Developer, Machine Learning, EMBO

IT and InfrastructureEMBL Heidelberg

EMBO (embo.org) stands for excellence in the life sciences. We support talented researchers at all stages of their careers in Europe and beyond, stimulate the exchange of scientific information, and help build a research environment where scientists can achieve their best work.

EMBO considers openness and transparency to be key values in scientific research and publishing. We are involved in shaping open science by actively working with the scientific communities and by developing technologies and standards that serve researchers.

EMBO Press (embopress.org) publishes four prestigious scientific research journals, The EMBO Journal, EMBO Reports, Molecular Systems Biology and EMBO Molecular Medicine and runs the journal-independent peer review platform Review Commons. EMBO Press has implemented numerous initiatives to promote transparency, reproducibility and efficiency in publishing.

SourceData (sourcedata.embo.org) is as an open platform developed by EMBO to make research data shown in published figures findable, accessible, inter-connected and reusable. SourceData implements Open Science principles at the heart of scientific publishing.

To support its multiple initiatives at the interface of scientific publishing, research policy and open science, EMBO is looking for a developer in machine learning to build tools and develop resources and technologies supporting the research community.

Your role

As Developer in Machine Learning you will be responsible for:

• Contributing to a new Wellcome Trust-funded project to extract and organize features from peer review reports in order to facilitate their exchange, display and findability.
• Developing further the SmartTag engine to automatically read scientific papers and organize them into an open knowledge graph (see http://github.com/source-data/soda-roberta, http://github.com/source-data/sd-graph and https://eeb.embo.org ).
• Maintaining and further developing tools for the editorial team at EMBO Press to use NLP (and possibly image analysis) to assist manuscript and data quality checks and automate repetitive tasks.
• In the context of responsibilities above, working on the following sites and code repositories: https://github.com/embo-press; https://github.com/source-data
• Coordinating with the EMBO IT team for systems administration.
• Additional tasks as required by the Head of SourceData, the Head of Scientific Publications or the EMBO Director.

This position will occasionally require working outside of the normal working hours, in the evenings or during the weekend.

You have

Your strength is solving complex problems and searching for the best possible solution while facing challenges and obstacles with ease. Proactivity and ownership are your crucial values when working on projects. You are motivated by a fast-changing environment that requires you to adapt to new scenarios as they unfold. You actively seek opportunities to learn new programming languages or to learn how to use new frameworks and new technologies. We love to work as a team and would like to welcome you as one of its key players.

We would like you to have a degree in computer science, computational biology, physics, maths or equivalent work experience. An MS in any related field will be strongly valued. The position requires experience in the following fields:

• Demonstrated expertise in structured, object-oriented and test-oriented programming in Python.
• Experience with a major deep learning framework such as PyTorch (preferred) or TensorFlow.
• Experience in natural language processing and text mining, using classical or deep learning frameworks (for example: nltk, spaCy, Gensim, BERT/transformers, …).
• Experience with data processing (for example: numpy, pandas, scikit-learn, …).
• Experience with relational databases (for example: PostgreSQL, MySQL…) and/or or graph database (for example: neo4j).
• Familiarity with version control systems such as Git.

You might also have

• Experience in graph data science and network analysis.
• A demonstrated involvement in Open Source development.
• A background in Linux system administration: bash scripting, server deployment and maintenance (e.g. systemd), cron jobs, backups, etc...

Why join us

EMBO is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment.

The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits. Excellent child care facility is available on campus.

The work at EMBO comes with

• Relocation package
• English is the working language
• Creative, diverse and international environment
• Flat hierarchies and freedom to make decisions and grow professionally
• Possibility for position extension of the position, up to 9 years
• Access to learning resources, training and budget for conference visit
• Broad spectrum of technological challenges
• Organized sport groups and social clubs
• German classes

What else you need to know

The Machine Learning Developer reports to the Head of SourceData.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.