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Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening
Wu, Nan, Phang, Jason, Park, Jungkyu, Shen, Yiqiu, Huang, Zhe, Zorin, Masha, Jastrzębski, Stanisław, Févry, Thibault, Katsnelson, Joe, Kim, Eric, Wolfson, Stacey, Parikh, Ujas, Gaddam, Sushma, Lin, Leng Leng Young, Ho, Kara, Weinstein, Joshua D., Reig, Beatriu, Gao, Yiming, Toth, Hildegard, Pysarenko, Kristine, Lewin, Alana, Lee, Jiyon, Airola, Krystal, Mema, Eralda, Chung, Stephanie, Hwang, Esther, Samreen, Naziya, Kim, S. Gene, Heacock, Laura, Moy, Linda, Cho, Kyunghyun, Geras, Krzysztof J.
This paper makes several contributions. Among these, only 20-40% yield a diagnosis of cancer (5). The authors declare no conflict of interest. To whom correspondence should be addressed. Work done while visiting NYU. In the reader study, we compared the performance of our best model to that of radiologists and found our model to be as accurate as radiologists both in terms of area under ROC curve (AUC) and area under precision-recall curve (PRAUC). We also found that a hybrid model, taking the average of the probabilities of malignancy predicted by a radiologist and by our neural network, yields more accurate predictions than either of the two separately. This suggests that our network and radiologists learned different aspects of the task and that our model could be effective as a tool providing radiologists a second reader. With this contribution, research groups that are working on improving screening mammography, which may not have access to a large training dataset like ours, will be able to directly use our model in their research or to use our pretrained weights as an initialization to train models with less data. By making our models public, we invite other groups to validate our results and test their robustness to shifts in the data distribution. The dataset includes 229,426 digital screening mammography exams (1,001,093 images) from 141,473 patients. For each breast, we assign two binary labels: from biopsies. We have 5,832 exams with at least one biopsy the absence/presence of malignant findings in a breast, performed within 120 days of the screening mammogram. With Among these, biopsies confirmed malignant findings for 985 left and right breasts, each exam has a total of four binary (8.4%) breasts and benign findings for 5,556 (47.6%) breasts.
Adaptive Hard Thresholding for Near-optimal Consistent Robust Regression
Suggala, Arun Sai, Bhatia, Kush, Ravikumar, Pradeep, Jain, Prateek
We study the problem of robust linear regression with response variable corruptions. We consider the oblivious adversary model, where the adversary corrupts a fraction of the responses in complete ignorance of the data. We provide a nearly linear time estimator which consistently estimates the true regression vector, even with $1-o(1)$ fraction of corruptions. Existing results in this setting either don't guarantee consistent estimates or can only handle a small fraction of corruptions. We also extend our estimator to robust sparse linear regression and show that similar guarantees hold in this setting. Finally, we apply our estimator to the problem of linear regression with heavy-tailed noise and show that our estimator consistently estimates the regression vector even when the noise has unbounded variance (e.g., Cauchy distribution), for which most existing results don't even apply. Our estimator is based on a novel variant of outlier removal via hard thresholding in which the threshold is chosen adaptively and crucially relies on randomness to escape bad fixed points of the non-convex hard thresholding operation.
Kernel-based Translations of Convolutional Networks
Jones, Corinne, Roulet, Vincent, Harchaoui, Zaid
Convolutional Neural Networks, as most artificial neural networks, are commonly viewed as methods different in essence from kernel-based methods. We provide a systematic translation of Convolutional Neural Networks (ConvNets) into their kernel-based counterparts, Convolutional Kernel Networks (CKNs), and demonstrate that this perception is unfounded both formally and empirically. We show that, given a Convolutional Neural Network, we can design a corresponding Convolutional Kernel Network, easily trainable using a new stochastic gradient algorithm based on an accurate gradient computation, that performs on par with its Convolutional Neural Network counterpart. We present experimental results supporting our claims on landmark ConvNet architectures comparing each ConvNet to its CKN counterpart over several parameter settings.
Residual Deep Convolutional Neural Network for EEG Signal Classification in Epilepsy
Epilepsy is the fourth most common neurological disorder, affecting about 1% of the population at all ages. As many as 60% of people with epilepsy experience focal seizures which originate in a certain brain area and are limited to part of one cerebral hemisphere. In focal epilepsy patients, a precise surgical removal of the seizure onset zone can lead to effective seizure control or even a seizure-free outcome. Thus, correct identification of the seizure onset zone is essential. For clinical evaluation purposes, electroencephalography (EEG) recordings are commonly used. However, their interpretation is usually done manually by physicians and is time-consuming and error-prone. In this work, we propose an automated epileptic signal classification method based on modern deep learning methods. In contrast to previous approaches, the network is trained directly on the EEG recordings, avoiding hand-crafted feature extraction and selection procedures. This exploits the ability of deep neural networks to detect and extract relevant features automatically, that may be too complex or subtle to be noticed by humans. The proposed network structure is based on a convolutional neural network with residual connections. We demonstrate that our network produces state-of-the-art performance on two benchmark data sets, a data set from Bonn University and the Bern-Barcelona data set. We conclude that modern deep learning approaches can reach state-of-the-art performance on epileptic EEG classification and automated seizure onset zone identification tasks when trained on raw EEG data. This suggests that such approaches have potential for improving clinical practice.
