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Register a new userImproving Interpretability in Medical Imaging Diagnosis using Adversarial Training
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Andrei Margeloiu
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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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.
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Recently, substantial progress has been made in language modeling by using deep neural networks. However, in practice, large scale neural language models have been shown to be prone to overfitting. In this paper, we present a simple yet highly effective adversarial training mechanism for regularizing neural language models. The idea is to introduce adversarial noise to the output embedding layer while training the models. We show that the optimal adversarial noise yields a simple closed-form solution, thus allowing us to develop a simple and time efficient algorithm. Theoretically, we show that our adversarial mechanism effectively encourages the diversity of the embedding vectors, helping to increase the robustness of models. Empirically, we show that our method improves on the single model state-of-the-art results for language modeling on Penn Treebank (PTB) and Wikitext-2, achieving test perplexity scores of 46.01 and 38.07, respectively. When applied to machine translation, our method improves over various transformer-based translation baselines in BLEU scores on the WMT14 English-German and IWSLT14 German-English tasks.
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.
Abbreviation disambiguation is important for automated clinical note processing due to the frequent use of abbreviations in clinical settings. Current models for automated abbreviation disambiguation are restricted by the scarcity and imbalance of labeled training data, decreasing their generalizability to orthogonal sources. In this work we propose a novel data augmentation technique that utilizes information from related medical concepts, which improves our models ability to generalize. Furthermore, we show that incorporating the global context information within the whole medical note (in addition to the traditional local context window), can significantly improve the models representation for abbreviations. We train our model on a public dataset (MIMIC III) and test its performance on datasets from different sources (CASI, i2b2). Together, these two techniques boost the accuracy of abbreviation disambiguation by almost 14% on the CASI dataset and 4% on i2b2.
One of the key challenges when developing a predictive model is the capability to describe the domain knowledge and the cause-effect relationships in a simple way. Decision rules are a useful and important methodology in this context, justifying their application in several areas, in particular in clinical practice. Several machine-learning classifiers have exploited the advantageous properties of decision rules to build intelligent prediction models, namely decision trees and ensembles of trees (ETs). However, such methodologies usually suffer from a trade-off between interpretability and predictive performance. Some procedures consider a simplification of ETs, using heuristic approaches to select an optimal reduced set of decision rules. In this paper, we introduce a novel step to those methodologies. We create a new component to predict if a given rule will be correct or not for a particular patient, which introduces personalization into the procedure. Furthermore, the validation results using three public clinical datasets show that it also allows to increase the predictive performance of the selected set of rules, improving the mentioned trade-off.
Diagnosing diseases such as leukemia or anemia requires reliable counts of blood cells. Hematologists usually label and count microscopy images of blood cells manually. In many cases, however, cells in different maturity states are difficult to distinguish, and in combination with image noise and subjectivity, humans are prone to make labeling mistakes. This results in labels that are often not reproducible, which can directly affect the diagnoses. We introduce TIMELY, a probabilistic model that combines pseudotime inference methods with inhomogeneous hidden Markov trees, which addresses this challenge of label inconsistency. We show first on simulation data that TIMELY is able to identify and correct wrong labels with higher precision and recall than baseline methods for labeling correction. We then apply our method to two real-world datasets of blood cell data and show that TIMELY successfully finds inconsistent labels, thereby improving the quality of human-generated labels.
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