PhD student position in multi-modal AI for biomolecular engineering

For this project, the PhD candidate will work on a novel, multi-modal deep learning approach to accelerate computational drug discovery, with a focus on degraders, ADME modeling, and generative AI. The PhD candidate will work in the AI Laboratory for Molecular Engineering, led by Assist. Prof. Rocío Mercado Oropeza at Chalmers. This position is funded by the Swedish Research Council.

Project description
Data-driven approaches to drug design, such as deep biomolecular generative models, have emerged as powerful strategies for engineering new molecules with desired properties and repurposing existing molecules for new tasks. As implied by the term “data-driven”, these methods require large amounts of data to make accurate predictions, ranging from structural and biochemical information about targets and ligands, to genomic and phenotypic data. Such data can be used to build computational models which improve our understanding of the complex relationships between molecular structure and biological function. By using machine learning, statistical modeling, and simulation, data-driven drug design can help identify new drug candidates, optimize leads, and predict drug efficacy and toxicity with greater accuracy and speed than with traditional rule-based methods.

One key advantage of data-driven drug design is its ability to account for the many factors that affect drug behavior in vivo, including pharmacokinetics, pharmacodynamics, and toxicity, before synthesizing and testing a compound. By integrating data from multiple sources and applying data-driven methods, generative models can propose new drug candidates which fulfill a desired property profile, or repurpose existing drugs for new indications, with greater efficiency and precision than traditional drug discovery approaches. Furthermore, data-driven drug design enables the development of personalized medicine by enabling the identification of patient subpopulations that may benefit from specific drugs, doses, or drug combinations.

Of particular interest in this project are new modalities for targeted protein degradation, such as PROteolysis TArgeting Chimeras (PROTACs), Regulated Induced Proximity TArgeting Chimeras (RIPTACs), etc. Multi-target therapeutic modalities such as these have become increasingly important for the treatment of complex diseases like cancer, cardiovascular disease, and neurodegenerative disorders. Unlike traditional single-target drugs that aim to modulate the activity of a single protein or pathway, multi-target drugs are designed to simultaneously interact with multiple targets involved in the disease pathway(s) that contribute to disease progression. By modulating multiple targets, multi-target drugs can achieve synergistic effects, reduce the risk of drug resistance, and improve therapeutic outcomes. Multi-target drugs can offer a more comprehensive approach to disease treatment than single-target drugs by addressing the complexity and heterogeneity of a range of diseases. They can, for instance, be used to target proteins without well-defined binding pockets, and their catalytic mechanism of action means lower doses could potentially be used to observe a desired therapeutic effect.

Information about the division and the department
The AI Laboratory for Molecular Engineering (AIME) is based in the Data Science & AI (DSAI) division in the Department of Computer Science and Engineering (CSE). Led by Dr. Rocío Mercado Oropeza, our group uses methods from machine learning and the life sciences to understand how molecules interact to form complex systems, and how we can use these insights to engineer molecular systems for therapeutic applications. We are currently focused on applying our computational tools to improving the understanding and design of molecular systems for drug discovery and materials applications. We interact closely with leading academic and industrial groups in computational chemistry, bioinformatics, materials science, and computer science. In AIME, we seek to create a vibrant and collaborative environment where students and postdocs are supported in their pursuit of challenging research questions at the forefront of machine learning and the molecular sciences.

The CSE department is a joint department at Chalmers University of Technology and the University of Gothenburg, with activities on two campuses in the city of Gothenburg. The department is divided into four divisions, and employs around 270 people from over 30 countries. Research in the department has a wide span, from theoretical foundations to applied systems development. We provide high quality education at the bachelor's, master's, and graduate levels, offering over 120 courses each year. We also have extensive national and international collaborations with academia, industry and society.

Our aim is to actively improve our gender balance in both our department and division. We therefore strongly encourage applicants from historically-excluded groups to our positions, such as women and non-binary individuals. As an employee of Chalmers and CSE department, students are given the opportunity to contribute to our active work within the field of equality and diversity.

Major responsibilities
The major responsibilities for a PhD student position in the division include conducting doctoral research and coursework. By the end of the PhD, students will be able to identify novel research directions and design the appropriate computational experiments to answer key questions. Students are expected to effectively communicate the results of their research verbally and in writing, and will receive specific training towards building these skills. This position also includes teaching at Chalmers' undergraduate level, or performing other teaching duties corresponding to 20% of working hours. The appointment is a full-time temporary employment for a period of not more than 5 years, funded by the Swedish Research Council.

Read more about doctoral studies at Chalmers here.

Qualifications
To qualify as a PhD student, applicants must have a master's level degree corresponding to at least 240 higher education credits in Computer Science, Chemistry, Biology, or a related field. The applicant should have strong background and experience in Python programming and deep learning. Previous experience in Generative AI and/or molecular modeling is a merit, but not required.

The position requires sound verbal and written communication skills in English. If Swedish is not your native language, Chalmers offers Swedish courses.

Contract terms
Full-time temporary employment. The position is limited to a maximum of five years.

We offer
Chalmers offers a cultivating and inspiring working environment in the coastal city of Gothenburg. 
Read more about working at Chalmers and our benefits for employees.

Chalmers aims to actively improve our gender balance. We work broadly with equality projects, for example the GENIE Initiative on gender equality for excellence. Equality and diversity are substantial foundations in all activities at Chalmers.

Application procedure
The application should be marked with reference number 20240442 and written in English. The application should be sent electronically and be attached as PDF-files, as below. Maximum size for each file is 40 MB. Please note that the system does not support Zip files.

CV: (Please name the document: CV, Family name, reference number)
• CV
• Other, for example previous employments or leadership qualifications and positions of trust.
• Two references that we can contact.

Personal letter: (Please name the document as: Personal letter, Family name, ref.number)
1-3 pages where you:
• Introduce yourself
• Describe your previous experience of relevance for the position (e.g. education, thesis work and, if applicable, any other research activities)
• Describe your future goals and future research focus

Other documents:
• Copies of bachelor and/or master’s thesis.
• Attested copies and transcripts of completed education, grades and other certificates, e.g. TOEFL test results.

Use the button at the foot of the page to reach the application form. 

Please note: The applicant is responsible for ensuring that the application is complete. Incomplete applications and applications sent by email will not be considered.

Application deadline: 2024-09-23

For questions, please contact:
Assistant professor Rocío Mercado, Data Science & AI division,
rocio.mercado@chalmers.se, +45 76 854 7752

*** Chalmers declines to consider all offers of further announcement publishing or other types of support for the recruiting process in connection with this position. *** 
   

Chalmers University of Technology in Gothenburg conducts research and education in technology and natural sciences at a high international level. The university has 3100 employees and 10,000 students, and offers education in engineering, science, shipping and architecture. With scientific excellence as a basis, Chalmers promotes knowledge and technical solutions for a sustainable world. Through global commitment and entrepreneurship, we foster an innovative spirit, in close collaboration with wider society.
Chalmers was founded in 1829 and has the same motto today as it did then: Avancez – forward.