Despite a plethora of prior explorations, conducting text adversarial attacks in practical settings is still challenging with the following constraints: black box -- the inner structure of the victim model is unknown; hard label -- the attacker only has access to the top-1 prediction results; and semantic preservation - the perturbation needs to preserve the original semantics. In this paper, we present PAT, a novel adversarial attack method employed under all these constraints. Specifically, PAT explicitly models the adversarial and non-adversarial prototypes and incorporates them to measure semantic changes for replacement selection in the hard-label black-box setting to generate high-quality samples. In each iteration, PAT finds original words that can be replaced back and selects better candidate words for perturbed positions in a geometry-aware manner guided by this estimation, which maximally improves the perturbation construction and minimally impacts the original semantics. Extensive evaluation with benchmark datasets and state-of-the-art models shows that PAT outperforms existing text adversarial attacks in terms of both attack effectiveness and semantic preservation. Moreover, we validate the efficacy of PAT against industry-leading natural language processing platforms in real-world settings.

Health risk prediction is a challenge task that aims to predict whether patients would suffer from a certain disease/condition in the near future based on their historical EHR data. Although existing approaches can achieve better performance, none of them can deal with the noise existing in the EHR data explicitly. In this paper, we hypothesize that automatically removing noise from EHR data should help the models further improve the performance. Correspondingly, we propose a novel model named MedSkim, which is able to automatically rule out irrelevant visits and codes by effectively skimming through the EHR data. In particular, the proposed model has a code selection module that can directly make a skipping decision to each individual diagnosis codes and then remove the target-irrelevant ones. A backward probing RNN (BPRNN) is designed to reversely process the EHR data and provide a coarse grained representation learning for visits. Besides, a forward skipping RNN (FSRNN) is proposed to read the EHR in a preceding way and dynamically select important visits and codes based on the results of previous two modules. Finally, the risk prediction module uses the output hidden states from FSRNN for generating the final representation to make predictions. Additionally, we also design an extra regularization term based on the skip rate of the model and combine it with standard cross entropy loss to train the model in an end-to-end setting. Experimental results show that MedSkim achieves the best performance on three real-world datasets compared with the state-of-the-art baselines in terms of PR-AUC, F1 and Cohen’s Kappa. Moreover, the ablation study and case study confirm that the proposed MedSkim is reasonable and effective for removing noise from EHR data1.1The source code of the proposed MedSkim is available at https://github.com/SH-Src/MedSkim

Generating text adversarial examples in the hard-label setting is a more realistic and challenging black-box adversarial attack problem, whose challenge comes from the fact that gradient cannot be directly calculated from discrete word replacements. Consequently, the effectiveness of gradient-based methods for this problem still awaits improvement. In this paper, we propose a gradient-based optimization method named LeapAttack to craft high-quality text adversarial examples in the hard-label setting. To specify, LeapAttack employs the word embedding space to characterize the semantic deviation between the two words of each perturbed substitution by their difference vector. Facilitated by this expression, LeapAttack gradually updates the perturbation direction and constructs adversarial examples in an iterative round trip: firstly, the gradient is estimated by transforming randomly sampled word candidates to continuous difference vectors after moving the current adversarial example near the decision boundary; secondly, the estimated gradient is mapped back to a new substitution word based on the cosine similarity metric. Extensive experimental results show that in the general case LeapAttack can efficiently generate high-quality text adversarial examples with the highest semantic similarity and the lowest perturbation rate in the hard-label setting.

The broad adoption of electronic health record (EHR) systems and the advances of deep learning technology have motivated the development of health risk prediction models, which mainly depend on the expressiveness and temporal modeling capacity of deep neural networks (DNNs) to improve prediction performance. Some further augment the prediction by using external knowledge, however, a great deal of EHR information inevitably loses during the knowledge mapping. In addition, prediction made by existing models usually lacks reliable interpretation, which undermines their reliability in guiding clinical decision-making. To solve these challenges, we propose MedRetriever, an effective and flexible framework that leverages unstructured medical text collected from authoritative websites to augment health risk prediction as well as to provide understandable interpretation. Besides, MedRetriever explicitly takes the target disease documents into consideration, which provide key guidance for the model to learn in a target-driven direction, i.e., from the target disease to the input EHR. To specify, MedRetriever can flexibly choose its backbone from major predictive models to learn the EHR embedding for each visit. After that, the EHR embedding and features of target disease documents are aggregated into a query by self-attention to retrieve highly relevant text segments from the medical text pool, which is stored in the dynamically updated text memory. Finally, the comprehensive EHR embedding and the text memory are used for prediction and interpretation. We evaluate MedRetriever against nine state-of-the-art approaches across three real-world EHR datasets, which consistently achieves the best performance in AUC and recall metrics and outperforms the best baseline by at least 4.8% in recall on three test datasets. Furthermore, we conduct case studies to show the easy-to-understand interpretation by MedRetriever.

