[Corpora-List] PhD Position in biomedical information extraction at Bielefeld University

Roman Klinger roman.klinger at uni-bielefeld.de
Wed Sep 2 16:12:59 CEST 2015

The Semantic Computing Group [1] at Bielefeld University has an opening for a PhD candidate to work on information extraction from bio-medical full text articles using machine learning methods, in particular probabilistic graphical models.

The position is available in the context of the project PSINK (Automatically Populating a Preclinical Spinal Cord Injury Knowledge Base to Support Clinical Translation) that is expected to be funded by the German Ministry of Education and Research (BMBF). The goal of the project is to develop novel methods for information extraction from bio-medical full text articles, in particular describing pre-clinical studies, to support the translation of pre-clinical knowledge into clinical practice. The goal of the project is to populate a large database of pre-clinical knowledge in the area of spinal cord injury to support informed decision making for the design of therapies that are potentially successful in human patients. This is a joint project with leading experts from the University of Düsseldorf and the Center for Neuronal Regeneration [2] who will bring in the medical expertise. Dr. Roman Klinger [3] from the Institute of Natural Language Processing in Stuttgart [4] will act as a co-principal investigator in this project.

The requirements of the position are the following:

* excellent Master’s degree in computer science or computational linguistics * advanced knowledge of machine learning methods * strong programming skills in an object-oriented language (Java, C++, …) and scripting languages (Perl, bash etc.) * advanced knowledge of natural language processing * good knowledge of database technology * excellent communication skills and interest in interdisciplinary work

The following skills will be considered as a plus, while not strictly mandatory:

* knowledge of undirected probabilistic graphical models, Markov chain Monte Carlo methods * experience in applying NLP techniques to the biomedical domain

Depending on grant approval, the position will be available for three years, starting from March 2016. The salary is according to the university payscale (TV-L 13, 100%) and amounts to about 3.500 EUR per month (pre-taxes). Working language of the project will be English, knowledge of German is not mandatory, but a plus.

The Semantic Computing group is part of the Cognitive Interaction Technology Center of Excellence [5] that hosts over 250 researchers working on intelligent systems in a highly interdisciplinary context.

Bielefeld University [6] is a young, very dynamic and fastly growing university. It is a campus university hosting more than 22.000 students. Housing and many other facilities offered directly on campus. With close to 330.000 inhabitants, Bielefeld [7] is one of the top 20 major cities in Germany. It has many leisure and cultural activities to offer and is at the center of the Teutoburg Forest [8], offering many possibilities for outdoor activities.

To apply, please send a full CV and letter of motivation (in one PDF document) to Prof. Philipp Cimiano (cimiano at cit-ec.uni-bielefeld.de) by October 2nd, 2015. For informal inquiries, please contact Matthias Hartung (mhartung at cit-ec.uni-bielefeld.de) or Roman Klinger (rklinger at cit-ec.uni-bielefeld.de).

[1] http://www.sc.cit-ec.uni-bielefeld.de/ [2] http://www.cnr.de [3] http://www.romanklinger.de/ [4] http://www.ims.uni-stuttgart.de/ [5] http://www.cit-ec.de [6] http://www.uni-bielefeld.de [7] http://www.bielefeld.de [8] https://en.wikipedia.org/wiki/Teutoburg_Forest

-- Dr. Roman Klinger Visiting Professor/Vertretungsprofessur Institut für Maschinelle Sprachverarbeitung University of Stuttgart Stuttgart/Germany Phone: +49 711 685 81406 Mail: roman.klinger at ims.uni-stuttgart.de

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