AMIA Summits on Translational Science Proceedings

We developed the Ochsner Emergency Department Overcrowding Scale (OEDOCS) to help us measure and respond to crowding among diverse-sized Emergency Departments (ED) within our network. Not satisfied with our current Emergency Department (ED) crowding score, we first surveyed our ED staff to report perceived crowding and then developed models to predict perceived crowding from our Electronic Health Record (EHR) data. Staff at two ED locations, one large and one small, were asked to report a perceived crowding level between 0-200 every four hours for over 3 months...

Kinship relationship estimation plays a significant role in today's genome studies. Since genetic data are mostly stored and protected in different silos, retrieving the desirable kinship relationships across federated data warehouses is a non-trivial problem. The ability to identify and connect related individuals is important for both research and clinical applications. In this work, we propose a new privacy-preserving kinship relationship estimation framework: Incremental Update Kinship Identification (INK)...

Intimate partner violence (IPV) involves physical, emotional, and sexual harm to the survivor. To characterize the relationship between mental health and IPV, we utilized electronic health records (EHR) data from IBM Explorys. Focusing on 15 mental health conditions and IPV, we queried cohorts of patients with these conditions to discover additional medical terms, including symptoms, findings, and diagnoses that are prevalent in these cohorts. We then systematically assessed the (i) direct association (co-occurrence, i...

Social media platforms are increasingly being used by intimate partner violence (IPV) victims to share experiences and seek support. If such information is automatically curated, it may be possible to conduct social media based surveillance and even design interventions over such platforms. In this paper, we describe the development of a supervised classification system that automatically characterizes IPV-related posts on the social network Reddit. We collected data from four IPV-related subreddits and manually annotated the data to indicate whether a post is a self-report of IPV or not...

The evidence is growing that machine and deep learning methods can learn the subtle differences between the language produced by people with various forms of cognitive impairment such as dementia and cognitively healthy individuals. Valuable public data repositories such as TalkBank have made it possible for researchers in the computational community to join forces and learn from each other to make significant advances in this area. However, due to variability in approaches and data selection strategies used by various researchers, results obtained by different groups have been difficult to compare directly...

Matrix-Assisted Laser Desorption Ionization mass spectrometry imaging (MALDI-MSI) is a mass spectrometry ionization technique that can be used to directly analyze tissues and has led the way in the development of biological and clinical applications for imaging mass spectrometry. One of its advantages is measuring the distribution of a large number of analytes at one time without destroying the sample, making it a useful method in tissue-based studies. However, analysis of the MALDI-MSI images from tissue microarrays (TMAs) remains less studied...

Early onset of seizure is a potential risk factor for Sudden Unexpected Death in Epilepsy (SUDEP). However, the first seizure onset information is often documented as clinical narratives in epilepsy monitoring unit (EMU) discharge summaries. Manually extracting first seizure onset time from discharge summaries is time consuming and labor-intensive. In this work, we developed a rule-based natural language processing pipeline for automatically extracting the temporal information of patients' first seizure onset from EMU discharge summaries...

Modeling with longitudinal electronic health record (EHR) data proves challenging given the high dimensionality, redundancy, and noise captured in EHR. In order to improve precision medicine strategies and identify predictors of disease risk in advance, evaluating meaningful patient disease trajectories is essential. In this study, we develop the algorithm D iseas E T rajectory f E ature extra CT ion ( DETECT) for feature extraction and trajectory generation in high-throughput temporal EHR data. This algorithm can 1) simulate longitudinal individual-level EHR data, specified to user parameters of scale, complexity, and noise and 2) use a convergent relative risk framework to test intermediate codes occurring between specified index code(s) and outcome code(s) to determine if they are predictive features of the outcome...

Advancements in technology have enabled diverse tools and medical devices that are able to improve the efficiency of diagnosis and detection of various health diseases. Rheumatoid arthritis is an autoimmune disease that affects multiple joints including the wrist, hands and feet. We used YOLOv5l6 to detect these joints in radiograph images. In this paper, we show that training YOLOv5l6 on joint images of healthy patients is able to achieve a high performance when used to evaluate joint images of patients with rheumatoid arthritis, even when there is a limited number of training samples...

Hotspotting may prevent high healthcare costs surrounding a minority of patients when void of issues such as availability, completeness, and accessibility of information in electronic health records (EHRs). We performed a descriptive study using Barnes-Jewish Hospital patients to assess the availability and accessibility of information that can predict negative outcomes. Manual electronic chart review produced descriptive statistics for a sample of 100 High Resource and 100 Control patient records. The majority of cases were not predictive...

