Machine Learning Scientist - Westerdijk Fungal Biodiversity Institute - Utrecht

The challenge
For this position, we seek a machine learning expert ready to tackle one of the most diverse and under-explored datasets in biology.

Our institute maintains one of the world’s richest fungal strain collections, and we are generating large in-house datasets that are multi-modal and paired with each sample:

• High-resolution images (morphology, microscopy);
• DNA sequences (barcodes, full genomes, transcriptomes); and
• Phenotypic and biochemical profiles (structured/tabular data).

Our datasets are not just big — they’re continuously expanding with tens of thousands of strains, each with matched image, sequence, and phenotype data. On top of our in-house resources, you’ll integrate with external repositories (e.g., GEO, MycoCosm, MIRRI-ERIC, etc.), giving you access to even more omics and microbial data.

You will design the next generation of AI algorithms to:

• Integrate image, sequence, and tabular data in a single modeling framework;
• Build correlation networks across biological and environmental variables;
• Develop scalable pipelines for classification, anomaly detection, and clustering
• Enable rapid, automated species identification at a speed the field has never seen; and
• Create a robust data infrastructure to connect internal and external datasets

“This means you can train and evaluate models on truly linked biological datasets — a rare opportunity in applied AI.”

Why This Matters?
Globally, only a tiny fraction of fungal species has been described. Your work will directly accelerate discovery — compressing what is currently a slow, manual process into an AI-assisted, high-throughput pipeline. By developing AI tools to discover species boundaries, rapidly and accurately identify species, detect pathogens, and predict traits, your work will directly contribute to protecting food security, preventing invasive species, improving early disease diagnosis, and enabling new biotechnological applications. You will not just be advancing AI research — you will deliver solutions with real societal and environmental impact.

"Working at the Westerdijk Fungal Biodiversity Institute — a world of knowledge, innovation, and growth"

What We Are Offering

• A full-time postdoc position in a leading fungal biodiversity institute;
• Opportunities to participate in internal training for soft skills development;
• To become part a cross-disciplinary bioinformatics cluster that blends existing biology expertise with new AI skills;
• Working as team to build a central data platform, integrating analysis pipelines into daily workflows, and making curated datasets openly available to the global research community;
• A chance to advance AI research and deliver solutions with real societal and environmental impact.

“You bring the technical expertise — we will provide the data, the domain experts,and the chance to make a measurable impact in both AI and science.”

You are a curious, enthusiastic, and independent working bioinformatician with experience in machine learning and developing deep learning AI pipelines for complex biological data.

Furthermore, you possess:

• A PhD in Computing Science, AI, or Bioinformatics;
• Demonstrable experience with programming language and deep learning libraries (e.g., Python with Keras, PyTorch, and/or TensorFlow);
• Demonstratable expertise in developing and implementing AI methodology;
• Experience with metadata handling, archiving, and FAIR data principles;
• Strong attention to detail, organizational skills, and communication skills;
• Fluency in English; Dutch language skills are a plus;
• Background in genomics or mycology is beneficial but not required.

Terms of employment
Depending on education and experience the minimum salary is [[salarisMin]] and the maximum salary is [[salarisMax]] gross per month for a full-time appointment (scale [[ufoSchaal]] cao Nederlandse Universiteiten/KNAW). This is exclusive of 8% vacation allowance, 8.3% year-end bonus, travel allowance, internet allowance, home working allowance and pension accrual with ABP.

The KNAW offers its staff an excellent package of secondary benefits. A package that meets the different needs of employees depending on their stage of life, lifestyle or career ambitions. For example, by working an extra two hours a week, it is possible to increase the number of days off from 29 to 41 days a year (with full-time employment).

For a complete overview of the terms of employment, please refer to the web page: werken bij de KNAW.

Applying for a Certificate of Good Conduct can be part of the employment procedure.

The Westerdijk Fungal Biodiversity Institute is a leading research institute of the Royal Netherlands Academy of Sciences, located at Utrecht Science Park. The institute focuses on the biodiversity of the entire fungal kingdom and plays a leading role in mycology worldwide. Researchers at Westerdijk Fungal Biodiversity Institute use a wide range of innovative techniques to study the biology, ecology, and genetics of fungi. With an exceptional collection of more than 100,000 living fungal strains, yeasts, and bacteria, Westerdijk Fungal Biodiversity Institute has a wealth of biological diversity and knowledge.
As an internationally recognized centre of mycological expertise, Westerdijk Fungal Biodiversity Institute contributes to solving pressing issues in health, agriculture, and industry.

Need more information? No problem at all. The director of the Westerdijk Fungal Biodiversity Institute will be happy to tell you more! He can be reached via email at: w.meyer@wi.knaw.nl