Thanks to the explosion of heterogeneous healthcare data and advanced machine learning and data mining techniques, specifically deep learning methods, we now have an opportunity to make difference in healthcare. In this tutorial, we will present state-of-the-art deep learning methods and their real-world applications, specifically focusing on exploring the unique characteristics of different types of healthcare data. The first half will be spent on introducing recent advances in mining structured healthcare data, including computational phenotyping, disease early detection/risk prediction and treatment recommendation. In the second half, we will focus on challenges specific to the unstructured healthcare data, and introduce advanced deep learning methods in automated ICD coding, understandable medical language translation, clinical trial mining, and medical report generation. This tutorial is intended for students, engineers and researchers who are interested in applying deep learning methods to healthcare, and prerequisite knowledge will be minimal. The tutorial will be concluded with open problems and a Q&A session.

The broad adoption of electronic health records (EHR) data and the availability of biomedical knowledge graphs (KGs) on the web have provided clinicians and researchers unprecedented resources and opportunities for conducting health risk predictions to improve healthcare quality and medical resource allocation. Existing methods have focused on improving the EHR feature representations using attention mechanisms, time-aware models, or external knowledge. However, they ignore the importance of using personalized information to make predictions. Besides, the reliability of their prediction interpretations needs to be improved since their interpretable attention scores are not explicitly reasoned from disease progression paths. In this paper, we propose MedPath to solve these challenges and augment existing risk prediction models with the ability to use personalized information and provide reliable interpretations inferring from disease progression paths. Firstly, MedPath extracts personalized knowledge graphs (PKGs) containing all possible disease progression paths from observed symptoms to target diseases from a large-scale online medical knowledge graph. Next, to augment existing EHR encoders for achieving better predictions, MedPath learns a PKG embedding by conducting multi-hop message passing from symptom nodes to target disease nodes through a graph neural network encoder. Since MedPath reasons disease progression by paths existing in PKGs, it can provide explicit explanations for the prediction by pointing out how observed symptoms can finally lead to target diseases. Experimental results on three real-world medical datasets show that MedPath is effective in improving the performance of eight state-of-the-art methods with higher F1 scores and AUCs. Our case study also demonstrates that MedPath can greatly improve the explicitness of the risk prediction interpretation.1

Risk prediction using electronic health records (EHR) is a challenging data mining task due to the two-level hierarchical structure of EHR data. EHR data consist of a set of time-ordered visits, and within each visit, there is a set of unordered diagnosis codes. Existing approaches focus on modeling temporal visits with deep neural network (DNN) techniques. However, they ignore the importance of modeling diagnosis codes within visits, and a lot of task-unrelated information within visits usually leads to unsatisfactory performance of existing approaches. To minimize the effect caused by noise information of EHR data, in this paper, we propose a novel DNN for risk prediction termed as LSAN, which consists of a Hierarchical Attention Module (HAM) and a Temporal Aggregation Module (TAM). Particularly, LSAN applies HAM to model the hierarchical structure of EHR data. Using the attention mechanism in the hierarchy of diagnosis code, HAM is able to retain diagnosis details and assign flexible attention weights to different diagnosis codes by their relevance to corresponding diseases. Moreover, the attention mechanism in the hierarchy of visit learns a comprehensive feature throughout the visit history by paying greater attention to visits with higher relevance. Based on the foundation laying by HAM, TAM uses a two-pathway structure to learn a robust temporal aggregation mechanism among all visits for LSAN. It extracts long-term dependencies by a Transformer encoder and short-term correlations by a parallel convolutional layer among different visits. With the construction of HAM and TAM, LSAN achieves the state-of-the-art performance on three real-world datasets with larger AUCs, recalls and F1 scores. Furthermore, the model analysis results demonstrate the effectiveness of the network construction with good interpretability and robustness of decision making by LSAN.

Deep learning methods especially recurrent neural network based models have demonstrated early success in disease risk prediction on longitudinal patient data. Existing works follow a strong assumption to implicitly assume the stationary disease progression during each time period, and thus, take a homogeneous way to decay the information from previous time steps for all patients. However,in reality, disease progression is non-stationary. Besides, the key time steps for a target disease vary among patients. To leverage time information for risk prediction in a more reasonable way, we propose a new hierarchical time-aware attention network, named HiTANet, which imitates the decision making process of doctors inrisk prediction. Particularly, HiTANet models time information in local and global stages. The local evaluation stage has a time aware Transformer that embeds time information into visit-level embed-ding and generates local attention weight for each visit. The global synthesis stage further adopts a time-aware key-query attention mechanism to assign global weights to different time steps. Finally, the two types of attention weights are dynamically combined to generate the patient representations for further risk prediction. We evaluate HiTANet on three real-world datasets. Compared with the best results among twelve competing baselines, HiTANet achieves over 7% in terms of F1 score on all datasets, which demonstrates the effectiveness of the proposed model and the necessity of modeling time information in risk prediction task.