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Results from Randomized Controlled Trials (RCTs) establish the comparative effectiveness of interventions, and are in turn critical inputs for evidence-based care. However, results from RCTs are presented in (often unstructured) natural…
The recent adoption of Electronic Health Records (EHRs) by health care providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in…
Within the intensive care unit (ICU), a wealth of patient data, including clinical measurements and clinical notes, is readily available. This data is a valuable resource for comprehending patient health and informing medical decisions, but…
Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on…
This paper addresses the challenges posed by the unstructured nature and high-dimensional semantic complexity of electronic health record texts. A deep learning method based on attention mechanisms is proposed to achieve unified modeling…
To reduce the large amount of time spent screening, identifying, and recruiting patients into clinical trials, we need prescreening systems that are able to automate the data extraction and decision-making tasks that are typically relegated…
Background: Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors…
Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden,…
Extracting relevant information from medical conversations and providing it to doctors and patients might help in addressing doctor burnout and patient forgetfulness. In this paper, we focus on extracting the Medication Regimen (dosage and…
This study introduces a novel teacher-student architecture utilizing Large Language Models (LLMs) to improve prostate cancer radiotherapy symptom extraction from clinical notes. Mixtral, the student model, initially extracts symptoms,…
A core component of precision medicine research involves optimizing individualized treatment rules (ITRs) based on patient characteristics. Many studies used to estimate ITRs are longitudinal in nature, collecting outcomes over time. Yet,…
Timing of clinical events is central to characterization of patient trajectories, enabling analyses such as process tracing, forecasting, and causal reasoning. However, structured electronic health records capture few data elements critical…
Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency,…
In this work we addressed the problem of capturing sequential information contained in longitudinal electronic health records (EHRs). Clinical notes, which is a particular type of EHR data, are a rich source of information and practitioners…
The Interaction between Drugs and Targets (DTI) in human body plays a crucial role in biomedical science and applications. As millions of papers come out every year in the biomedical domain, automatically discovering DTI knowledge from…
A common practice in the medical industry is the use of clinical notes, which consist of detailed patient observations. However, electronic health record systems frequently do not contain these observations in a structured format, rendering…
We extended dynamic time warping (DTW) into interval-based dynamic time warping (iDTW), including (A) interval-based representation (iRep): [1] abstracting raw, time-stamped data into interval-based abstractions, [2] comparison-period…
This report describes a minimalistic set of methods engineered to anchor clinical events onto a temporal space. Specifically, we describe methods to extract clinical events (e.g., Problems, Treatments and Tests), temporal expressions (i.e.,…
Although cancer patients survive years after oncologic therapy, they are plagued with long-lasting or permanent residual symptoms, whose severity, rate of development, and resolution after treatment vary largely between survivors. The…
Medical research, particularly in predicting patient outcomes, heavily relies on medical time series data extracted from Electronic Health Records (EHR), which provide extensive information on patient histories. Despite rigorous…