving decision making in an autonomous driving system. Previous works often adopt physical variables such as driving speed, acceleration and so forth for lane change classification. However, physical variables do not contain semantic information. Although 3D CNNs have been developing rapidly, the number of methods utilising action recognition models and appearance feature for lane change recognition is low, and they all require additional information to pre-process data. In this work, we propose an end-to-end framework including two action recognition methods for lane change recognition, using video data collected by cameras. Our method achieves the best lane change classification results using only the RGB video data of the PREVENTION dataset. Class activation maps demonstrate that action recognition models can efficiently extract lane change motions. A method to better extract motion clues is also proposed in this paper.

Wenbo Wei, Jun Wang, Abhir Bhalerao

To help address the occlusion problem in panoptic segmentation and image understanding, this paper proposes a new large-scale dataset named COCO-OLAC (COCO Occlusion Labels for All Computer Vision Tasks), which is derived from the COCO dataset by manually labelling images into three perceived occlusion levels. Using COCO-OLAC, we systematically assess and quantify the impact of occlusion on panoptic segmentation on samples having different levels of occlusion. Comparative experiments with SOTA panoptic models demonstrate that the presence of occlusion significantly affects performance, with higher occlusion levels resulting in notably poorer performance. Additionally, we propose a straightforward yet effective method as an initial attempt to leverage the occlusion annotation using contrastive learning to render a model that learns a more robust representation capturing different severities of occlusion. Experimental results demonstrate that the proposed approach boosts the performance of the baseline model and achieves SOTA performance on the proposed COCO-OLAC dataset.

Jun Wang, Lixing Zhu, Abhir Bhalerao et al.

Radiology report generation aims to automatically provide clinically meaningful descriptions of radiology images such as MRI and X-ray. Although great success has been achieved in natural scene image captioning tasks, radiology report generation remains challenging and requires prior medical knowledge. In this paper, we propose PromptRRG, a method that utilizes prompt learning to activate a pretrained model and incorporate prior knowledge. Since prompt learning for radiology report generation has not been explored before, we begin with investigating prompt designs and categorise them based on varying levels of knowledge: common, domain-specific and disease-enriched prompts. Additionally, we propose an automatic prompt learning mechanism to alleviate the burden of manual prompt engineering. This is the first work to systematically examine the effectiveness of prompt learning for radiology report generation. Experimental results on the largest radiology report generation benchmark, MIMIC-CXR, demonstrate that our proposed method achieves state-of-the-art performance. Code will be available upon the acceptance.

Saif Anwar, Nathan Griffiths, Abhir Bhalerao et al.

The trustworthiness of Machine Learning (ML) models can be difficult to assess, but is critical in high-risk or ethically sensitive applications. Many models are treated as a `black-box' where the reasoning or criteria for a final decision is opaque to the user. To address this, some existing Explainable AI (XAI) approaches approximate model behaviour using perturbed data. However, such methods have been criticised for ignoring feature dependencies, with explanations being based on potentially unrealistic data. We propose a novel framework, CHILLI, for incorporating data context into XAI by generating contextually aware perturbations, which are faithful to the training data of the base model being explained. This is shown to improve both the soundness and accuracy of the explanations.

Saif Anwar, Nathan Griffiths, Abhir Bhalerao et al.

Existing local Explainable AI (XAI) methods, such as LIME, select a region of the input space in the vicinity of a given input instance, for which they approximate the behaviour of a model using a simpler and more interpretable surrogate model. The size of this region is often controlled by a user-defined locality hyperparameter. In this paper, we demonstrate the difficulties associated with defining a suitable locality size to capture impactful model behaviour, as well as the inadequacy of using a single locality size to explain all predictions. We propose a novel method, MASALA, for generating explanations, which automatically determines the appropriate local region of impactful model behaviour for each individual instance being explained. MASALA approximates the local behaviour used by a complex model to make a prediction by fitting a linear surrogate model to a set of points which experience similar model behaviour. These points are found by clustering the input space into regions of linear behavioural trends exhibited by the model. We compare the fidelity and consistency of explanations generated by our method with existing local XAI methods, namely LIME and CHILLI. Experiments on the PHM08 and MIDAS datasets show that our method produces more faithful and consistent explanations than existing methods, without the need to define any sensitive locality hyperparameters.

Jun Wang, Lixing Zhu, Abhir Bhalerao et al.

Radiology report generation (RRG) methods often lack sufficient medical knowledge to produce clinically accurate reports. The scene graph contains rich information to describe the objects in an image. We explore enriching the medical knowledge for RRG via a scene graph, which has not been done in the current RRG literature. To this end, we propose the Scene Graph aided RRG (SGRRG) network, a framework that generates region-level visual features, predicts anatomical attributes, and leverages an automatically generated scene graph, thus achieving medical knowledge distillation in an end-to-end manner. SGRRG is composed of a dedicated scene graph encoder responsible for translating the scene graph, and a scene graph-aided decoder that takes advantage of both patch-level and region-level visual information. A fine-grained, sentence-level attention method is designed to better dis-till the scene graph information. Extensive experiments demonstrate that SGRRG outperforms previous state-of-the-art methods in report generation and can better capture abnormal findings.

Jun Wang, Lixing Zhu, Xiaohan Yu et al.

