In recent years, the landscape of digital biomedicine and healthcare has been reshaped due to the disruptive breakthroughs in AIfacilitated by tremendous data and high-performance computers, large language models (LLMs) have transformed information technology from accessing data to performing analytical tasks.While demonstrating unprecedented capabilities, LLMs have been found unreliable in tasks requiring factual knowledge and rigorous reasoning.Biomedicine and healthcare, as an important vertical domain rapidly benefitting from progress in AI, necessitates strict requirements on the accuracy, controllability, and interpretability of analytical models, posing critical challenges for LLMs.Despite recent studies addressing the hallucination problem of LLMs, research on empowering LLMs with the ability to plan, reason, and ground with explicit knowledge has also started to prosper, especially in the biomedicine and healthcare domain.On the other hand, biomedical data are enormous and notoriously complex, coming from various sources (e.g., biomedical knowledge bases, online literature, and hospitals) and bearing various modalities (e.g., tables, texts, images and time-series).Healthcare professionals have spent decades collecting, cleaning, and curating various types of data.The processes are extremely costly, producing various datasets with different data schemas, coding systems, and quality standards, many privately

KDD ’25, August 3–7, 2025, Toronto, ON, Canada

Synthesizing electronic health records (EHR) data has become a preferred strategy to address data scarcity, improve data quality, and model fairness in healthcare. However, existing approaches for EHR data generation predominantly rely on state-of-the-art generative techniques like generative adversarial networks, variational autoencoders, and language models. These methods typically replicate input visits, resulting in inadequate modeling of temporal dependencies between visits and overlooking the generation of time information, a crucial element in EHR data. Moreover, their ability to learn visit representations is limited due to simple linear mapping functions, thus compromising generation quality. To address these limitations, we propose a novel EHR data generation model called EHRPD. It is a diffusion-based model designed to predict the next visit based on the current one while also incorporating time interval estimation. To enhance generation quality and diversity, we introduce a novel time-aware visit embedding module and a pioneering predictive denoising diffusion probabilistic model (P-DDPM). Additionally, we devise a predictive U-Net (PU-Net) to optimize P-DDPM. We conduct experiments on two public datasets and evaluate EHRPD from fidelity, privacy, and utility perspectives. The experimental results demonstrate the efficacy and utility of the proposed EHRPD in addressing the aforementioned limitations and advancing EHR data generation.

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.

A comprehensive patient health history is essential for patient care and healthcare research. However, due to the distributed nature of healthcare services, patient health records are often scattered across multiple systems. Existing record linkage approaches primarily rely on patient identifiers, which have inherent limitations such as privacy invasion and identifier discrepancies. To tackle this problem, we propose linking de-identified patient health records by matching health patterns without strictly relying on sensitive patient identifiers. Our model MedLink solves two challenges faced with the patient linkage task: (1) the challenge of identifying the same patients based on data collected in different timelines as disease progression makes the record matching difficult, and (2) the challenge of identifying distinct health patterns as common medical codes dominate health records and overshadow the more informative low-prevalence codes. To address these challenges, MedLink utilizes bi-directional health prediction to predict future codes forwardly and past codes backwardly, thus accounting for the health progression. MedLink also has a prevalence-aware retrieval design to focus more on the low-prevalence but informative codes during learning. MedLink can be trained end-to-end and is lightweight for efficient inference on large patient databases. We evaluate MedLink against leading baselines on real-world patient datasets, including the critical care dataset MIMIC-III and a large health claims dataset. Results show that MedLink outperforms the best baseline by 4% in top-1 accuracy with only 8% memory cost. Additionally, when combined with existing identifier-based linkage approaches, MedLink can improve their performance by up to 15%.

Population-level disease prediction estimates the number of potential patients of particular diseases in some location at a future time based on (frequently updated) historical disease statistics. Existing approaches often assume the existing disease statistics are reliable and will not change. However, in practice, data collection is often time-consuming and has time delays, with both historical and current disease statistics being updated continuously. In this work, we propose a real-time population-level disease prediction model which captures data latency (PopNet) and incorporates the updated data for improved predictions. To achieve this goal, PopNet models real-time data and updated data using two separate systems, each capturing spatial and temporal effects using hybrid graph attention networks and recurrent neural networks. PopNet then fuses the two systems using both spatial and temporal latency-aware attentions in an end-to-end manner. We evaluate PopNet on real-world disease datasets and show that PopNet consistently outperforms all baseline disease prediction and general spatial-temporal prediction models, achieving up to 47% lower root mean squared error and 24% lower mean absolute error compared with the best baselines.

