Machine-Learning-Based Multiple Abnormality Prediction with Large-Scale Chest Computed Tomography Volumes

Machine learning models for radiology benefit from large-scale data sets with high quality labels for abnormalities. We curated and analyzed a chest computed tomography (CT) data set of 36,316 volumes from 19,993 unique patients. This is the largest multiply-annotated volumetric medical imaging data set reported. To annotate this data set, we developed a rule-based method for automatically extracting abnormality labels from free-text radiology reports with an average F-score of 0.976 (min 0.941, max 1.0). We also developed a model for multi-organ, multi-disease classification of chest CT volumes that uses a deep convolutional neural network (CNN). This model reached a classification performance of AUROC greater than 0.90 for 18 abnormalities, with an average AUROC of 0.773 for all 83 abnormalities, demonstrating the feasibility of learning from unfiltered whole volume CT data. We show that training on more labels improves performance significantly: for a subset of 9 labels - nodule, opacity, atelectasis, pleural effusion, consolidation, mass, pericardial effusion, cardiomegaly, and pneumothorax - the model's average AUROC increased by 10% when the number of training labels was increased from 9 to all 83. All code for volume preprocessing, automated label extraction, and the volume abnormality prediction model will be made publicly available. The 36,316 CT volumes and labels will also be made publicly available pending institutional approval.

Object Detection as a Positive-Unlabeled Problem

As with other deep learning methods, label quality is important for learning modern convolutional object detectors. However, the potentially large number and wide diversity of object instances that can be found in complex image scenes makes constituting complete annotations a challenging task; objects missing annotations can be observed in a variety of popular object detection datasets. These missing annotations can be problematic, as the standard cross-entropy loss employed to train object detection models treats classification as a positive-negative (PN) problem: unlabeled regions are implicitly assumed to be background. As such, any object missing a bounding box results in a confusing learning signal, the effects of which we observe empirically. To remedy this, we propose treating object detection as a positive-unlabeled (PU) problem, which removes the assumption that unlabeled regions must be negative. We demonstrate that our proposed PU classification loss outperforms the standard PN loss on PASCAL VOC and MS COCO across a range of label missingness, as well as on Visual Genome and DeepLesion with full labels.

Learning Autoencoders with Relational Regularization

A new algorithmic framework is proposed for learning autoencoders of data distributions. We minimize the discrepancy between the model and target distributions, with a \emph{relational regularization} on the learnable latent prior. This regularization penalizes the fused Gromov-Wasserstein (FGW) distance between the latent prior and its corresponding posterior, allowing one to flexibly learn a structured prior distribution associated with the generative model. Moreover, it helps co-training of multiple autoencoders even if they have heterogeneous architectures and incomparable latent spaces. We implement the framework with two scalable algorithms, making it applicable for both probabilistic and deterministic autoencoders. Our relational regularized autoencoder (RAE) outperforms existing methods, $e.g.$, the variational autoencoder, Wasserstein autoencoder, and their variants, on generating images. Additionally, our relational co-training strategy for autoencoders achieves encouraging results in both synthesis and real-world multi-view learning tasks.

Nested-Wasserstein Self-Imitation Learning for Sequence Generation

Reinforcement learning (RL) has been widely studied for improving sequence-generation models. However, the conventional rewards used for RL training typically cannot capture sufficient semantic information and therefore render model bias. Further, the sparse and delayed rewards make RL exploration inefficient. To alleviate these issues, we propose the concept of nested-Wasserstein distance for distributional semantic matching. To further exploit it, a novel nested-Wasserstein self-imitation learning framework is developed, encouraging the model to exploit historical high-rewarded sequences for enhanced exploration and better semantic matching. Our solution can be understood as approximately executing proximal policy optimization with Wasserstein trust-regions. Experiments on a variety of unconditional and conditional sequence-generation tasks demonstrate the proposed approach consistently leads to improved performance.

