Postdoctoral researcher on AI for drug design

About Ghent University

Ghent University is a world of its own. Employing more than 8,000 people, it is actively involved in education and research, management and administration, as well as technical and social service provision on a daily basis. It is one of the largest, most exciting employers in the area and offers great career opportunities. With its 11 faculties and more than 80 departments offering state-of-the-art study programmes grounded in research in a wide range of academic fields, Ghent University is a logical choice for its staff and students.

About IDLAB

The IDLab Ghent research group from Ghent University - imec in Belgium is extending its interdisciplinary research cluster focusing on artificial intelligence for bio-informatics, within a new collaboration project between academia and industry, focusing on the AI-driven generation and optimization of proteins for therapeutic purposes.
This vacancy encompasses 3 different two-year post-doc positions within the same project, focusing on developing machine learning models and training strategies for the creation and adaptation of antibodies and nanobodies, with the following postdoc projects:

Postdoc project 1: finetuning of protein language models 

The first focus of this postdoc project will be on encoder-only protein language models, with the reproduction of published benchmark results in a comparison of existing models (including the recently released ESM3-open), on downstream tasks related to antibody design (including transfer learning for improved developability prediction models).  A comprehensive nanobody sequence collection will be composed from multiple public sources. It will be used for achieving state-of-the-art results on nanobody representation learning, through continued pretraining and/or (low-rank) finetuning of the encoders. 
The second focus will be on autoregressive protein language models, again aiming at achieving the best possible model for nanobody generation tasks, in a comparison between low-rank finetuning of large-scale models vs. full finetuning of smaller antibody-specific models.

Postdoc project 2: design of antibody diffusion models

The first goal of this postdoc project is to evaluate and compare recent antibody diffusion models on sequence-conditioned structure prediction, as well as joint sequence and structure prediction, for antibodies in the presence of an antigen, both for optimization and full infilling (e.g., of CDR regions in antibodies).  Recent models will be studied, and a reproducible benchmark will be composed. The second goal is finetuning such models on a newly aggregated nanobody dataset, aiming at achieving new state-of-the-art results to be validated in industrial nanobody use cases.

Postdoc project 3: research and proof-of-concept validation of protein developability property prediction models.

This postdoc project focuses on predictive modeling of a number of common developability properties in the largely wetlab dominated area of antibody and nanobody engineering. Setting up baselines (benchmark datasets, and reproducing existing models) will be an important part of the work, as well as investigating the design of improved models, including in a multi-task setting.  The key properties to be studied are (1) thermostability, for which we will gather a unique industrial dataset in collaboration with the partners, (2) spatial aggregation propensity, (3) immunogenicity, and (4) the presence of sequence liabilities (deamidation, isomerization, oxidation).  Frequent contacts with industrial experts will be an important part of the validation efforts.

We are seeking highly motivated and recently graduated PhDs to join the AI-bioinformatics research cluster, with profs. Thomas Demeester, Jan Fostier, and Kathleen Marchal, combining their respective expertise in machine learning, high-performance computing in bioinformatics, and AI for biology.  

The postdoc projects fit within the recently launched imec Health Mission, a strategic research track aiming to advance the discovery and development of novel therapeutics over the next 10 years.  IDLab Ghent is a key partner in the Health Mission, and leads the first mission project ADAPT (for "Affinity and Developability through AI for Protein Therapeutics"). ADAPT aims to develop AI-based models to design and optimize antibodies and nanobodies with high binding affinity and optimal developability properties, in a collaboration between several imec research groups and key industrial partners from the Ghent area specialized in nanobody technology.

The main tasks for the postdoctoral researchers will include:

• At least 70% of your assignment will be spent on academic research.
• Daily dedicated research (including coding and experimentation), as well as co-supervising and collaborating with junior PhD students on the respective projects.  
• Collaborating with the PIs at IDLab (profs. Demeester, Fostier, Marchal), and other senior researchers to achieve the goals of the project, as well as maintaining frequent contacts with the academic and industrial project partners (through recurring consortium meetings and ad hoc one-on-one meetings).
• Building proof-of-concept implementations involving the created models for validation by experts in the domain of antibody engineering.
• Writing high quality publications, targeting top journals and international conferences.

