Clinical trial analysis is one of the main business directions and services in IQVIA, and reviewing past similar studies is one of the most critical steps before starting a commercial clinical trial. The current review process is manual and time-consuming, requiring a clinical trial analyst to manually search through an extensive clinical trial database and then review all candidate studies. Therefore, it is of great interest to develop an automatic retrieval algorithm to select similar studies by giving new study information. To achieve this goal, we propose a novel group-based trial similarity learning network named GTSLNet, consisting of two kinds of similarity learning modules. The pair-wise section-level similarity learning module aims to compare the query trial and the candidate trial from the abstract semantic level via the proposed section transformer. Meanwhile, a word-level similarity learning module uses the word similarly matrix to capture the low-level similarity information. Additionally, an aggregation module combines these similarities. To address potential false negatives and noisy data, we introduce a variance-regularized group distance loss function. Experiment results show that the proposed GTSLNet significantly and consistently outperforms state-of-the-art baselines.

Clinical trials aim to study new tests and evaluate their effects on human health outcomes, which has a huge market size. However, carrying out clinical trials is expensive and time-consuming and often ends in no results. It will revolutionize clinical practice if we can develop an effective model to automatically estimate the status of a clinical trial and find out possible failure reasons. However, it is challenging to develop such a model because of the lack of a benchmark dataset. To address these challenges, in this paper, we first build a new dataset by extracting the publicly available clinical trial reports from ClinicalTrials.gov. The associated status of each report is treated as the status label. To analyze the failure reasons, domain experts help us manually annotate each failed report based on the description associated with it. More importantly, we examine several state-of-the-art text classification baselines on this task and find out that the unique format of the clinical trial protocols plays an essential role in affecting prediction accuracy, demonstrating the need for specially designed clinical trial classification models.

Predicting adverse drug reactions (ADRs) of drugs is one of the most critical steps in drug development. By pre-estimating the adverse reactions, researchers and drug development companies can greatly prevent the potential ADR risks and tragedies. However, the current ADR prediction methods suffer from several limitations. First, the prediction results are based on pure drug-related information, which makes them impossible to be directly applied for the personalized ADR prediction task. The lack of personalization of models also makes rare adverse events hard to be predicted. Therefore, it is of great interest to develop a new personalized ADR prediction method by introducing additional sources, e.g., patient health records. However, few methods have tried to use additional sources. In the meantime, the variety of different source formats and structures makes this task more challenging. To address the above challenges, we propose a novel personalized multi-sourced-based drug adverse reaction prediction model named pADR. pADR first works on every single source to transform them into proper representations. Next, a hierarchical multi-sourced Transformer is designed to automatically model the interactions between different sources and fuse them together for the final adverse event prediction. Experimental results on a new multi-sourced ADR prediction dataset show that PADR outperforms state-of-the-art drug-based baselines. Moreover, the case and ablation studies also illustrate the effectiveness of our proposed fusion strategies and the reasonableness of each module design.

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

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.

In this paper, we propose a multi-task learning approach for cross-modal image-text retrieval. First, a correlation network is proposed for relation recognition task, which helps learn the complicated relations and common information of different modalities. Then, we propose a correspondence cross-modal autoencoder for cross-modal input reconstruction task, which helps correlate the hidden representations of two uni-modal autoencoders. In addition, to further improve the performance of cross-modal retrieval, two regularization terms (variance and consistency constraints) are introduced to the cross-modal embeddings such that the learned common information has large variance and is modality invariant. Finally, to enable large-scale cross-modal similarity search, a flexible binary transform network is designed to convert the text and image embeddings into binary codes. Extensive experiments on two benchmark datasets demonstrate that our model has robust superiority over the compared strong baseline methods. Source code is available at \urlhttps://github.com/daerv/DAEVR.