Learning medical visual representations from image-report pairs through joint learning has garnered increasing research attention due to its potential to alleviate the data scarcity problem in the medical domain. The primary challenges stem from the lengthy reports that feature complex discourse relations and semantic pathologies. Previous works have predominantly focused on instance-wise or token-wise cross-modal alignment, often neglecting the importance of pathological-level consistency. This paper presents a novel framework PLACE that promotes the Pathological-Level Alignment and enriches the fine-grained details via Correlation Exploration without additional human annotations. Specifically, we propose a novel pathological-level cross-modal alignment (PCMA) approach to maximize the consistency of pathology observations from both images and reports. To facilitate this, a Visual Pathology Observation Extractor is introduced to extract visual pathological observation representations from localized tokens. The PCMA module operates independently of any external disease annotations, enhancing the generalizability and robustness of our methods. Furthermore, we design a proxy task that enforces the model to identify correlations among image patches, thereby enriching the fine-grained details crucial for various downstream tasks. Experimental results demonstrate that our proposed framework achieves new state-of-the-art performance on multiple downstream tasks, including classification, image-to-text retrieval, semantic segmentation, object detection and report generation.

Saif Anwar, Nathan Griffiths, Thomas Popham et al.

Recent improvements in the expressive power of spatio-temporal models have led to performance gains in many real-world applications, such as traffic forecasting and social network modelling. However, understanding the predictions from a model is crucial to ensure reliability and trustworthiness, particularly for high-risk applications, such as healthcare and transport. Few existing methods are able to generate explanations for models trained on continuous-time dynamic graph data and, of these, the computational complexity and lack of suitable explanation objectives pose challenges. In this paper, we propose $\textbf{S}$patio-$\textbf{T}$emporal E$\textbf{X}$planation $\textbf{Search}$ (STX-Search), a novel method for generating instance-level explanations that is applicable to static and dynamic temporal graph structures. We introduce a novel search strategy and objective function, to find explanations that are highly faithful and interpretable. When compared with existing methods, STX-Search produces explanations of higher fidelity whilst optimising explanation size to maintain interpretability.

Robert Jewsbury, Ruoyu Wang, Abhir Bhalerao et al.

Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight cellular components in the images. We propose a new approach, StainFuser, which treats this problem as a style transfer task using a novel Conditional Latent Diffusion architecture, eliminating the need for handcrafted color components. With this method, we curate SPI-2M the largest stain normalization dataset to date of over 2 million histology images with neural style transfer for high-quality transformations. Trained on this data, StainFuser outperforms current state-of-the-art deep learning and handcrafted methods in terms of the quality of normalized images and in terms of downstream model performance on the CoNIC dataset.

Rob Jewsbury, Abhir Bhalerao, Nasir Rajpoot

The field of computational pathology presents many challenges for computer vision algorithms due to the sheer size of pathology images. Histopathology images are large and need to be split up into image tiles or patches so modern convolutional neural networks (CNNs) can process them. In this work, we present a method to generate an interpretable image representation of computational pathology images using quadtrees and a pipeline to use these representations for highly accurate downstream classification. To the best of our knowledge, this is the first attempt to use quadtrees for pathology image data. We show it is highly accurate, able to achieve as good results as the currently widely adopted tissue mask patch extraction methods all while using over 38% less data.

Noorul Wahab, Islam M Miligy, Katherine Dodd et al.

Recent advances in whole slide imaging (WSI) technology have led to the development of a myriad of computer vision and artificial intelligence (AI) based diagnostic, prognostic, and predictive algorithms. Computational Pathology (CPath) offers an integrated solution to utilize information embedded in pathology WSIs beyond what we obtain through visual assessment. For automated analysis of WSIs and validation of machine learning (ML) models, annotations at the slide, tissue and cellular levels are required. The annotation of important visual constructs in pathology images is an important component of CPath projects. Improper annotations can result in algorithms which are hard to interpret and can potentially produce inaccurate and inconsistent results. Despite the crucial role of annotations in CPath projects, there are no well-defined guidelines or best practices on how annotations should be carried out. In this paper, we address this shortcoming by presenting the experience and best practices acquired during the execution of a large-scale annotation exercise involving a multidisciplinary team of pathologists, ML experts and researchers as part of the Pathology image data Lake for Analytics, Knowledge and Education (PathLAKE) consortium. We present a real-world case study along with examples of different types of annotations, diagnostic algorithm, annotation data dictionary and annotation constructs. The analyses reported in this work highlight best practice recommendations that can be used as annotation guidelines over the lifecycle of a CPath project.

Talha Qaiser, Abhik Mukherjee, Chaitanya Reddy Pb et al.

Evaluating expression of the Human epidermal growth factor receptor 2 (Her2) by visual examination of immunohistochemistry (IHC) on invasive breast cancer (BCa) is a key part of the diagnostic assessment of BCa due to its recognised importance as a predictive and prognostic marker in clinical practice. However, visual scoring of Her2 is subjective and consequently prone to inter-observer variability. Given the prognostic and therapeutic implications of Her2 scoring, a more objective method is required. In this paper, we report on a recent automated Her2 scoring contest, held in conjunction with the annual PathSoc meeting held in Nottingham in June 2016, aimed at systematically comparing and advancing the state-of-the-art Artificial Intelligence (AI) based automated methods for Her2 scoring. The contest dataset comprised of digitised whole slide images (WSI) of sections from 86 cases of invasive breast carcinoma stained with both Haematoxylin & Eosin (H&E) and IHC for Her2. The contesting algorithms automatically predicted scores of the IHC slides for an unseen subset of the dataset and the predicted scores were compared with the 'ground truth' (a consensus score from at least two experts). We also report on a simple Man vs Machine contest for the scoring of Her2 and show that the automated methods could beat the pathology experts on this contest dataset. This paper presents a benchmark for comparing the performance of automated algorithms for scoring of Her2. It also demonstrates the enormous potential of automated algorithms in assisting the pathologist with objective IHC scoring.