The goal of molecular optimization is to generate molecules similar to a target molecule but with better chemical properties. Deep generative models have shown great success in molecule optimization. However, due to the iterative local generation process of deep generative models, the resulting molecules can significantly deviate from the input in molecular similarity and size, leading to poor chemical properties. The key issue here is that the existing deep generative models restrict their attention on substructure-level generation without considering the entire molecule as a whole. To address this challenge, we propose Molecule-Level Reward functions (MOLER) to encourage (1) the input and the generated molecule to be similar, and to ensure (2) the generated molecule has a similar size to the input. The proposed method can be combined with various deep generative models. Policy gradient technique is introduced to optimize reward-based objectives with small computational overhead. Empirical studies show that MOLER achieves up to 20.2% relative improvement in success rate over the best baseline method on several properties, including QED, DRD2 and LogP.

There is a growing interest in applying deep learning (DL) to healthcare, driven by the availability of data with multiple feature channels inrich-dataenvironments (e.g., intensive care units). However, in many other practical situations, we can only access data with much fewer feature channels in apoor-dataenvironments (e.g., at home), which often results in predictive models with poor performance. How can we boost the performance of models learned from suchpoor-dataenvironment by leveraging knowledge extracted from existing models trained usingrich datain a related environment? To address this question, we develop a knowledge infusion framework namedCHEERthat can succinctly summarize suchrich modelinto transferable representations, which can be incorporated into thepoor modelto improve its performance. The infused model is analyzed theoretically and evaluated empirically on several datasets. Our empirical results showed thatCHEERoutperformed baselines by 5.60 to 46.80 percent in terms of the macro-F1 score on multiple physiological datasets.

We propose CUP, a new method for compressing and accelerating deep neural networks. At its core, CUP achieves compression by clustering and pruning similar filters in each layer. For clustering, CUP uses hierarchical clustering which allows for an elegant parameterization of model capacity through a single hyper-parameter t. We observe that by increasing t, CUP can dynamically reduce model capacity through non-uniform layer-wise pruning leading to two advantages. First, CUP can effectively compress a model to within the desired compute budget through a simple line-search on t. Second, through a simple extension, CUP can obtain the pruned model in a single training pass leading to large savings in training time. On Imagenet, CUP leads to a 2.47× FLOPS reduction on Resnet-50 with less than 1% drop in top-5 accuracy. Notably, in the retrain-free setting, CUP-RF saves over 10 hours of training time on 3 GPUs, in comparison to state-of-the-art methods. The code for CUP is open sourced1.

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.

Drug discovery aims at finding promising drug molecules for treating target diseases. Existing computational drug discovery methods mainly depend on molecule databases, ignoring valuable data collected from clinical trials. In this work, we propose PRIME to leverage high-quality drug molecules and drug-disease relations in historical clinical trials to narrow down the molecular search space in drug discovery. PRIME also introduces time dependency constraints to model evolving drug-disease relations using a probabilistic deep learning model that can quantify model uncertainty. We evaluated PRIME against leading models on both de novo design and drug repurposing tasks. Results show that compared with the best baselines, PRIME achieves 25.9% relative improvement (i.e., reduction) in average hit-ranking on drug repurposing and 47.6% relative improvement in success rate on de novo design.

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.

Existing tensor completion formulation mostly relies on partial observations from a single tensor. However, tensors extracted from real-world data often are more complex due to: (i) Partial observation: Only a small subset of tensor elements are available. (ii) Coarse observation: Some tensor modes only present coarse and aggregated patterns (e.g., monthly summary instead of daily reports). In this paper, we are given a subset of the tensor and some aggregated/coarse observations (along one or more modes) and seek to recover the original fine-granular tensor with low-rank factorization. We formulate a coupled tensor completion problem and propose an efficient Multi-resolution Tensor Completion model (MTC) to solve the problem. Our MTC model explores tensor mode properties and leverages the hierarchy of resolutions to recursively initialize an optimization setup, and optimizes on the coupled system using alternating least squares. MTC ensures low computational and space complexity. We evaluate our model on two COVID-19 related spatio-temporal tensors. The experiments show that MTC could provide 65.20% and 75.79% percentage of fitness (PoF) in tensor completion with only 5% fine granular observations, which is 27.96% relative improvement over the best baseline. To evaluate the learned low-rank factors, we also design a tensor prediction task for daily and cumulative disease case predictions, where MTC achieves 50% in PoF and 30% relative improvements over the best baseline.

