Postdoc In AI Foundation Models For Crop Microbiomes
18 сентября 2026 г.
Офис
Senior
Utrecht, Netherlands
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Описание
A postdoctoral researcher is sought to take a leading technical role in the EU-funded EIC Pathfinder project NOAH, developing ARCA, an AI foundation model for crop microbiomes. The work sits at the interface of deep learning, bioinformatics and microbial ecology, using large-scale microbiome and genome data to learn contextual representations of microbes and communities. It covers both foundation-model pretraining and downstream predictive and generative applications tested in greenhouse and field settings. The position is embedded in an interdisciplinary research environment with access to GPU/HPC infrastructure and curated microbiome datasets.
Обязанности
Design, implement and benchmark foundation-model architectures for microbiome data, including transformer-based and masked-autoencoder approaches
Develop representations that integrate microbial identity and abundance with genomic or functional information and contextual metadata such as crop genotype, soil and environmental conditions
Define and evaluate self-supervised learning objectives and embedding strategies, benchmarking their added value against simpler machine-learning baselines
Train and evaluate ARCA on large-scale microbiome datasets, addressing sparsity, batch effects, scalability, generalisation across studies and uncertainty
Fine-tune ARCA for tasks including microbial root competence and crop-relevant outcomes, iteratively improving it with Design-Build-Test-Learn data from project partners
Develop a generative ARCA component using autoencoder- and/or diffusion-based approaches for ecologically plausible microbiome configurations
Apply interpretable and explainable AI approaches to identify microbial taxa, functions and contextual features driving model predictions
Develop reproducible training and evaluation workflows and work with project partners to make models and tools usable beyond the immediate research setting
Требования
PhD, or a PhD close to completion, in machine learning, artificial intelligence, computational biology, bioinformatics, computer science or a closely related field
Strong hands-on experience with deep learning and modern representation learning, preferably including transformers, self-supervised learning, foundation models or autoencoders
Strong programming skills in Python and experience with a deep-learning framework such as PyTorch, including training and evaluating models on GPU/HPC infrastructure
Experience with high-dimensional biological, omics, ecological or similarly sparse and heterogeneous data, or a clear motivation to develop this expertise
Interest in interpretable AI, rigorous benchmarking and reproducible research
Ability to collaborate across AI, bioinformatics, microbiology and crop science
Experience with microbiome data, microbial genomics, metagenomics or multimodal biological data is an advantage, but not required
Условия
Central role in developing ARCA, the core AI technology of the five-year EIC Pathfinder project NOAH
Position available from January 2027, initially for 1 year, extended with 3 years after a positive evaluation
Gross monthly salary from €3,706 to €5,760 (salary scale 10, CAO NU), based on a 38-hour working week
8% holiday pay and 8.3% year-end bonus
Pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU
Additional benefits including personal and professional growth, flexible leave arrangements and extra vacation days