MOTIVATION: Electronic health records (EHRs) represent a comprehensive resource of a patient's medical history. EHRs are essential for utilizing advanced technologies such as deep learning (DL), enabling healthcare providers to analyze extensive data, extract valuable insights, and make precise and data-driven clinical decisions. DL methods such as recurrent neural networks (RNN) have been utilized to analyze EHR to model disease progression and predict diagnosis. However, these methods do not address some inherent irregularities in EHR data such as irregular time intervals between clinical visits. Furthermore, most DL models are not interpretable. In this study, we propose two interpretable DL architectures based on RNN, namely time-aware RNN (TA-RNN) and TA-RNN-autoencoder (TA-RNN-AE) to predict patient's clinical outcome in EHR at the next visit and multiple visits ahead, respectively. To mitigate the impact of irregular time intervals, we propose incorporating time embedding of the elapsed times between visits. For interpretability, we propose employing a dual-level attention mechanism that operates between visits and features within each visit. RESULTS: The results of the experiments conducted on Alzheimer's Disease Neuroimaging Initiative (ADNI) and National Alzheimer's Coordinating Center (NACC) datasets indicated the superior performance of proposed models for predicting Alzheimer's Disease (AD) compared to state-of-the-art and baseline approaches based on F2 and sensitivity. Additionally, TA-RNN showed superior performance on the Medical Information Mart for Intensive Care (MIMIC-III) dataset for mortality prediction. In our ablation study, we observed enhanced predictive performance by incorporating time embedding and attention mechanisms. Finally, investigating attention weights helped identify influential visits and features in predictions. AVAILABILITY AND IMPLEMENTATION: https://github.com/bozdaglab/TA-RNN.

MOTIVATION: Alzheimer's disease (AD) is a neurodegenerative disease that affects millions of people worldwide. Mild cognitive impairment (MCI) is an intermediary stage between cognitively normal state and AD. Not all people who have MCI convert to AD. The diagnosis of AD is made after significant symptoms of dementia such as short-term memory loss are already present. Since AD is currently an irreversible disease, diagnosis at the onset of the disease brings a huge burden on patients, their caregivers, and the healthcare sector. Thus, there is a crucial need to develop methods for the early prediction AD for patients who have MCI. Recurrent neural networks (RNN) have been successfully used to handle electronic health records (EHR) for predicting conversion from MCI to AD. However, RNN ignores irregular time intervals between successive events which occurs common in electronic health record data. In this study, we propose two deep learning architectures based on RNN, namely Predicting Progression of Alzheimer's Disease (PPAD) and PPAD-Autoencoder. PPAD and PPAD-Autoencoder are designed for early predicting conversion from MCI to AD at the next visit and multiple visits ahead for patients, respectively. To minimize the effect of the irregular time intervals between visits, we propose using age in each visit as an indicator of time change between successive visits. RESULTS: Our experimental results conducted on Alzheimer's Disease Neuroimaging Initiative and National Alzheimer's Coordinating Center datasets showed that our proposed models outperformed all baseline models for most prediction scenarios in terms of F2 and sensitivity. We also observed that the age feature was one of top features and was able to address irregular time interval problem. AVAILABILITY AND IMPLEMENTATION: https://github.com/bozdaglab/PPAD.

While machine learning technologies have been remarkably advanced over the past several years, one of the fundamental requirements for the success of learning-based approaches would be the availability of high-quality data that thoroughly represent individual classes in a problem space. Unfortunately, it is not uncommon to observe a significant degree of class imbalance with only a few instances for minority classes in many datasets, including network traffic traces highly skewed toward a large number of normal connections while very small in quantity for attack instances. A well-known approach to addressing the class imbalance problem is data augmentation that generates synthetic instances belonging to minority classes. However, traditional statistical techniques may be limited since the extended data through statistical sampling should have the same density as original data instances with a minor degree of variation. This paper takes a learning-based approach to data augmentation to enable effective network anomaly detection. One of the critical challenges for the learning-based approach is the mode collapse problem resulting in a limited diversity of samples, which was also observed from our preliminary experimental result. To this end, we present a novel "Divide-Augment-Combine" (DAC) strategy, which groups the instances based on their characteristics and augments data on a group basis to represent a subset independently using a generative adversarial model. Our experimental results conducted with two recently collected public network datasets (UNSW-NB15 and IDS-2017) show that the proposed technique enhances performances up to 21.5% for identifying network anomalies.