Successful health risk prediction demands accuracy and reliability of the model. Existing predictive models mainly depend on mining electronic health records (EHR) with advanced deep learning techniques to improve model accuracy. However, they all ignore the importance of publicly available online health data, especially socioeconomic status, environmental factors, and detailed demographic information for each location, which are all strong predictive signals and can definitely augment precision medicine. To achieve model reliability, the model needs to provide accurate prediction and uncertainty score of the prediction. However, existing uncertainty estimation approaches often failed in handling high-dimensional data, which are present in multi-sourced data.

This paper presents an active distillation method for a local institution (e.g., hospital) to find the best queries within its given budget to distill an on-server black-box model’s predictive knowledge into a local surrogate with transparent parameterization. This allows local institutions to understand better the predictive reasoning of the black-box model in its own local context or to further customize the distilled knowledge with its private dataset that cannot be centralized and fed into the server model. The proposed method thus addresses several challenges of deploying machine learning (ML) in many industrial settings (e.g., healthcare analytics) with strong proprietary constraints. These include: (1) the opaqueness of the server model’s architecture which prevents local users from understanding its predictive reasoning in their local data contexts; (2) the increasing cost and risk of uploading local data on the cloud for analysis; and (3) the need to customize the server model with private onsite data. We evaluated the proposed method on both benchmark and real-world healthcare data where significant improvements over existing local distillation methods were observed. A theoretical analysis of the proposed method is also presented.

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

Clinical narratives that describe complex medical events are often accompanied by meta-information such as a patient’s demographics, diagnoses and medications. This structured information implicitly relates to the logical and semantic structure of the entire narrative, and thus affects vocabulary choices for the narrative composition. To leverage this meta-information, we propose a supervised topic compositional neural language model, called MeTRNN, that integrates the strength of supervised topic modeling in capturing global semantics with the capacity of contextual recurrent neural networks (RNN) in modeling local word dependencies. MeTRNN generates interpretable topics from global meta-information and uses them to facilitate contextual RNNs in modeling local dependencies of text. For efficient training of MeTRNN, we develop an autoencoding variational Bayes inference method. We evaluate MeTRNN on the word prediction tasks using public text datasets. MeTRNN consistently outperforms all baselines across all datasets in perplexity ranging from 5% to 40%. Our case studies on real world electronic health records (EHR) data show that MeTRNN can learn and benefit from meaningful topics.

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.

Clinical trials play important roles in drug development but often suffer from expensive, inaccurate and insufficient patient recruitment. The availability of massive electronic health records (EHR) data and trial eligibility criteria (EC) bring a new opportunity to data driven patient recruitment. One key task named patient-trial matching is to find qualified patients for clinical trials given structured EHR and unstructured EC text (both inclusion and exclusion criteria). How to match complex EC text with longitudinal patient EHRs? How to embed many-to-many relationships between patients and trials? How to explicitly handle the difference between inclusion and exclusion criteria? In this paper, we proposed CrOss-Modal PseudO-SiamEse network (COMPOSE) to address these challenges for patient-trial matching. One path of the network encodes EC using convolutional highway network. The other path processes EHR with multi-granularity memory network that encodes structured patient records into multiple levels based on medical ontology. Using the EC embedding as query, COMPOSE performs attentional record alignment and thus enables dynamic patient-trial matching. COMPOSE also introduces a composite loss term to maximize the similarity between patient records and inclusion criteria while minimize the similarity to the exclusion criteria. Experiment results show COMPOSE can reach 98.0% AUC on patient-criteria matching and 83.7% accuracy on patient-trial matching, which leads 24.3% improvement over the best baseline on real-world patient-trial matching tasks.

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.

Generating clinical reports from raw recordings such as X-rays and electroencephalogram (EEG) is an essential and routine task for doctors. However, it is often time-consuming to write accurate and detailed reports. Most existing methods try to generate the whole reports from the raw input with limited success because 1) generated reports often contain errors that need manual review and correction, 2) it does not save time when doctors want to write additional information into the report, and 3) the generated reports are not customized based on individual doctors’ preference. We propose CLinicAl Report Auto-completion (, an interactive method that generates reports in a sentence by sentence fashion based on doctors’ anchor words and partially completed sentences. earches for most relevant sentences from existing reports as the template for the current report. The retrieved sentences are sequentially modified by combining with the input feature representations to create the final report. In our experimental evaluation chieved 0.393 CIDEr and 0.248 BLEU-4 on X-ray reports and 0.482 CIDEr and 0.491 BLEU-4 for EEG reports for sentence-level generation, which is up to 35% improvement over the best baseline. Also via our qualitative evaluation, s shown to produce reports which have a significantly higher level of approval by doctors in a user study (3.74 out of 5 for s 2.52 out of 5 for the baseline).

