Bioinformatics Commons^™

Ordinal Convolutional Neural Networks For Predicting Rdoc Positive Valence Psychiatric Symptom Severity Scores, Anthony Rios, Ramakanth Kavuluru

Computer Science Faculty Publications

Background—The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) provided a set of 1000 neuropsychiatric notes to participants as part of a competition to predict psychiatric symptom severity scores. This paper summarizes our methods, results, and experiences based on our participation in the second track of the shared task.

Objective—Classical methods of text classification usually fall into one of three problem types: binary, multi-class, and multi-label classification. In this effort, we study ordinal regression problems with text data where misclassifications are penalized differently based on how far apart the ground truth and model predictions are …

Predicting Mental Conditions Based On "History Of Present Illness" In Psychiatric Notes With Deep Neural Networks, Tung Tran, Ramakanth Kavuluru

Computer Science Faculty Publications

Background—Applications of natural language processing to mental health notes are not common given the sensitive nature of the associated narratives. The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) changed this scenario by providing the first set of neuropsychiatric notes to participants. This study summarizes our efforts and results in proposing a novel data use case for this dataset as part of the third track in this shared task.

Objective—We explore the feasibility and effectiveness of predicting a set of common mental conditions a patient has based on the short textual description of patient’s history …

Immune Checkpoint Inhibition And The Prevalence Of Autoimmune Disorders Among Patients With Lung And Renal Cancer, Sherif M. El-Refai

Pharmaceutical Sciences Faculty Publications

PURPOSE: Immune checkpoint inhibition reactivates the immune response against cancer cells in multiple tissue types and has been shown to induce durable responses. However, for patients with autoimmune disorders, their conditions can worsen with this reactivation. We sought to identify, among patients with lung and renal cancer, how many harbor a comorbid autoimmune condition and may be at risk of worsening their condition while on immune checkpoint inhibitors such as nivolumab and pembrolizumab.

METHODS: An administrative health care claims database, Truven MarketScan, was used to identify patients diagnosed with lung and renal cancer from 2010 to 2013. We assessed patients …

Cross-Talk Between Clinical And Host-Response Parameters Of Periodontitis In Smokers, Radha Nagarajan, Craig S. Miller, Dolph R. Dawson Iii, Mohanad Al-Sabbagh, Jeffrey L. Ebersole

Institute for Biomedical Informatics Faculty Publications

Background and Objective

Periodontal diseases are a major public health concern leading to tooth loss and have also been shown to be associated with several chronic systemic diseases. Smoking is a major risk factor for the development of numerous systemic diseases, as well as periodontitis. While it is clear that smokers have a significantly enhanced risk for developing periodontitis leading to tooth loss, the population varies regarding susceptibility to disease associated with smoking. This investigation focused on identifying differences in four broad sets of variables, consisting of: (i) host‐response molecules; (ii) periodontal clinical parameters; (iii) antibody responses to periodontal pathogens …

A Fast And Efficient Python Library For Interfacing With The Biological Magnetic Resonance Data Bank, Andrey Smelter, Morgan Astra, Hunter N. B. Moseley

Center for Environmental and Systems Biochemistry Faculty Publications

Background: The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis.

Results:To aid in the use of this public resource, we have developed a package called …

Roadmap To A Comprehensive Clinical Data Warehouse For Precision Medicine Applications In Oncology, David J. Foran, Wenjin Chen, Huiqi Chu, Evita Sadimin, Doreen Loh, Gregory Riedlinger, Lauri A. Goodell, Shridar Ganesan, Kim Hirshfield, Lorna Rodriguez, Robert S. Dipaola

Internal Medicine Faculty Publications

Leading institutions throughout the country have established Precision Medicine programs to support personalized treatment of patients. A cornerstone for these programs is the establishment of enterprise-wide Clinical Data Warehouses. Working shoulder-to-shoulder, a team of physicians, systems biologists, engineers, and scientists at Rutgers Cancer Institute of New Jersey have designed, developed, and implemented the Warehouse with information originating from data sources, including Electronic Medical Records, Clinical Trial Management Systems, Tumor Registries, Biospecimen Repositories, Radiology and Pathology archives, and Next Generation Sequencing services. Innovative solutions were implemented to detect and extract unstructured clinical information that was embedded in paper/text documents, including synoptic …