arXiv subjects

Krzysztof J. Geras

Publications and source records attributed to Krzysztof J. Geras.

34 records · Page 2Linked to original sources

arXiv2020

An artificial intelligence system for predicting the deterioration of COVID-19 patients in the emergency department

During the coronavirus disease 2019 (COVID-19) pandemic, rapid and accurate triage of patients at the emergency department is critical to inform decision-making. We propose a data-driven approach for automatic prediction of deterioration risk using a deep neural network that learns from chest X-ray images and a gradient boosting model that learns from routine clinical variables. Our AI prognosis system, trained using data from 3,661 patients, achieves an area under the receiver operating characteristic curve (AUC) of 0.786 (95% CI: 0.745-0.830) when predicting deterioration within 96 hours. The deep neural network extracts informative areas of chest X-ray images to assist clinicians in interpreting the predictions and performs comparably to two radiologists in a reader study. In order to verify performance in a real clinical setting, we silently deployed a preliminary version of the deep neural network at New York University Langone Health during the first wave of the pandemic, which produced accurate predictions in real-time. In summary, our findings demonstrate the potential of the proposed system for assisting front-line physicians in the triage of COVID-19 patients.

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arXiv2020

Investigating and Simplifying Masking-based Saliency Methods for Model Interpretability

Saliency maps that identify the most informative regions of an image for a classifier are valuable for model interpretability. A common approach to creating saliency maps involves generating input masks that mask out portions of an image to maximally deteriorate classification performance, or mask in an image to preserve classification performance. Many variants of this approach have been proposed in the literature, such as counterfactual generation and optimizing over a Gumbel-Softmax distribution. Using a general formulation of masking-based saliency methods, we conduct an extensive evaluation study of a number of recently proposed variants to understand which elements of these methods meaningfully improve performance. Surprisingly, we find that a well-tuned, relatively simple formulation of a masking-based saliency model outperforms many more complex approaches. We find that the most important ingredients for high quality saliency map generation are (1) using both masked-in and masked-out objectives and (2) training the classifier alongside the masking model. Strikingly, we show that a masking model can be trained with as few as 10 examples per class and still generate saliency maps with only a 0.7-point increase in localization error.

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arXiv2020

Reducing false-positive biopsies with deep neural networks that utilize local and global information in screening mammograms

Breast cancer is the most common cancer in women, and hundreds of thousands of unnecessary biopsies are done around the world at a tremendous cost. It is crucial to reduce the rate of biopsies that turn out to be benign tissue. In this study, we build deep neural networks (DNNs) to classify biopsied lesions as being either malignant or benign, with the goal of using these networks as second readers serving radiologists to further reduce the number of false positive findings. We enhance the performance of DNNs that are trained to learn from small image patches by integrating global context provided in the form of saliency maps learned from the entire image into their reasoning, similar to how radiologists consider global context when evaluating areas of interest. Our experiments are conducted on a dataset of 229,426 screening mammography exams from 141,473 patients. We achieve an AUC of 0.8 on a test set consisting of 464 benign and 136 malignant lesions.

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arXiv2020

Classifier-agnostic saliency map extraction

Currently available methods for extracting saliency maps identify parts of the input which are the most important to a specific fixed classifier. We show that this strong dependence on a given classifier hinders their performance. To address this problem, we propose classifier-agnostic saliency map extraction, which finds all parts of the image that any classifier could use, not just one given in advance. We observe that the proposed approach extracts higher quality saliency maps than prior work while being conceptually simple and easy to implement. The method sets the new state of the art result for localization task on the ImageNet data, outperforming all existing weakly-supervised localization techniques, despite not using the ground truth labels at the inference time. The code reproducing the results is available at https://github.com/kondiz/casme . The final version of this manuscript is published in Computer Vision and Image Understanding and is available online at https://doi.org/10.1016/j.cviu.2020.102969 .

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arXiv2020

Understanding the robustness of deep neural network classifiers for breast cancer screening

Deep neural networks (DNNs) show promise in breast cancer screening, but their robustness to input perturbations must be better understood before they can be clinically implemented. There exists extensive literature on this subject in the context of natural images that can potentially be built upon. However, it cannot be assumed that conclusions about robustness will transfer from natural images to mammogram images, due to significant differences between the two image modalities. In order to determine whether conclusions will transfer, we measure the sensitivity of a radiologist-level screening mammogram image classifier to four commonly studied input perturbations that natural image classifiers are sensitive to. We find that mammogram image classifiers are also sensitive to these perturbations, which suggests that we can build on the existing literature. We also perform a detailed analysis on the effects of low-pass filtering, and find that it degrades the visibility of clinically meaningful features called microcalcifications. Since low-pass filtering removes semantically meaningful information that is predictive of breast cancer, we argue that it is undesirable for mammogram image classifiers to be invariant to it. This is in contrast to natural images, where we do not want DNNs to be sensitive to low-pass filtering due to its tendency to remove information that is human-incomprehensible.