IndyLSTMs: Independently Recurrent LSTMs
Gonnet, Pedro, Deselaers, Thomas
We introduce Independently Recurrent Long Short-term Memory cells: IndyLSTMs. These differ from regular LSTM cells in that the recurrent weights are not modeled as a full matrix, but as a diagonal matrix, i.e.\ the output and state of each LSTM cell depends on the inputs and its own output/state, as opposed to the input and the outputs/states of all the cells in the layer. The number of parameters per IndyLSTM layer, and thus the number of FLOPS per evaluation, is linear in the number of nodes in the layer, as opposed to quadratic for regular LSTM layers, resulting in potentially both smaller and faster models. We evaluate their performance experimentally by training several models on the popular \iamondb and CASIA online handwriting datasets, as well as on several of our in-house datasets. We show that IndyLSTMs, despite their smaller size, consistently outperform regular LSTMs both in terms of accuracy per parameter, and in best accuracy overall. We attribute this improved performance to the IndyLSTMs being less prone to overfitting.
Ensemble Clustering for Graphs: Comparisons and Applications
Poulin, Valérie, Théberge, François
We recently proposed a new ensemble clustering algorithm for graphs (ECG) based on the concept of consensus clustering. We validated our approach by replicating a study comparing graph clustering algorithms over benchmark graphs, showing that ECG outperforms the leading algorithms. In this paper, we extend our comparison by considering a wider range of parameters for the benchmark, generating graphs with different properties. We provide new experimental results showing that the ECG algorithm alleviates the well-known resolution limit issue, and that it leads to better stability of the partitions. We also illustrate how the ensemble obtained with ECG can be used to quantify the presence of community structure in the graph, and to zoom in on the sub-graph most closely associated with seed vertices. Finally, we illustrate further applications of ECG by comparing it to previous results for community detection on weighted graphs, and community-aware anomaly detection.
An Evaluation of Bitcoin Address Classification based on Transaction History Summarization
Lin, Yu-Jing, Wu, Po-Wei, Hsu, Cheng-Han, Tu, I-Ping, Liao, Shih-wei
Bitcoin is a cryptocurrency that features a distributed, decentralized and trustworthy mechanism, which has made Bitcoin a popular global transaction platform. The transaction efficiency among nations and the privacy benefiting from address anonymity of the Bitcoin network have attracted many activities such as payments, investments, gambling, and even money laundering in the past decade. Unfortunately, some criminal behaviors which took advantage of this platform were not identified. This has discouraged many governments to support cryptocurrency. Thus, the capability to identify criminal addresses becomes an important issue in the cryptocurrency network. In this paper, we propose new features in addition to those commonly used in the literature to build a classification model for detecting abnormality of Bitcoin network addresses. These features include various high orders of moments of transaction time (represented by block height) which summarizes the transaction history in an efficient way. The extracted features are trained by supervised machine learning methods on a labeling category data set. The experimental evaluation shows that these features have improved the performance of Bitcoin address classification significantly. We evaluate the results under eight classifiers and achieve the highest Micro-F1/Macro-F1 of 87%/86% with LightGBM.
NeuralHydrology - Interpreting LSTMs in Hydrology
Kratzert, Frederik, Herrnegger, Mathew, Klotz, Daniel, Hochreiter, Sepp, Klambauer, Günter
Despite the huge success of Long Short-Term Memory networks, their applications in environmental sciences are scarce. We argue that one reason is the difficulty to interpret the internals of trained networks. In this study, we look at the application of LSTMs for rainfall-runoff forecasting, one of the central tasks in the field of hydrology, in which the river discharge has to be predicted from meteorological observations. LSTMs are particularly well-suited for this problem since memory cells can represent dynamic reservoirs and storages, which are essential components in state-space modelling approaches of the hydrological system. On basis of two different catchments, one with snow influence and one without, we demonstrate how the trained model can be analyzed and interpreted. In the process, we show that the network internally learns to represent patterns that are consistent with our qualitative understanding of the hydrological system.
Adaptivity, Variance and Separation for Adversarial Bandits
Pogodin, Roman, Lattimore, Tor
We make three contributions to the theory of k-armed adversarial bandits. First, we prove a first-order bound for a modified variant of the INF strategy by Audibert and Bubeck [2009], without sacrificing worst case optimality or modifying the loss estimators. Second, we provide a variance analysis for algorithms based on follow the regularised leader, showing that without adaptation the variance of the regret is typically {\Omega}(n^2) where n is the horizon. Finally, we study bounds that depend on the degree of separation of the arms, generalising the results by Cowan and Katehakis [2015] from the stochastic setting to the adversarial and improving the result of Seldin and Slivkins [2014] by a factor of log(n)/log(log(n)).
Compressed Sensing: From Research to Clinical Practice with Data-Driven Learning
Cheng, Joseph Y., Chen, Feiyu, Sandino, Christopher, Mardani, Morteza, Pauly, John M., Vasanawala, Shreyas S.
Compressed sensing in MRI enables high subsampling factors while maintaining diagnostic image quality. This technique enables shortened scan durations and/or improved image resolution. Further, compressed sensing can increase the diagnostic information and value from each scan performed. Overall, compressed sensing has significant clinical impact in improving the diagnostic quality and patient experience for imaging exams. However, a number of challenges exist when moving compressed sensing from research to the clinic. These challenges include hand-crafted image priors, sensitive tuning parameters, and long reconstruction times. Data-driven learning provides a solution to address these challenges. As a result, compressed sensing can have greater clinical impact. In this tutorial, we will review the compressed sensing formulation and outline steps needed to transform this formulation to a deep learning framework. Supplementary open source code in python will be used to demonstrate this approach with open databases. Further, we will discuss considerations in applying data-driven compressed sensing in the clinical setting.