Research Assistant - Clinical NLP (m/f/d)

Heidelberg University Hospital

Germany

December 22, 2021

Description

Research Assistant - Clinical NLP (m/f/d)

full time – JobID: P0035V331

as soon as possible searched for The division of Bioinformatics and Systems Cardiology ( www. dieterichlab.org ) at the Klaus Tschira Institute for Integrative Computational Cardiology / Department of Internal Medicine III .

The position is initially limited to 2 years with option of further extension. The salary is paid according to the German TV-L system (the salary agreement for public service employees). The position is also suitable for part-time employment.

The Klaus Tschira Institute for Integrative Computational Cardiology / Internal Medicine III offers a full-time position for a research assistant in clinical natural language processing (NLP).

The Bioinformatics and Systems Cardiology Lab at the Klaus Tschira Institute for Integrative Computational Cardiology develops software to study the causes of cardiac disorders (https: // github.com/dieterich-lab). In medicine in general and in cardiology in particular, much treatment-relevant information is still stored in unstructured free text. In this context we make use of recent advancements in NLP, applying deep neural networks for information extraction from unstructured texts.

Tasks

The successful applicant will enter a collaborative research environment and contribute to the group's NLP portfolio. The successful applicant will basically work on noisy unstructured clinical data in German language, applying state-of-the-art NLP methods to extract clinical information.

  • Preparation and curation of data sets for clinical information extraction tasks
  • Data cleaning and data preprocessing
  • Designing and performing machine learning experiments using state-of-the- art NLP methods
  • Developing end-to-end information extraction pipelines, ready-to-use in clinical routine
  • Required Qualifications

  • BA/MA degree in computational linguistics, computer science or comparable relevant background and level of expertise
  • Strong Python programming skills
  • Proven record using the Python data science and NLP stack
  • Strong experiences using machine learning methods for information extraction tasks
  • Experience handling noisy and large-scale unstructured data sets
  • Good Linux administration skills (i.e. software management, shell and scripting languages)
  • Experience using deep learning libraries for NLP is a plus (i.e. PyTorch, huggingface)
  • Experience handling multi-user annotation projects is a plus (i.e. via WebAnno/brat)
  • Experience using MS Windows for software development is a plus
  • Familiar with agile software development tools (i.e. Github, Redmine)
  • Ability to communicate and collaborate with experts from various scientific domains
  • Good spoken and written German and English is expected
  • Your expertise is complemented by essential soft skills, the ability to communicate and work in teams, flexibility and targeted action.

    We offer

    The Dieterich Lab (www. dieterichlab.org) offers a stimulating, diverse and international research environment. We are embedded in a vibrant community of clinical NLP and collaborate with many NLP research teams in the Heidelberg area.

  • Target-oriented individual further education and training opportunities
  • Targeted training on the job
  • Ticket for public transport
  • Possibility of child care (crèche and kindergarten) as well as subsidy for holiday care for school children
  • Active health promotion
  • Company pension scheme
  • Access to the university library and other university facilities (e.g. university sports)
  • Contact & Application

    Please do not hesitate to contact us if you have any further questions via Email sekretariat.dieterich@med.uni-heidelberg.de .

    Interested?

    Applications will be accepted until December 22, 2021 direct online. Please send a covering letter and a CV.

    Universitätsklinikum Heidelberg Zentrum für Innere Medizin Klinik für Kardiologie, Angiologie, Pneumologie (Innere Medizin III) Prof. Dr. rer. nat. Christoph Dieterich - Section of Bioinformatics & Systems Cardiology Im Neuenheimer Feld 669 69120 Heidelberg sekretariat.dieterich@med.uni-heidelberg.de

    Published: 24.11.2021

    Wir stehen für Chancengleichheit. Schwerbehinderte werden bei gleicher Eignung vorrangig eingestellt. Das Universitätsklinikum strebt eine generelle Erhöhung des Frauenanteils in allen Bereichen und Positionen an, in denen Frauen unterrepräsentiert sind. Qualifizierte Frauen sind daher besonders aufgefordert, sich zu bewerben. Vollzeitstellen sind grundsätzlich teilbar, soweit dienstliche oder rechtliche Gründe nicht entgegenstehen.

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