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Register a new userQuantifying Explainers of Graph Neural Networks in Computational Pathology
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Added by
Guillaume Jaume
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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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.
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Stain variation is a phenomenon observed when distinct pathology laboratories stain tissue slides that exhibit similar but not identical color appearance. Due to this color shift between laboratories, convolutional neural networks (CNNs) trained with images from one lab often underperform on unseen images from the other lab. Several techniques have been proposed to reduce the generalization error, mainly grouped into two categories: stain color augmentation and stain color normalization. The former simulates a wide variety of realistic stain variations during training, producing stain-invariant CNNs. The latter aims to match training and test color distributions in order to reduce stain variation. For the first time, we compared some of these techniques and quantified their effect on CNN classification performance using a heterogeneous dataset of hematoxylin and eosin histopathology images from 4 organs and 9 pathology laboratories. Additionally, we propose a novel unsupervised method to perform stain color normalization using a neural network. Based on our experimental results, we provide practical guidelines on how to use stain color augmentation and stain color normalization in future computational pathology applications.
The spatial homogeneity of an urban road network (URN) measures whether each distinct component is analogous to the whole network and can serve as a quantitative manner bridging network structure and dynamics. However, given the complexity of cities, it is challenging to quantify spatial homogeneity simply based on conventional network statistics. In this work, we use Graph Neural Networks to model the 11,790 URN samples across 30 cities worldwide and use its predictability to define the spatial homogeneity. The proposed measurement can be viewed as a non-linear integration of multiple geometric properties, such as degree, betweenness, road network type, and a strong indicator of mixed socio-economic events, such as GDP and population growth. City clusters derived from transferring spatial homogeneity can be interpreted well by continental urbanization histories. We expect this novel metric supports various subsequent tasks in transportation, urban planning, and geography.
AI technology has made remarkable achievements in computational pathology (CPath), especially with the help of deep neural networks. However, the network performance is highly related to architecture design, which commonly requires human experts with domain knowledge. In this paper, we combat this challenge with the recent advance in neural architecture search (NAS) to find an optimal network for CPath applications. In particular, we use differentiable architecture search (DARTS) for its efficiency. We first adopt a probing metric to show that the original DARTS lacks proper hyperparameter tuning on the CIFAR dataset, and how the generalization issue can be addressed using an adaptive optimization strategy. We then apply our searching framework on CPath applications by searching for the optimum network architecture on a histological tissue type dataset (ADP). Results show that the searched network outperforms state-of-the-art networks in terms of prediction accuracy and computation complexity. We further conduct extensive experiments to demonstrate the transferability of the searched network to new CPath applications, the robustness against downscaled inputs, as well as the reliability of predictions.
Graph neural networks (GNNs) have witnessed an unprecedented proliferation in tackling several problems in computer vision, computer-aided diagnosis, and related fields. While prior studies have focused on boosting the model accuracy, quantifying the reproducibility of the most discriminative features identified by GNNs is still an intact problem that yields concerns about their reliability in clinical applications in particular. Specifically, the reproducibility of biological markers across clinical datasets and distribution shifts across classes (e.g., healthy and disordered brains) is of paramount importance in revealing the underpinning mechanisms of diseases as well as propelling the development of personalized treatment. Motivated by these issues, we propose, for the first time, reproducibility-based GNN selection (RG-Select), a framework for GNN reproducibility assessment via the quantification of the most discriminative features (i.e., biomarkers) shared between different models. To ascertain the soundness of our framework, the reproducibility assessment embraces variations of different factors such as training strategies and data perturbations. Despite these challenges, our framework successfully yielded replicable conclusions across different training strategies and various clinical datasets. Our findings could thus pave the way for the development of biomarker trustworthiness and reliability assessment methods for computer-aided diagnosis and prognosis tasks. RG-Select code is available on GitHub at https://github.com/basiralab/RG-Select.
We address the problem of recognizing situations in images. Given an image, the task is to predict the most salient verb (action), and fill its semantic roles such as who is performing the action, what is the source and target of the action, etc. Different verbs have different roles (e.g. attacking has weapon), and each role can take on many possible values (nouns). We propose a model based on Graph Neural Networks that allows us to efficiently capture joint dependencies between roles using neural networks defined on a graph. Experiments with different graph connectivities show that our approach that propagates information between roles significantly outperforms existing work, as well as multiple baselines. We obtain roughly 3-5% improvement over previous work in predicting the full situation. We also provide a thorough qualitative analysis of our model and influence of different roles in the verbs.
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