Machine Learning Scientist (f/m/x)

  • Contract
  • Germany
  • Posted 2 months ago

Helmholtz Munich

Area of research:

Scientific / postdoctoral posts

Job description:

Our mission as research center: Discover personalized medical solutions for environmentally triggered diseases to promote a healthier society in a rapidly changing world.

The Institute of Computational Biology is globally recognized for innovations in data analysis and modeling of biological systems and diseases, anchored at Helmholtz Munich and the Technical University Munich. The Theis Lab has a long-standing reputation for pioneering machine learning and AI methods in molecular biology, in particular on single-cell genomics and microscopy.

scArches is one of the leading toolkits for reference-based analysis of single-cell data.


is compatible with deep learning models integrating datasets across different modalities and labs while allowing users to update the integrated reference using concepts from life-long learning continually. scArches

provide different capabilities, from querying cells to see if they were changed after the disease, mapping cells to gene programs, building cell hierarchies, and spatial organization of the tissue. We plan to extend


by developing base models supporting different data modalities in addition to improving the performance and speed of reference mapping using advanced life-long learning. The ideal candidate will work with a high degree of independence and have several opportunities to shape scArches

according to your own ideas and contributions. You will work in a highly collaborative environment with a young and agile team, and will receive direct and tangible feedback on your work in a very inclusive and skilled community.

Full time, Part time

Neuherberg near Munich

Professionals, Graduates & Entry-level Professionals, Postdocs, PhD

Your responsibilities

  • Propose, develop, train and evaluate existing and new machine learning models extending scArches

capabilities to other modalities

  • Propose and implement solutions to speed up single-cell reference mapping for online settings
  • Deploy your advanced solutions into open-source, easy-to-install packages with documentation that facilitates the usage of your solution for downstream users, including biologists and bioinformaticians
  • Develop and maintain scArches

repository and software infrastructure together with the backend team

  • Organize and overhaul test suites and increase test coverage for scArches

Your qualifications

  • Bachelor / Master / PhD degree in Computer Science, Software Engineering, or related fields
  • Extensive knowledge of scientific computing and machine learning ecosystem in Python (Pytorch, Tensorflow, NumPy, SciPy, Scikit-Learn, Pandas)
  • Familiarity with MLOps and hyper-performance computing using GPUs
  • Extensive knowledge of continuous integration and testing suite maintenance (GitHub actions, tox, readthedocs etc.)

Desirable qualifications

  • Familiar with basic data analysis in single-cell or biological data

What we offer you

work-life balance
flexible working hours & working-time models
continuous education and training
30 days annual leave
on-site health management service
home office options
on-site nursery & holiday care
elder care company pension scheme discounted public transport ticket
Munich, with its numerous lakes and its vicinity to the Alps, is considered to be one of the cities with the best quality of life worldwide. With its first-class universities and world-leading research institutions it offers an intellectually stimulating environment.

Salary and social benefits are based on the collective agreement for the federal public service (TVöD). The position is (initially) limited until 31.12.2023, under certain circumstances an extension can be arranged.

To promote diversity, we welcome applications from talented people regardless of gender, cultural background, nationality, ethnicity, sexual identity, physical abilities, religion and age. Qualified applicants with physical disabilities will be given preference.
If you have obtained a university degree abroad, we require further documents from you regarding the recognition of the degree. Please request the recognition as early as possible.

Interested?If you have further questions, simply contact Dr. Anna Sacher, 089 3187-2926, who will be happy to be of assistance. Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Institute of Computational Biology
Ingolstädter Landstraße 1

85764 Oberschleißheim

Total E-Quality Award for excellent gender equality policy for women and men: Helmholtz Munich is particularly committed to promoting professional equality between women and men. It therefore aims to increase the proportion of the underrepresented sex in the respective field. Helmholtz Munich is part of the Helmholtz Association, Germany’s largest scientific organization. Altogether 43.000 people currently work in its 18 scientific-technical and biological-medical research centers. The Association’s annual budget amounts to around 5 billion Euros.

This research center is part of the Helmholtz Association of German Research Centers. With more than 42,000 employees and an annual budget of over € 5 billion, the Helmholtz Association is Germany’s largest scientific organisation.

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