In recent years, significant attention has been devoted towards integrating deep learning technologies in the healthcare domain. However, to safely and practically deploy deep learning models for home health monitoring, two significant challenges must be addressed: the models should be (1) robust against noise; and (2) compact and energy-efficient. We propose Rest , a new method that simultaneously tackles both issues via 1) adversarial training and controlling the Lipschitz constant of the neural network through spectral regularization while 2) enabling neural network compression through sparsity regularization. We demonstrate that Rest produces highly-robust and efficient models that substantially outperform the original full-sized models in the presence of noise. For the sleep staging task over single-channel electroencephalogram (EEG), the Rest model achieves a macro-F1 score of 0.67 vs. 0.39 achieved by a state-of-the-art model in the presence of Gaussian noise while obtaining 19 × parameter reduction and 15 × MFLOPS reduction on two large, real-world EEG datasets. By deploying these models to an Android application on a smartphone, we quantitatively observe that Rest allows models to achieve up to 17 × energy reduction and 9 × faster inference. We open source the code repository with this paper: https://github.com/duggalrahul/REST.

Deep learning has demonstrated success in health risk prediction especially for patients with chronic and progressing conditions. Most existing works focus on learning disease patterns from longitudinal patient data, but pay little attention to the disease progression stage itself. To fill the gap, we propose a Stage-aware neural Network (StageNet) model to extract disease stage information from patient data and integrate it into risk prediction. StageNet is enabled by (1) a stage-aware long short-term memory (LSTM) module that extracts health stage variations unsupervisedly; (2) a stage-adaptive convolutional module that incorporates stage-related progression patterns into risk prediction. We evaluate StageNet on two real-world datasets and show that StageNet outperforms state-of-the-art models in risk prediction task and patient subtyping task. Compared to the best baseline model, StageNet achieves up to 12% higher AUPRC for risk prediction task on two real-world patient datasets. StageNet also achieves over 58% higher Calinski-Harabasz score (a cluster quality metric) for a patient subtyping task.

Clinical trials are essential for drug development but often suffer from expensive, inaccurate and insufficient patient recruitment. The core problem of patient-trial matching is to find qualified patients for a trial, where patient information is stored in electronic health records (EHR) while trial eligibility criteria (EC) are described in text documents available on the web. How to represent longitudinal patient EHR? How to extract complex logical rules from EC? Most existing works rely on manual rule-based extraction, which is time consuming and inflexible for complex inference. To address these challenges, we proposed a cross-modal inference learning model to jointly encode enrollment criteria (text) and patients records (tabular data) into a shared latent space for matching inference. pplies a pre-trained Bidirectional Encoder Representations from Transformers(BERT) model to encode clinical trial information into sentence embedding. And uses a hierarchical embedding model to represent patient longitudinal EHR. In addition, s augmented by a numerical information embedding and entailment module to reason over numerical information in both EC and EHR. These encoders are trained jointly to optimize patient-trial matching score. We evaluated n the trial-patient matching task with demonstrated on real world datasets. utperformed the best baseline by up to 12.4% in average F1.

Knowledge transfer has been of great interest in current machine learning research, as many have speculated its importance in modeling the human ability to rapidly generalize learned models to new scenarios. Particularly in cases where training samples are limited, knowledge transfer shows improvement on both the learning speed and generalization performance of related tasks. Recently, Learning Using Privileged Information (LUPI) has presented a new direction in knowledge transfer by modeling the transfer of prior knowledge as a Teacher-Student interaction process. Under LUPI, a Teacher model uses Privileged Information (PI) that is only available at training time to improve the sample complexity required to train a Student learner for a given task. In this work, we present a LUPI formulation that allows privileged information to be retained in a multi-task learning setting. We propose a novel feature matching algorithm that projects samples from the original feature space and the privilege information space into a joint latent space in a way that informs similarity between training samples. Our experiments show that useful knowledge from PI is maintained in the latent space and greatly improves the sample efficiency of other related learning tasks. We also provide an analysis of sample complexity of the proposed LUPI method, which under some favorable assumptions can achieve a greater sample efficiency than brute force methods.

In silico modeling of medicine refers to the direct use of computational methods in support of drug discovery and development. Machine learning and data mining methods have become an integral part of in silico modeling and demonstrated promising performance at various phases of the drug discovery and development process. In this tutorial we will introduce data analytic methods in drug discovery and development. For the first half, we will provide an overview about related data and analytic tasks, and then present the enabling data analytic methods for these tasks. For the second half, we will describe concrete applications of each of those tasks. The tutorial will be concluded with open problems and a Q&A session.

