Medical imaging is widely used in clinical practice for diagnosis and treatment. Report-writing can be error-prone for unexperienced physicians, and timeconsuming and tedious for experienced physicians. To address these issues, we study the automatic generation of medical imaging reports. This task presents several challenges. First, a complete report contains multiple heterogeneous forms of information, including findings and tags. Second, abnormal regions in medical images are difficult to identify. Third, the reports are typically long, containing multiple sentences. To cope with these challenges, we (1) build a multi-task learning framework which jointly performs the prediction of tags and the generation of paragraphs, (2) propose a co-attention mechanism to localize regions containing abnormalities and generate narrations for them, (3) develop a hierarchical LSTM model to generate long paragraphs. We demonstrate the effectiveness of the proposed methods on two publicly available datasets.

Combining deep neural networks with structured logic rules is desirable to harness flexibility and reduce uninterpretability of the neural models. We propose a general framework capable of enhancing various types of neural networks (e.g., CNNs and RNNs) with declarative first-order logic rules. Specifically, we develop an iterative distillation method that transfers the structured information of logic rules into the weights of neural networks. We deploy the framework on a CNN for sentiment analysis, and an RNN for named entity recognition. With a few highly intuitive rules, we obtain substantial improvements and achieve state-of-the-art or comparable results to previous best-performing systems.

We consider the problem of estimating a sparse multi-response regression function, with an application to expression quantitative trait locus (eQTL) mapping, where the goal is to discover genetic variations that influence gene-expression levels. In particular, we investigate a shrinkage technique capable of capturing a given hierarchical structure over the responses, such as a hierarchical clustering tree with leaf nodes for responses and internal nodes for clusters of related responses at multiple granularity, and we seek to leverage this structure to recover covariates relevant to each hierarchically-defined cluster of responses. We propose a tree-guided group lasso, or tree lasso, for estimating such structured sparsity under multi-response regression by employing a novel penalty function constructed from the tree. We describe a systematic weighting scheme for the overlapping groups in the tree-penalty such that each regression coefficient is penalized in a balanced manner despite the inhomogeneous multiplicity of group memberships of the regression coefficients due to overlaps among groups. For efficient optimization, we employ a smoothing proximal gradient method that was originally developed for a general class of structured-sparsity-inducing penalties. Using simulated and yeast data sets, we demonstrate that our method shows a superior performance in terms of both prediction errors and recovery of true sparsity patterns, compared to other methods for learning a multivariate-response regression.

We propose a family of statistical models for social network evolution over time, which represents an extension of Exponential Random Graph Models (ERGMs). Many of the methods for ERGMs are readily adapted for these models, including maximum likelihood estimation algorithms. We discuss models of this type and their properties, and give examples, as well as a demonstration of their use for hypothesis testing and classification. We believe our temporal ERG models represent a useful new framework for modeling time-evolving social networks, and rewiring networks from other domains such as gene regulation circuitry, and communication networks.

Coronavirus disease 2019 (COVID-19) has infected more than 1.3 million individuals all over the world and caused more than 106,000 deaths. One major hurdle in controlling the spreading of this disease is the inefficiency and shortage of medical tests. There have been increasing efforts on developing deep learning methods to diagnose COVID-19 based on CT scans. However, these works are difficult to reproduce and adopt since the CT data used in their studies are not publicly available. Besides, these works require a large number of CTs to train accurate diagnosis models, which are difficult to obtain. In this paper, we aim to address these two problems. We build a publicly-available dataset containing hundreds of CT scans positive for COVID-19 and develop sample-efficient deep learning methods that can achieve high diagnosis accuracy of COVID-19 from CT scans even when the number of training CT images are limited. Specifically, we propose an Self-Trans approach, which synergistically integrates contrastive self-supervised learning with transfer learning to learn powerful and unbiased feature representations for reducing the risk of overfitting. Extensive experiments demonstrate the superior performance of our proposed Self-Trans approach compared with several state-of-the-art baselines. Our approach achieves an F1 of 0.85 and an AUC of 0.94 in diagnosing COVID-19 from CT scans, even though the number of training CTs is just a few hundred.