Jakub Chłędowski

Jungkyu Park, Jakub Chłędowski, Stanisław Jastrzębski et al.

3D imaging enables accurate diagnosis by providing spatial information about organ anatomy. However, using 3D images to train AI models is computationally challenging because they consist of 10x or 100x more pixels than their 2D counterparts. To be trained with high-resolution 3D images, convolutional neural networks resort to downsampling them or projecting them to 2D. We propose an effective alternative, a neural network that enables efficient classification of full-resolution 3D medical images. Compared to off-the-shelf convolutional neural networks, our network, 3D Globally-Aware Multiple Instance Classifier (3D-GMIC), uses 77.98%-90.05% less GPU memory and 91.23%-96.02% less computation. While it is trained only with image-level labels, without segmentation labels, it explains its predictions by providing pixel-level saliency maps. On a dataset collected at NYU Langone Health, including 85,526 patients with full-field 2D mammography (FFDM), synthetic 2D mammography, and 3D mammography, 3D-GMIC achieves an AUC of 0.831 (95% CI: 0.769-0.887) in classifying breasts with malignant findings using 3D mammography. This is comparable to the performance of GMIC on FFDM (0.816, 95% CI: 0.737-0.878) and synthetic 2D (0.826, 95% CI: 0.754-0.884), which demonstrates that 3D-GMIC successfully classified large 3D images despite focusing computation on a smaller percentage of its input compared to GMIC. Therefore, 3D-GMIC identifies and utilizes extremely small regions of interest from 3D images consisting of hundreds of millions of pixels, dramatically reducing associated computational challenges. 3D-GMIC generalizes well to BCS-DBT, an external dataset from Duke University Hospital, achieving an AUC of 0.848 (95% CI: 0.798-0.896).

Benjamin Stadnick, Jan Witowski, Vishwaesh Rajiv et al.

Artificial intelligence (AI) is showing promise in improving clinical diagnosis. In breast cancer screening, recent studies show that AI has the potential to improve early cancer diagnosis and reduce unnecessary workup. As the number of proposed models and their complexity grows, it is becoming increasingly difficult to re-implement them. To enable reproducibility of research and to enable comparison between different methods, we release a meta-repository containing models for classification of screening mammograms. This meta-repository creates a framework that enables the evaluation of AI models on any screening mammography data set. At its inception, our meta-repository contains five state-of-the-art models with open-source implementations and cross-platform compatibility. We compare their performance on seven international data sets. Our framework has a flexible design that can be generalized to other medical image analysis tasks. The meta-repository is available at https://www.github.com/nyukat/mammography_metarepository.

Kangning Liu, Yiqiu Shen, Nan Wu et al.

In the last few years, deep learning classifiers have shown promising results in image-based medical diagnosis. However, interpreting the outputs of these models remains a challenge. In cancer diagnosis, interpretability can be achieved by localizing the region of the input image responsible for the output, i.e. the location of a lesion. Alternatively, segmentation or detection models can be trained with pixel-wise annotations indicating the locations of malignant lesions. Unfortunately, acquiring such labels is labor-intensive and requires medical expertise. To overcome this difficulty, weakly-supervised localization can be utilized. These methods allow neural network classifiers to output saliency maps highlighting the regions of the input most relevant to the classification task (e.g. malignant lesions in mammograms) using only image-level labels (e.g. whether the patient has cancer or not) during training. When applied to high-resolution images, existing methods produce low-resolution saliency maps. This is problematic in applications in which suspicious lesions are small in relation to the image size. In this work, we introduce a novel neural network architecture to perform weakly-supervised segmentation of high-resolution images. The proposed model selects regions of interest via coarse-level localization, and then performs fine-grained segmentation of those regions. We apply this model to breast cancer diagnosis with screening mammography, and validate it on a large clinically-realistic dataset. Measured by Dice similarity score, our approach outperforms existing methods by a large margin in terms of localization performance of benign and malignant lesions, relatively improving the performance by 39.6% and 20.0%, respectively. Code and the weights of some of the models are available at https://github.com/nyukat/GLAM

Jakub Chłędowski, Adam Polak, Bartosz Szabucki et al.

Effective caching is crucial for the performance of modern-day computing systems. A key optimization problem arising in caching -- which item to evict to make room for a new item -- cannot be optimally solved without knowing the future. There are many classical approximation algorithms for this problem, but more recently researchers started to successfully apply machine learning to decide what to evict by discovering implicit input patterns and predicting the future. While machine learning typically does not provide any worst-case guarantees, the new field of learning-augmented algorithms proposes solutions that leverage classical online caching algorithms to make the machine-learned predictors robust. We are the first to comprehensively evaluate these learning-augmented algorithms on real-world caching datasets and state-of-the-art machine-learned predictors. We show that a straightforward method -- blindly following either a predictor or a classical robust algorithm, and switching whenever one becomes worse than the other -- has only a low overhead over a well-performing predictor, while competing with classical methods when the coupled predictor fails, thus providing a cheap worst-case insurance.

Tomasz Dwojak, Michał Pietruszka, Łukasz Borchmann et al.

This paper investigates various Transformer architectures on the WikiReading Information Extraction and Machine Reading Comprehension dataset. The proposed dual-source model outperforms the current state-of-the-art by a large margin. Next, we introduce WikiReading Recycled-a newly developed public dataset and the task of multiple property extraction. It uses the same data as WikiReading but does not inherit its predecessor's identified disadvantages. In addition, we provide a human-annotated test set with diagnostic subsets for a detailed analysis of model performance.

Tomasz Dwojak, Michał Pietruszka, Łukasz Borchmann et al.

In this paper, we investigate the Dual-source Transformer architecture on the WikiReading information extraction and machine reading comprehension dataset. The proposed model outperforms the current state-of-the-art by a large margin. Next, we introduce WikiReading Recycled - a newly developed public dataset, supporting the task of multiple property extraction. It keeps the spirit of the original WikiReading but does not inherit the identified disadvantages of its predecessor.