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arXiv2020

An interpretable classifier for high-resolution breast cancer screening images utilizing weakly supervised localization

Medical images differ from natural images in significantly higher resolutions and smaller regions of interest. Because of these differences, neural network architectures that work well for natural images might not be applicable to medical image analysis. In this work, we extend the globally-aware multiple instance classifier, a framework we proposed to address these unique properties of medical images. This model first uses a low-capacity, yet memory-efficient, network on the whole image to identify the most informative regions. It then applies another higher-capacity network to collect details from chosen regions. Finally, it employs a fusion module that aggregates global and local information to make a final prediction. While existing methods often require lesion segmentation during training, our model is trained with only image-level labels and can generate pixel-level saliency maps indicating possible malignant findings. We apply the model to screening mammography interpretation: predicting the presence or absence of benign and malignant lesions. On the NYU Breast Cancer Screening Dataset, consisting of more than one million images, our model achieves an AUC of 0.93 in classifying breasts with malignant findings, outperforming ResNet-34 and Faster R-CNN. Compared to ResNet-34, our model is 4.1x faster for inference while using 78.4% less GPU memory. Furthermore, we demonstrate, in a reader study, that our model surpasses radiologist-level AUC by a margin of 0.11. The proposed model is available online: https://github.com/nyukat/GMIC.

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arXiv2019

fastMRI: An Open Dataset and Benchmarks for Accelerated MRI

Accelerating Magnetic Resonance Imaging (MRI) by taking fewer measurements has the potential to reduce medical costs, minimize stress to patients and make MRI possible in applications where it is currently prohibitively slow or expensive. We introduce the fastMRI dataset, a large-scale collection of both raw MR measurements and clinical MR images, that can be used for training and evaluation of machine-learning approaches to MR image reconstruction. By introducing standardized evaluation criteria and a freely-accessible dataset, our goal is to help the community make rapid advances in the state of the art for MR image reconstruction. We also provide a self-contained introduction to MRI for machine learning researchers with no medical imaging background.

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arXiv2019

Globally-Aware Multiple Instance Classifier for Breast Cancer Screening

Deep learning models designed for visual classification tasks on natural images have become prevalent in medical image analysis. However, medical images differ from typical natural images in many ways, such as significantly higher resolutions and smaller regions of interest. Moreover, both the global structure and local details play important roles in medical image analysis tasks. To address these unique properties of medical images, we propose a neural network that is able to classify breast cancer lesions utilizing information from both a global saliency map and multiple local patches. The proposed model outperforms the ResNet-based baseline and achieves radiologist-level performance in the interpretation of screening mammography. Although our model is trained only with image-level labels, it is able to generate pixel-level saliency maps that provide localization of possible malignant findings.

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arXiv2019

Improving localization-based approaches for breast cancer screening exam classification

We trained and evaluated a localization-based deep CNN for breast cancer screening exam classification on over 200,000 exams (over 1,000,000 images). Our model achieves an AUC of 0.919 in predicting malignancy in patients undergoing breast cancer screening, reducing the error rate of the baseline (Wu et al., 2019a) by 23%. In addition, the models generates bounding boxes for benign and malignant findings, providing interpretable predictions.

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arXiv2019

Screening Mammogram Classification with Prior Exams

Radiologists typically compare a patient's most recent breast cancer screening exam to their previous ones in making informed diagnoses. To reflect this practice, we propose new neural network models that compare pairs of screening mammograms from the same patient. We train and evaluate our proposed models on over 665,000 pairs of images (over 166,000 pairs of exams). Our best model achieves an AUC of 0.866 in predicting malignancy in patients who underwent breast cancer screening, reducing the error rate of the corresponding baseline.