Symptom information is primarily documented in free-text clinical notes and is not directly accessible for downstream applications. To address this challenge, information extraction approaches that can handle clinical language variation across different institutions and specialties are needed. In this paper, we present domain generalization for symptom extraction using pretraining and fine-tuning data that differs from the target domain in terms of institution and/or specialty and patient population. We extract symptom events using a transformer-based joint entity and relation extraction method...

Exposure to Intimate Partner Violence (IPV) has lasting adverse effects on the physical, behavioral, cognitive, and emotional health of survivors. To this end, it is critical to understand the effectiveness of IPV treatment strategies in reducing IPV and its debilitating effects. Meta-analyses designed to comprehensively describe the effectiveness of treatments offer unique advantages. However, the heterogeneity within and between studies poses challenges in interpreting findings. Meta-analyses are therefore unlikely to identify the factors that underlie disparities in treatment efficacy...

The 21st Century Cures Act allows the US Food and Drug Administration to consider real world data (RWD) for new indications or post approval study requirements. However, there is limited guidance as to the relative quality of different RWD types. The ACE-RWD program will compare the quality of EHR clinical data, EHR billing data, and linked healthcare claims data to traditional clinical trial data collection methods. ACE-RWD is being conducted alongside 5-10 ancillary studies, with five sponsors, across multiple therapeutic areas...

Advances in technology have made continuous/remote monitoring of digital health data possible, which can enable the early detection and treatment of age-related cognitive and health declines. Using Arksey and O'Malley's methodology, this scoping review evaluated potential barriers to the collection of mobile and wearable device data to monitor health and cognitive status in older adults with and without mild cognitive impairment (MCI). Selected articles were US based and focused on experienced or perceived barriers to the collection of mobile and wearable device data by adults 55 years of age or older...

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia in clinical practice and has a well-established association with coronary artery bypass graft (CABG) surgery. Being able to predict post-operative AF (POAF) may improve surgical outcomes. This study retrospectively assembled a large cohort of 3,807 first-time CABG patients with no prior AF to study factors that contribute to occurrence of POAF, in addition to testing models that may predict its incidence. Several clinical features with established relevance to POAF were extracted from the EHR, along with a record of medications administered intra-operatively...

Alzheimer's Disease (AD) is a multifactorial disease that shares common etiologies with its multiple comorbidities, especially vascular diseases. To predict repurposable drugs for AD utilizing the relatively well-investigated comorbidities' knowledge, we proposed a multi-task graph neural network (GNN)-based pipeline that incorporates the corresponding biomedical interactome of these diseases with their genetic markers and effective therapeutics. Our pipeline can accurately capture the interactions and disease classification in the network...

Exploring the neural basis of intelligence and the corresponding associations with brain network has been an active area of research in network neuroscience. Up to now, the majority of explorations mining human intelligence in brain connectomics leverages whole-brain functional connectivity patterns. In this study, structural connectivity patterns are instead used to explore relationships between brain connectivity and different behavioral/cognitive measures such as fluid intelligence. Specifically, we conduct a study using the 397 unrelated subjects from Human Connectome Project (Young Adults) dataset to estimate individual level structural connectivity matrices...

Self-controlled case series (SCCS) is a statistical method in epidemiological study design that uses individuals as their own controls, with comparisons made within the same individuals at different time points of observation. SCCS has been applied in settings where it is difficult to identify comparison or control groups. To provide computational support for SCCS, we introduce a query engine called Self-Controlled Case Query (SCCQ) and use it to extract cohorts of self-controlled case series from a large-scale COVID-19 Electronic Health Records (EHR) dataset...

Place-based exposures, termed "geomarkers", are powerful determinants of health but are often understudied because of a lack of open data and integration tools. Existing DeGAUSS (Decentralized Geomarker Assessment for Multisite Studies) software has been successfully implemented in multi-site studies, ensuring reproducibility and protection of health information. However, DeGAUSS relies on transporting geomarker data, which is not feasible for high-resolution spatiotemporal data too large to store locally or download over the internet...

Gender stereotyping is the practice of assigning or ascribing specific characteristics, differences, or identities to a person solely based on their gender. Biased conceptions of gender can create barriers to equality and need to be proactively identified and addressed. In biomedical education, letters of recommendation (LOR) are considered an important source for evaluating candidates' past performance. Because LOR is subjective and has no standard formatting requirements for the writer, potential language bias can be introduced...