ETUDE for easy and efficient NLP application evaluation

November 14, 2018

NLP development and evaluation requires tools to compare annotations, analyze differences, and compute accuracy metrics.

None of the few existing tools allows consuming the output of any NLP system, comparing it with reference annotations in any format (both with configuration),  setting comparison rules, counting matches and computing accuracy metrics, visually displaying matching and erroneous annotations, changing the displayed information for analysis on the fly, exporting evaluation results, etc.

ETUDE (Evaluation Tool for Unstructured Data and Extractions) is a collaborative development by the MUSC TBIC (Paul Heider, for the engine) and by Clinacuity, Inc.

It offers the following functionalities:

  • Import of annotations (system output and reference standard) in multiple configurable formats
  • Drag-and-drop creation of evaluation configuration files (i.e., specification of annotation categories and attributes to match and compare) 
  • Customizable annotation comparison settings (base includes exact, partial, and fully-contained matches)
  • Count and comparison of annotations, computing descriptive statistics, a confusion matrix of matches and mismatches, and computing accuracy metrics (recall, precision, F-measure) 
  • Show side-by-side reference and system annotations in the original document context with easy exploration of matches and errors 
  • Export of evaluation results in various configurable formats

ETUDE is available with an open source license and available for download on GitHub at https://github.com/MUSC-TBIC/etude-engine and https://github.com/Clinacuity/etude-viewer.

SCRA Announces New SC Launch Client Companies

February 21, 2018

Press release available at http://www.scra.org/media-center/new-sc-launch-client-companies-jan

 

Summerville, S.C. – SCRA announced the recent acceptance of five Client Companies into its entrepreneurial program, SC Launch. Client Companies receive mentoring and support services and may also be eligible for grants, matching funds and investments.

Lowcountry Companies

Clinacuity’s solutions extract critical information from patient electronic healthcare records. The data extracted provides clarity and efficiency to improve patient care as well as provides de-identified information to researchers that will enhance treatment outcomes. The company is developing two product prototypes with funding from the National Cancer Institute and the National Institute of General Medical Sciences with clinical impact evaluations by Hollings Cancer Center at the Medical University of South Carolina and the University of Utah.

 

National Institutes of Health Commercialization Accelerator Program (CAP)

October 5, 2017

Clinacuity has been selected to participate in the biennial NIH Commercialization Accelerator Program (CAP) for 2017-2018, an excellent opportunity for our company!
The CAP is designed to help NIH technology transfer funding awardees transition their SBIR/STTR developed products into the marketplace through a contract with Larta Inc.
It will provide companies with individualized assistance toward accomplishing their commercialization goals.

Clinacuity’s CEO moves to a new academic position

August 22, 2016
Stephane Meystre, Clinacuity’s CEO moved from the University of Utah to the Medical University of South Carolina (MUSC) and Health Sciences South Carolina in August 2016. He was awarded a SmartState Endowed Chair in Translational Biomedical Informatics position, as Associate Professor at MUSC. He will create and develop a new Translational Biomedical Informatics center at MUSC.
Stephane Meystre also started as Interim Chief Technology Officer for Health Sciences South Carolina, a statewide health collaborative including the state’s largest research-intensive universities (Clemson University, MUSC and the University of South Carolina) along with the largest health systems (AnMed Health, Greenville Health System, McLeod Health, MUSC Health, Palmetto Health, Self Regional Healthcare, and Spartanburg Regional Healthcare System).

NIGMS awards Clinacuity a new technology transfer grant

February 10, 2016
The National Institute of General Medical Sciences (NIGMS) has awarded a new technology transfer (STTR) grant to Clinacuity, to develop a new system to automatically de-identify clinical narrative text in the Electronic Health Record (CliniDeid), to then improve the availability of clinical text for secondary uses, as well as ameliorate the protection of patient data confidentiality. This project is realized in collaboration with the Scientific Computing and Imaging Institute, the Department of Biomedical Informatics at the University of Utah, the University of Utah Healthcare IT services, and the Huntsman Cancer Institute.