Although deep learning models trained on electronic health records (EHR) data have shown state-of-the-art performance in many predictive clinical tasks, the discovery of adversarial examples (i.e., input data that are engineered to cause misclassification) has exposed vulnerabilities with lab and imaging data. We specifically consider adversarial examples with longitudinal EHR data, an area that has not been previously examined because of the challenges with temporal high-dimensional and sparse features. We propose Longitudinal AdVersarial Attack (, a saliency score based adversarial example using a method that requires a minimal number of perturbations and that automatically minimizes the likelihood of detection. Features are selected and modified by jointly modeling a saliency map and attention mechanism. Experimental results with longitudinal EHR data show that an substantially reduce model performance for attention-based target models (from AUPR = 0.5 to AUPR = 0.08).

Heterogeneous hyper-networks is used to represent multi-modal and composite interactions between data points. In such networks, several different types of nodes form a hyperedge. Heterogeneous hyper-network embedding learns a distributed node representation under such complex interactions while preserving the network structure. However, this is a challenging task due to the multiple modalities and composite interactions. In this study, a deep approach is proposed to embed heterogeneous attributed hyper-networks with complicated and non-linear node relationships. In particular, a fully-connected and graph convolutional layers are designed to project different types of nodes into a common low-dimensional space, a tuple-wise similarity function is proposed to preserve the network structure, and a ranking based loss function is used to improve the similarity scores of hyperedges in the embedding space. The proposed approach is evaluated on synthetic and real world datasets and a better performance is obtained compared with baselines.

Leveraging massive electronic health records (EHR) brings tremendous promises to advance clinical and precision medicine informatics research. However, it is very challenging to directly work with multifaceted patient information encoded in their EHR data. Deriving effective representations of patient EHRs is a crucial step to bridge raw EHR information and the endpoint analytical tasks, such as risk prediction or disease subtyping. In this paper, we propose Health-ATM, a novel and integrated deep architecture to uncover patients' comprehensive health information from their noisy, longitudinal, heterogeneous and irregular EHR data. Health-ATM extracts comprehensive multifaceted patient information patterns with attentive and time-aware modulars (ATM) and a hybrid network structure composed of both Recurrent Neural Network (RNN) and Convolutional Neural Network (CNN). The learned features are finally fed into a prediction layer to conduct the risk prediction task. We evaluated the Health-ATM on both artificial and real world EHR corpus and demonstrated its promising utility and efficacy on representation learning and disease onset predictions.

In the study of various diseases, heterogeneity among patients usually leads to different progression patterns and may require different types of therapeutic intervention. Therefore, it is important to study patient subtyping, which is grouping of patients into disease characterizing subtypes. Subtyping from complex patient data is challenging because of the information heterogeneity and temporal dynamics. Long-Short Term Memory (LSTM) has been successfully used in many domains for processing sequential data, and recently applied for analyzing longitudinal patient records. The LSTM units are designed to handle data with constant elapsed times between consecutive elements of a sequence. Given that time lapse between successive elements in patient records can vary from days to months, the design of traditional LSTM may lead to suboptimal performance. In this paper, we propose a novel LSTM unit called Time-Aware LSTM (T-LSTM) to handle irregular time intervals in longitudinal patient records. We learn a subspace decomposition of the cell memory which enables time decay to discount the memory content according to the elapsed time. We propose a patient subtyping model that leverages the proposed T-LSTM in an auto-encoder to learn a powerful single representation for sequential records of patients, which are then used to cluster patients into clinical subtypes. Experiments on synthetic and real world datasets show that the proposed T-LSTM architecture captures the underlying structures in the sequences with time irregularities.

Parkinson's disease (PD) is a chronic disease that develops over years and varies dramatically in its clinical manifestations. A preferred strategy to resolve this heterogeneity and thus enable better prognosis and targeted therapies is to segment out more homogeneous patient sub-populations. However, it is challenging to evaluate the clinical similarities among patients because of the longitudinality and temporality of their records. To address this issue, we propose a deep model that directly learns patient similarity from longitudinal and multi-modal patient records with an Recurrent Neural Network (RNN) architecture, which learns the similarity between two longitudinal patient record sequences through dynamically matching temporal patterns in patient sequences. Evaluations on real world patient records demonstrate the promising utility and efficacy of the proposed architecture in personalized predictions.