In addition to these primary research responsibilities, the postdoctoral researchers will get the chance to contribute to the ongoing research efforts in related areas in the research group, in order to maximally build a strong academic CV over the two-year post-doc period.  This includes collaborating on publications, joining high-quality international scientific events, and the supervision of master theses on their respective topics. Candidates are encouraged to apply for additional (inter)national funding and fellowships, and will receive support to do so. 

What can we offer

We offer the opportunity to do the postdoc project in an international and stimulating environment. Ghent University consistently ranks among the best 100 universities in the world. Located in the heart of Europe,  Ghent is a beautiful and welcoming city  with plenty of cultural and leisure activities. 
(https://www.lonelyplanet.com/belgium/flanders/ghent)

• We offer you a contract of indefinite duration with a maximum term of 2 years.
• Your remuneration will be determined by salary scale PD1. Click here for more information about our salary scales.
• All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 35 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, a bicycle allowance and eco vouchers. Click here for a complete overview of all the staff benefits (in Dutch).

The selected candidates will be offered employment from October 2024 (or later, depending on the hiring procedure) up to September 2026. 

Job profile

We are looking for highly creative and motivated postdoctoral researchers with the following qualifications and skills:

• You hold a thesis-based doctorate (obtained max. 6 years ago. This term of 6 years is determined by the date written on the above-mentioned required diploma). 
• You have (or will obtain by the starting date) a Ph.D. in computer science, artificial intelligence, bioinformatics, bioengineering, or equivalent. 
• You have an excellent publication record (with at least one first-author contribution in the main track of a top AI conference, or in a top journal in bioinformatics or bioengineering).
• You have excellent coding skills.  
• You have experience in collaborative research, and excellent verbal and written English communication and interpersonal skills.
• You have a genuine interest and commitment to advancing scientific knowledge and innovation.

Any of the following skills on top of your core skillset represent a significant plus:

• Hands-on experience in deep learning frameworks such as PyTorch or Tensorflow, and with Hugging Face repositories.
• Expert knowledge of large-scale language model finetuning.
• Expert knowledge of training diffusion probabilistic models.
• Expertise in application-specific custom neural network design.
• Expertise in antibody engineering, especially with in-silico methods.
• Expertise in molecular dynamics simulations.

If you have expertise in related areas not explicitly listed above (e.g., in rational design for protein engineering, experience in bio-chemistry,...), please clearly describe these as well, they could also represent a plus.

How to apply

Apply online through the e-recruitment system before the application deadline (https://jobs.ugent.be/). We do not accept late applications or applications that are not submitted through the online system.

Your application must include the following documents:

• In the field ‘CV’: your CV and an overview of your study results (merged into one pdf file), An academic/professional resume, tailored towards the described job profile (see above) and including your full bibliography.
• In the field ‘Cover letter’: your application letter in pdf format,  motivation letter (highlighting why you believe you are a suitable candidate for the position & why you want this position). Please clearly mention the specific postdoc project(s) you are most interested in (see above).
• In the field ‘Diploma’: a transcript of the required degree (if already in your possession). If you have a foreign diploma in a language other than our national languages (Dutch, French or German) or English, please add a translation in one of the mentioned languages.
• In the field “other documents”: An academic/professional resume, tailored towards the described job profile (see above) and including your full bibliography. An overview of your top three most relevant publications for the envisioned postdoc project(s), with a motivation for your selection and description of your contributions to these publications. At least two reference contacts.

Note that the maximum file size for each field is 10 MB.

As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.

More information

For additional information, please contact profs. Demeester (thomas.demeester@ugent.be) and Fostier (jan.fostier@ugent.be). 
Important: do NOT send your application by email, but apply online.
After a first screening, selected candidates will be invited for an interview (in person or remotely via MS Teams).
Start of the postdoctoral project:  as early as October 2024, or the subsequent months.