Toward Automatic Threat Recognition for Airport X-ray Baggage Screening with Deep Convolutional Object Detection

For the safety of the traveling public, the Transportation Security Administration (TSA) operates security checkpoints at airports in the United States, seeking to keep dangerous items off airplanes. At these checkpoints, the TSA employs a fleet of X-ray scanners, such as the Rapiscan 620DV, so Transportation Security Officers (TSOs) can inspect the contents of carry-on possessions. However, identifying and locating all potential threats can be a challenging task. As a result, the TSA has taken a recent interest in deep learning-based automated detection algorithms that can assist TSOs. In a collaboration funded by the TSA, we collected a sizable new dataset of X-ray scans with a diverse set of threats in a wide array of contexts, trained several deep convolutional object detection models, and integrated such models into the Rapiscan 620DV, resulting in functional prototypes capable of operating in real time. We show performance of our models on held-out evaluation sets, analyze several design parameters, and demonstrate the potential of such systems for automated detection of threats that can be found in airports.

Enhancing Cross-task Black-Box Transferability of Adversarial Examples with Dispersion Reduction

Neural networks are known to be vulnerable to carefully crafted adversarial examples, and these malicious samples often transfer, i.e., they remain adversarial even against other models. Although great efforts have been delved into the transferability across models, surprisingly, less attention has been paid to the cross-task transferability, which represents the real-world cybercriminal's situation, where an ensemble of different defense/detection mechanisms need to be evaded all at once. In this paper, we investigate the transferability of adversarial examples across a wide range of real-world computer vision tasks, including image classification, object detection, semantic segmentation, explicit content detection, and text detection. Our proposed attack minimizes the ``dispersion'' of the internal feature map, which overcomes existing attacks' limitation of requiring task-specific loss functions and/or probing a target model. We conduct evaluation on open source detection and segmentation models as well as four different computer vision tasks provided by Google Cloud Vision (GCV) APIs, to show how our approach outperforms existing attacks by degrading performance of multiple CV tasks by a large margin with only modest perturbations linf=16.

Graph-Driven Generative Models for Heterogeneous Multi-Task Learning

We propose a novel graph-driven generative model, that unifies multiple heterogeneous learning tasks into the same framework. The proposed model is based on the fact that heterogeneous learning tasks, which correspond to different generative processes, often rely on data with a shared graph structure. Accordingly, our model combines a graph convolutional network (GCN) with multiple variational autoencoders, thus embedding the nodes of the graph i.e., samples for the tasks) in a uniform manner while specializing their organization and usage to different tasks. With a focus on healthcare applications (tasks), including clinical topic modeling, procedure recommendation and admission-type prediction, we demonstrate that our method successfully leverages information across different tasks, boosting performance in all tasks and outperforming existing state-of-the-art approaches.

Syntax-Infused Transformer and BERT models for Machine Translation and Natural Language Understanding

Attention-based models have shown significant improvement over traditional algorithms in several NLP tasks. The Transformer, for instance, is an illustrative example that generates abstract representations of tokens inputted to an encoder based on their relationships to all tokens in a sequence. Recent studies have shown that although such models are capable of learning syntactic features purely by seeing examples, explicitly feeding this information to deep learning models can significantly enhance their performance. Leveraging syntactic information like part of speech (POS) may be particularly beneficial in limited training data settings for complex models such as the Transformer. We show that the syntax-infused Transformer with multiple features achieves an improvement of 0.7 BLEU when trained on the full WMT 14 English to German translation dataset and a maximum improvement of 1.99 BLEU points when trained on a fraction of the dataset. In addition, we find that the incorporation of syntax into BERT fine-tuning outperforms baseline on a number of downstream tasks from the GLUE benchmark.

Collaborative Filtering with A Synthetic Feedback Loop

We propose a novel learning framework for recommendation systems, assisting collaborative filtering with a synthetic feedback loop. The proposed framework consists of a "recommender" and a "virtual user." The recommender is formulizd as a collaborative-filtering method, recommending items according to observed user behavior. The virtual user estimates rewards from the recommended items and generates the influence of the rewards on observed user behavior. The recommender connected with the virtual user constructs a closed loop, that recommends users with items and imitates the unobserved feedback of the users to the recommended items. The synthetic feedback is used to augment observed user behavior and improve recommendation results. Such a model can be interpreted as the inverse reinforcement learning, which can be learned effectively via rollout (simulation). Experimental results show that the proposed framework is able to boost the performance of existing collaborative filtering methods on multiple datasets.