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Job Req ID:  94178

Software Engineer

The Institute for Clinical and Translational Research is seeking an NLP Software Engineer who will be responsible for extracting and transforming relevant data stored in unstructured clinical notes from electronic health information systems using Natural Language Processing (NLP) tools and techniques.

As an NLP expert, this position will interact with the Hopkins medical research community to analyze clinical text, deliver analysis results, and communicate findings. Data must be delivered in a secure manner, following all applicable institutional policies and State and Federal regulations for privacy, security, and the conduct of human subject research.

Job Scope/Complexity:

  • Will require a significant level of collaboration with other engineers and data scientists at Johns Hopkins University.  It will also require working closely with our Medical Director/Honest Broker on specific projects and techniques.  


  • Will design and develop algorithms and techniques using text analytics, best-in-class open source Natural Language Processing tools, and machine learning. This position will support collection/annotation of data for algorithm development and develop criteria for testing those algorithms.

Specific Systems, Applications, and Projects for which the Position is Responsible:

  • Will leverage the large corpus of original clinical text, including format, structure, and emphases, harmonized into an HL7 Clinical Document Architecture (CDAv2) warehouse. 
  • Will work on NLP projects which could last in duration from several weeks to several months, as well as other programming tasks to support the Institute for Clinical and Translational Research’s Informatics Core.
  • The major systems with which the position interfaces are: 
    • Epic Clarity, Epic Data Warehouse, Precision Medicine Analytics Platform on Azure Databricks, and DataMart/CaseMix.

Scale/Size of area, Project and/or System Supported:

  • Could work with about one hundred different users annually, primarily from the Johns Hopkins School of Medicine, but also from the Johns Hopkins School of Public Health, Nursing, and the Engineering Program.  
  • Most complex part of this job is learning about the nuances of the data in large institutional databases, with data for about 5.5 million patients.

Minimum Qualifications (Mandatory)

  • Bachelor’s degree in computer science or a related field
  • Experience using open source NLP tools 
  • Experience with at least one programming language (Python, Java, C++ etc.)
  • Development experience in at least one scripting language (PHP, Perl, Python, etc.)

JHU Equivalency Formula: 30 undergraduate degree credits (semester hours) or 18 graduate degree credits may substitute for one year of experience.  Additional related experience may substitute for the required education on the same basis. For jobs where equivalency is permitted, up to two years of non-related college course work may be applied towards the total minimum education/experience required for the respective job. 

** Applicants who do not meet the posted requirements but are completing their final academic semester/quarter will be considered eligible for employment and may be asked to provide additional information confirming their academic completion date. 


Preferred Qualifications:

  • Strong analytical thinking and problem-solving skills.
  • Experience with clinical data, having applied NLP and machine learning techniques on unstructured data in EMRs.
  • Experience in text mining, natural language processing techniques, clustering, text classifiers, advanced text parsing, parts of speech tagging, semantic analysis, and machine learning is highly desired.
  • Coursework in Data Science and/or Machine Learning.
  • Experience using R, SAS, or a Python stack including Numpy, Scipy, Scikits, Spyder, Matplotlib, Flask, Bokeh.
  • Demonstrated communication and cross-functional collaboration skills



Classified Title: Software Engineer
Role/Level/Range: ATP/04/PE  
Starting Salary Range: Commensurate with experience  
Employee group: Full Time 
Schedule: M-F, 8:30 am-5:00 pm 
Exempt Status: Exempt 
Location: Remote  
Department name: SOM ICTR Inst Clin Translational Resrch 

Personnel area: School of Medicine 



The successful candidate(s) for this position will be subject to a pre-employment background check.


The Johns Hopkins University values diversity, equity and inclusion and advances these through our key strategic framework, the JHU Roadmap on Diversity and Inclusion.


Equal Opportunity Employer

All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or status as a protected veteran.


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Accommodation Information

If you are interested in applying for employment with The Johns Hopkins University and require special assistance or accommodation during any part of the pre-employment process, please contact the Talent Acquisition Office at For TTY users, call via Maryland Relay or dial 711. For more information about workplace accommodations or accessibility at Johns Hopkins University, please visit


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The following additional provisions may apply, depending on campus. Your recruiter will advise accordingly.

The pre-employment physical for positions in clinical areas, laboratories, working with research subjects, or involving community contact requires documentation of immune status against Rubella (German measles), Rubeola (Measles), Mumps, Varicella (chickenpox), Hepatitis B and documentation of having received the Tdap (Tetanus, diphtheria, pertussis) vaccination. This may include documentation of having two (2) MMR vaccines; two (2) Varicella vaccines; or antibody status to these diseases from laboratory testing. Blood tests for immunities to these diseases are ordinarily included in the pre-employment physical exam except for those employees who provide results of blood tests or immunization documentation from their own health care providers. Any vaccinations required for these diseases will be given at no cost in our Occupational Health office.


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