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arXiv2019

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening

We present a deep convolutional neural network for breast cancer screening exam classification, trained and evaluated on over 200,000 exams (over 1,000,000 images). Our network achieves an AUC of 0.895 in predicting whether there is a cancer in the breast, when tested on the screening population. We attribute the high accuracy of our model to a two-stage training procedure, which allows us to use a very high-capacity patch-level network to learn from pixel-level labels alongside a network learning from macroscopic breast-level labels. To validate our model, we conducted a reader study with 14 readers, each reading 720 screening mammogram exams, and find our model to be as accurate as experienced radiologists when presented with the same data. Finally, we show that a hybrid model, averaging probability of malignancy predicted by a radiologist with a prediction of our neural network, is more accurate than either of the two separately. To better understand our results, we conduct a thorough analysis of our network's performance on different subpopulations of the screening population, model design, training procedure, errors, and properties of its internal representations.

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arXiv2018

High-Resolution Breast Cancer Screening with Multi-View Deep Convolutional Neural Networks

Advances in deep learning for natural images have prompted a surge of interest in applying similar techniques to medical images. The majority of the initial attempts focused on replacing the input of a deep convolutional neural network with a medical image, which does not take into consideration the fundamental differences between these two types of images. Specifically, fine details are necessary for detection in medical images, unlike in natural images where coarse structures matter most. This difference makes it inadequate to use the existing network architectures developed for natural images, because they work on heavily downscaled images to reduce the memory requirements. This hides details necessary to make accurate predictions. Additionally, a single exam in medical imaging often comes with a set of views which must be fused in order to reach a correct conclusion. In our work, we propose to use a multi-view deep convolutional neural network that handles a set of high-resolution medical images. We evaluate it on large-scale mammography-based breast cancer screening (BI-RADS prediction) using 886,000 images. We focus on investigating the impact of the training set size and image size on the prediction accuracy. Our results highlight that performance increases with the size of training set, and that the best performance can only be achieved using the original resolution. In the reader study, performed on a random subset of the test set, we confirmed the efficacy of our model, which achieved performance comparable to a committee of radiologists when presented with the same data.

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arXiv2017

Breast density classification with deep convolutional neural networks

Breast density classification is an essential part of breast cancer screening. Although a lot of prior work considered this problem as a task for learning algorithms, to our knowledge, all of them used small and not clinically realistic data both for training and evaluation of their models. In this work, we explore the limits of this task with a data set coming from over 200,000 breast cancer screening exams. We use this data to train and evaluate a strong convolutional neural network classifier. In a reader study, we find that our model can perform this task comparably to a human expert.

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arXiv2017

Do Deep Convolutional Nets Really Need to be Deep and Convolutional?

Yes, they do. This paper provides the first empirical demonstration that deep convolutional models really need to be both deep and convolutional, even when trained with methods such as distillation that allow small or shallow models of high accuracy to be trained. Although previous research showed that shallow feed-forward nets sometimes can learn the complex functions previously learned by deep nets while using the same number of parameters as the deep models they mimic, in this paper we demonstrate that the same methods cannot be used to train accurate models on CIFAR-10 unless the student models contain multiple layers of convolution. Although the student models do not have to be as deep as the teacher model they mimic, the students need multiple convolutional layers to learn functions of comparable accuracy as the deep convolutional teacher.

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arXiv2016

Blending LSTMs into CNNs

We consider whether deep convolutional networks (CNNs) can represent decision functions with similar accuracy as recurrent networks such as LSTMs. First, we show that a deep CNN with an architecture inspired by the models recently introduced in image recognition can yield better accuracy than previous convolutional and LSTM networks on the standard 309h Switchboard automatic speech recognition task. Then we show that even more accurate CNNs can be trained under the guidance of LSTMs using a variant of model compression, which we call model blending because the teacher and student models are similar in complexity but different in inductive bias. Blending further improves the accuracy of our CNN, yielding a computationally efficient model of accuracy higher than any of the other individual models. Examining the effect of "dark knowledge" in this model compression task, we find that less than 1% of the highest probability labels are needed for accurate model compression.

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arXiv2015

Scheduled denoising autoencoders

We present a representation learning method that learns features at multiple different levels of scale. Working within the unsupervised framework of denoising autoencoders, we observe that when the input is heavily corrupted during training, the network tends to learn coarse-grained features, whereas when the input is only slightly corrupted, the network tends to learn fine-grained features. This motivates the scheduled denoising autoencoder, which starts with a high level of noise that lowers as training progresses. We find that the resulting representation yields a significant boost on a later supervised task compared to the original input, or to a standard denoising autoencoder trained at a single noise level. After supervised fine-tuning our best model achieves the lowest ever reported error on the CIFAR-10 data set among permutation-invariant methods.

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