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PhD Researcher on concept recognition and disambiguation in biomedical literature and clinical records

Added on Feb 24, 2010

Employer description

More information about the Erasmus Medical Centre, Medical Informatics Group can be found here.

Job description

The PhD researcher will investigate, develop, and evaluate natural language processing techniques for the unambiguous and accurate detection of entities in text, using user feedback to automatically improve detection performance. The main application domain will be genomics with its highly ambiguous nomenclature.

Project description
A lot of scientific knowledge is contained in unstructured text, such as the scientific literature. The first step in extracting this knowledge is identifying the relevant concepts mentioned in the text. Concept recognition in the biomedical domain is extremely difficult due to a wide use of synonyms (several names for the same entity) and homonyms (several entities with the same name). In this project, the PhD student will investigate ways to improve the recognition of concepts by using a wide range of information sources, such as the text around the ambiguous terms, background knowledge about concepts, and background knowledge about the text (e.g. the journal or the author). A key element will be user feedback: users will be able to correct the system, and the system should learn from this feedback. 

Job requirements

  • Master degree in computer science, mathematics, or a related field.
  • Affinity with text-mining or machine learning.
  • Ability to program, preferably in Java.

What we look for
An enthusiastic young researcher interested in natural language processing and machine learning, and willing to gain a background understanding of the biomedical domain.

Job benefits

The position will be in in the Biosemantics group (http://biosemantics.org), a multidisciplinary group spanning the Medical Informatics department at the ErasmusMC and the Human Genetics department at the Leiden University Medical Center. This group has a strong international track record in applying text-mining in the biomedical domain, and has an extensive text-mining software and hardware infrastructure.

Appointment, salary, location
The appointment will be at the Erasmus University Medical Center of Rotterdam, and will initially be for 1 year. After successful evaluation, the appointment will be extended by another 3 years, resulting in a dissertation. The gross salary starts at EUR 2.435 per month. 

Apply information

Additional information can be obtained from:

If you are interested in this position you can apply using one of the following methods: 

  • E-mail: m.schuemie@removethis.erasmusmc.nl 
  • letter:
    Erasmus University Medical Center of Rotterdam
    Biosemantics group
    Attn. Martijn Schuemie
    Dr. Molewaterplein 50
    3015 GE Rotterdam
    The Netherlands
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