PhD Position in Computational Methods for Digital Twins of Embryonic Development & Disease

The Computational Biology Group (Prof Dagmar Iber) at D-BSSE develops digital twins of embryonic development and reproductive health using image-based mechanistic modelling and simulation.

Project background

Digital twins of living systems are a hard computational problem: nonlinear, high-dimensional models with uncertain parameters that must be fitted to noisy data, and simulations so expensive that fitting them demands new algorithms and scalable software. We apply this to real questions, from how tissues self-organise during embryonic development to digital twins that support IVF treatment planning. You will build the algorithmic infrastructure that makes this possible, working with modellers, experimentalists and clinicians, and building on our open-source simulation tools.

Job description

The PhD position focuses on developing the algorithmic infrastructure behind our digital twins. You will:

• develop and benchmark methods for parameter estimation and uncertainty quantification, from classical optimisation and Bayesian inference to physics-informed neural networks (PINNs) and other machine-learning approaches
• build and extend our simulation environment, with a focus on performance, scalability and reproducibility
• apply your methods to real models and data, from imaging-based models of tissue development to our digital twin of the hormonal cycle and IVF treatment, together with the modellers, experimentalists and clinical collaborators in the group
• publish your results and present them at international conferences
• contribute to the group's open-source software and to teaching

Profile

We are looking for a self-motivated candidate who is enthusiastic about developing algorithms and software for data-based modelling of biological systems. The position suits someone with training in computer science, scientific computing or a related quantitative field, and an interest in applying it to biology and biomedicine.

You should have:

• a Master's degree in Computer Science, Computational Science and Engineering, Applied Mathematics, Physics or a related field
• strong programming skills, e.g. in Python, Julia or C++, and experience in writing clean, well-tested code
• experience in numerical methods, optimisation, statistical inference or machine learning, gained through coursework, a thesis or a project
• an interest in biology and biomedicine and the willingness to learn the biological background of the project; prior knowledge of biology is not required
• good written and spoken English

Experience with PDE-based simulations, finite element methods, high-performance computing or deep-learning frameworks (e.g. PyTorch, JAX) is an advantage.

We offer

• A PhD position in an interdisciplinary, international research environment at the interface of mathematics, computing and biology
• Close collaboration with leading experimental groups and clinical partners
• Excellent infrastructure and computing resources at ETH Zurich
• Support for your scientific development, including conference travel and training
• Competitive ETH doctoral salary and conditions

Application

We look forward to receiving your online application with the following documents:

• A letter of motivation
• CV
• BSc & MSc diplomas and transcripts
• Contact details of 2 referees

Applications will be reviewed on a rolling basis until the position is filled. Questions regarding the position should be directed to Prof Dagmar Iber, dagmar.iber@bsse.ethz.ch (no applications). Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.