Causality in biomedicine: going beyond associations

This course provides an introduction to causal inference and causal representation learning, offering both theoretical foundations and hands-on training. You will learn how to apply these methodologies to various biomedical data types, including clinical, genotype-phenotype, molecular, and multimodal data.

Causal inference and causal representation learning are emerging fields in AI and biomedical data science, enabling a shift from associational to cause-and-effect reasoning. These approaches have significant applications in biomedicine, such as evaluating treatment effectiveness, understanding causal mechanisms, identifying genetic risk factors, and uncovering causal relationships in complex molecular datasets. For instance, they can help answer questions like how effective a treatment is in preventing disease, whether its effects are direct or mediated by intermediate variables, and which genetic variants causally increase disease risk and can be targeted by drugs.

Gain practical experience using widely adopted tools and resources to apply causal techniques in real-world biomedical contexts. This EMBO Practical Course will also feature keynote talks that will provide insights into the role of causality in genomic, molecular, and computational biology, highlighting recent advancements and future directions in the field.

Funded by EMBO for excellence in the life sciences. 
This event has been granted the following EMBO sustainability badge:

Grade 2 of 3

Who is this course for?

This course is for you if you are a PhD student, post-doctoral researcher, or research scientist currently working with clinical healthcare and/or molecular data. You will find the event of interest if you are keen to gain a better knowledge of causal inference approaches and how these can be leveraged to understand biological and biomedical problems. You should be relatively new to the application of causality in biomedicine, and be working as a computational biologist or bioinformatician, quantitative molecular biologist, statistical geneticist, AI/ML and biostatistics researcher, or similar.

You will be expected to have a working knowledge of the Linux operating system and the ability to use the command line. Basic use of R, Python, or Julia programming languages are required. 

While the course will make use of simple coding or streamlined approaches such as R Markdowns or Python notebooks, higher levels of competency will allow participants to focus on the scientific methodologies rather than the practical aspects of coding and how they can be applied in their own research.

We recommend these free tutorials:

• Basic introduction to the Unix environment 
• Introduction and exercises for Linux 
• Python tutorial
• R tutorial 
• Julia tutorial

Regardless of your current knowledge, we encourage you to use these to prepare for attending the EMBO Practical Course, if you are successfully selected. You may  also be sent materials prior to the course if the trainers believe this would be helpful to your prior understanding of the topics. These might include pre-recorded talks and required reading that will be essential to fully understand the course.

What will I learn?

Learning outcomes

After the course, you should be able to:

• Assess the difference between causal and associational estimation 
• Explain the difference between randomised experiments vs observational studies in the context of public health and the human ecosystem
• Perform nonparametric estimation techniques on real-world health data to estimate causal effects on biomedical data
• Examine challenges of causal discovery for high-throughput molecular studies
• Assess whether causality can be extracted from data and, if so, apply the appropriate technique to extract causality in experimental and observational settings
• Apply causal representation learning to extract causal (latent) features from molecular/imaging data

Course content

During this course, you will learn about: 

• Causal inference and applications to clinical and genotype-phenotype data
  • Estimating causal effects: why correlations alone are misleading
  • Data in causality: randomised trials vs observational data
  • Estimation techniques for causal effects, e.g., targeted learning
  • Applications in simple clinical settings 
• Causal representation learning and application to multimodal molecular data
  • Extracting causal structure from observations: assumptions and challenges
  • Multimodal learning for causal (latent) feature discovery
  • Application of these methods to multimodal molecular data
  • Synergies of causal inference and representation learning in biomedicine

Trainers

Please read our support page before starting your application. To be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59 UK time on 21 June 2026. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 6 July 2026.  If you have any questions regarding the application process, please contact Sophie Spencer.

Registration fees 
Payment must be completed within 14 days of receiving your acceptance email. Failure to do so may result in your place being offered to someone else on the waitlist.

Your registration fee includes:

• Catering as detailed in the course programme
• Accommodation for five nights (4, 5, 6, 7, and 8 October 2026) 
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Secure virtual machines for the practical sessions listed in the programme
• Shuttle bus on the final course day to Cambridge train station 

* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Officer for more information.

Posters
If selected for this course, you will be asked to submit your poster upon registration. We expect the posters to act as a talking point between you, other attendees, and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the group.

All posters should:

• be A2 in size – 420mm x 594 mm
•  be in a portrait orientation
• include your photograph and contact information

Flash talks
If selected for this course, you will be asked to submit your flash talk upon registration. This should be a short presentation about your research work, providing you with an opportunity to share your research with the other attendees and provide a forum for discussion.

Financial assistance
Limited financial assistance is provided by EMBO in the form of registration fee waivers, travel grants and childcare grants. 

Registration fee waiver and travel grant

The travel grant and fee waiver can be used to cover the cost of travel (airfare, train, bus, taxi, accommodation, visa) and/or course registration fees and is provided up to specified caps, which are normally as follows:

• up to €500.00 for any participant travelling to Hinxton to attend the course
• up to €1000.00 for any participant working in Chile, India, Singapore or Taiwan, travelling to Hinxton to attend the course

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their bursary amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. 

Childcare grant
There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. There is a limited amount of funding available for the childcare grants, and funds will be distributed amongst eligible applicants. Childcare grant is up to €500.00.

Accessibility grants
These grants cover additional costs for supporting participants or speakers with access needs, e.g. to adapt the conference environment, or to be accompanied by someone to assist the participants where necessary. Maximally €500.00 per participant can be allocated.

Sustainable travels
Limited financial assistance is available to support sustainable travel.

We encourage you to travel by train or other sustainable transport methods where possible. Therefore, if the cost of travelling by sustainable methods is higher than travelling by plane, we will aim to offset the difference in fares between the flight and the more expensive sustainable method of transport. 

We will also be providing Amazon gift vouchers for delegates who choose to travel by train. Further details on this will be shared at registration.

Bursaries terms and conditions

• Application process:
  • Apply for the fee waiver and/or travel grant, childcare grant, or accessibility grant alongside your course application.
  • Provide a brief explanation of why you require any of the above and how attending the course will benefit your career.
  • You will be informed of your bursary status at the same time as the outcome of your course application.
• Selection process: 
  • Recipients of financial assistance will be selected by the scientific organisers during the course application review.
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Reimbursement process:
  • Participants must pay upfront for their travel costs.
  • A reimbursement form will be provided upon course completion.
  • Submit the completed form with receipts to your Event Organiser within one month of travel completion.
• Fair consideration: Applying for financial assistance will not impact the outcome of your course application.