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Register a new userDeep Learning Under the Microscope: Improving the Interpretability of Medical Imaging Neural Networks
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Magdalini Paschali
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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In this paper, we propose a novel interpretation method tailored to histological Whole Slide Image (WSI) processing. A Deep Neural Network (DNN), inspired by Bag-of-Features models is equipped with a Multiple Instance Learning (MIL) branch and trained with weak supervision for WSI classification. MIL avoids label ambiguity and enhances our models expressive power without guiding its attention. We utilize a fine-grained logit heatmap of the models activations to interpret its decision-making process. The proposed method is quantitatively and qualitatively evaluated on two challenging histology datasets, outperforming a variety of baselines. In addition, two expert pathologists were consulted regarding the interpretability provided by our method and acknowledged its potential for integration into several clinical applications.
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Interpretability of deep neural networks (DNNs) is essential since it enables users to understand the overall strengths and weaknesses of the models, conveys an understanding of how the models will behave in the future, and how to diagnose and correct potential problems. However, it is challenging to reason about what a DNN actually does due to its opaque or black-box nature. To address this issue, we propose a novel technique to improve the interpretability of DNNs by leveraging the rich semantic information embedded in human descriptions. By concentrating on the video captioning task, we first extract a set of semantically meaningful topics from the human descriptions that cover a wide range of visual concepts, and integrate them into the model with an interpretive loss. We then propose a prediction difference maximization algorithm to interpret the learned features of each neuron. Experimental results demonstrate its effectiveness in video captioning using the interpretable features, which can also be transferred to video action recognition. By clearly understanding the learned features, users can easily revise false predictions via a human-in-the-loop procedure.
We investigate the influence of adversarial training on the interpretability of convolutional neural networks (CNNs), specifically applied to diagnosing skin cancer. We show that gradient-based saliency maps of adversarially trained CNNs are significantly sharper and more visually coherent than those of standardly trained CNNs. Furthermore, we show that adversarially trained networks highlight regions with significant color variation within the lesion, a common characteristic of melanoma. We find that fine-tuning a robust network with a small learning rate further improves saliency maps sharpness. Lastly, we provide preliminary work suggesting that robustifying the first layers to extract robust low-level features leads to visually coherent explanations.
Deep Convolutional Neural Networks (CNNs) have been one of the most influential recent developments in computer vision, particularly for categorization. There is an increasing demand for explainable AI as these systems are deployed in the real world. However, understanding the information represented and processed in CNNs remains in most cases challenging. Within this paper, we explore the use of new information theoretic techniques developed in the field of neuroscience to enable novel understanding of how a CNN represents information. We trained a 10-layer ResNet architecture to identify 2,000 face identities from 26M images generated using a rigorously controlled 3D face rendering model that produced variations of intrinsic (i.e. face morphology, gender, age, expression and ethnicity) and extrinsic factors (i.e. 3D pose, illumination, scale and 2D translation). With our methodology, we demonstrate that unlike humans network overgeneralizes face identities even with extreme changes of face shape, but it is more sensitive to changes of texture. To understand the processing of information underlying these counterintuitive properties, we visualize the features of shape and texture that the network processes to identify faces. Then, we shed a light into the inner workings of the black box and reveal how hidden layers represent these features and whether the representations are invariant to pose. We hope that our methodology will provide an additional valuable tool for interpretability of CNNs.
Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.
Medical imaging is playing a more and more important role in clinics. However, there are several issues in different imaging modalities such as slow imaging speed in MRI, radiation injury in CT and PET. Therefore, accelerating MRI, reducing radiation dose in CT and PET have been ongoing research topics since their invention. Usually, acquiring less data is a direct but important strategy to address these issues. However, less acquisition usually results in aliasing artifacts in reconstructions. Recently, deep learning (DL) has been introduced in medical image reconstruction and shown potential on significantly speeding up MR reconstruction and reducing radiation dose. In this paper, we propose a general framework on combining the reconstruction model with deep learning to maximize the potential of deep learning and model-based reconstruction, and give the examples to demonstrate the performance and requirements of unrolling different algorithms using deep learning.
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