Senior AI Research Scientist
About AQEMIA
AQEMIA is a drug invention company dedicated to creating entirely new medicines to address major unmet medical needs. At the core of our mission is QEMI, our proprietary molecule-invention platform, which uniquely combines cutting-edge science with advanced technology. Powered by physics-based modeling, statistical mechanics, and generative AI, QEMI allows our teams to design novel drug candidates from first principles.
What makes AQEMIA different is our commitment to true innovation: our research is dedicated to the invention of new molecular entities, not the refinement of existing ones. We focus on inventing never-before-seen molecules, without relying on experimental data, and advancing them into a growing pipeline of proprietary programs and strategic partnerships with leading pharmaceutical companies.
Our most advanced preclinical programs are currently in vivo optimization, targeting diseases still waiting for effective treatments, offering our teams the opportunity to work on science that can make a real difference in people’s lives.
For more information, visit AQEMIA.com and our LinkedIn.
About our Team
AQEMIA brings together a diverse, multidisciplinary team of 80+ professionals based in Paris and London. Our scientists and engineers, including chemists, physicists, machine learning experts, and software engineers, work side by side to push the boundaries of early-stage drug discovery.
This close collaboration across disciplines is central to our approach, enabling us to tackle complex scientific challenges from first principles and translate cutting-edge ideas into novel therapeutic candidates. At AQEMIA, team members are encouraged to contribute their expertise, learn from one another, and play an active role in shaping the future of drug invention.
The Platform Department
The Platform team (~20 people) brings together multidisciplinary teams working on the scientific core of Aqemia’s drug discovery engine. Its mission is to build scalable and reproducible workflows enabling multiple drug discovery programs to run in parallel with minimal manual intervention.
The team combines expertise to build predictive models, physics-based simulations, and extensive scientific pipelines for Aqemia’s discovery engine. This diverse group integrates expertise from several key areas:
Artificial Intelligence and Machine Learning (application and research)
Data science
Physics: Statistical mechanics and molecular simulations
Computational chemistry/CADD
At the center of this ecosystem is the “Rocket Launcher” process: an industrialized workflow continuously launching, testing, and improving drug discovery projects through iterative scientific feedback loops.
The role
As a Senior AI Research Scientist, you’ll join one of Aqemia’s Drug Discovery Platform AI teams and develop cutting-edge AI models to predict molecular properties and protein–ligand interactions. You’ll be a hands-on technical expert pushing the boundaries of what AI can do for drug discovery: from improving on AlphaFold approaches for protein–ligand structure prediction, to building probabilistic models that power our multi-fidelity Bayesian optimisation engine. You’ll own a key project on the ML team roadmap, mentor others, and make sure new AI methods become practical tools used in real drug discovery programmes.
Responsibilities
Develop novel ML models to predict molecular properties and protein–ligand interactions, with a focus on accuracy, uncertainty and generalisation to unseen chemical spaces.
Contribute to improving the state of the art in protein–ligand structure prediction, building on and significantly improving open-source AlphaFold implementations.
Contribute to Aqemia’s multi-fidelity Bayesian optimisation engine by building probabilistic deep learning models that capture uncertainty, in collaboration with our data scientists.
Own a key project on the ML team roadmap, from research and prototyping through to production.
Stay at the forefront of the literature: identify relevant publications, benchmark promising ideas and propose model or pipeline improvements.
Collaborate with AI researchers, computational chemists and drug discovery teams to turn AI models into actionable scientific insights.
Mentor team members on model design, implementation, debugging and good research and coding practices.
Qualifications
PhD in Computer Science, Mathematics, Physics, AI/Machine Learning or a related quantitative field.
8+ years of experience in AI/ML research, in academia or in research-intensive industry (any sector).
A track record of pushing the state of the art: you’ve developed ML models from scratch and understand how they work in theory and in practice.
Strong programming skills in Python and deep learning frameworks (e.g. PyTorch, JAX, TensorFlow).
Ownership of research projects, and the drive to turn research into something used in production.
Strong problem-solving skills, a collaborative mindset and clear communication.
Nice‑to‑Have
Experience applying ML to drug discovery on the chemistry side (proteins, small molecules, protein–ligand modelling).
Hands-on experience with scientific computing libraries (e.g. RDKit, OpenMM).
Experience with Bayesian optimisation or uncertainty quantification.
Experience productionising models or with software engineering best practices.
Preferred Mindset
At Aqemia, we believe that great science thrives in the right mindset and culture. We are looking for candidates who embody the following principles:
Pragmatic and Impact-Driven – Focused on delivering solutions that work in real-world applications, balancing scientific rigor with practical usability.
Eagerness to Learn – A strong curiosity for scientific advancements and a willingness to continuously expand your expertise.
Love for High Scientific Challenges – Enthusiasm for tackling complex problems at the frontier of AI and drug discovery.
Team-Oriented – A collaborative spirit, thriving in an interdisciplinary environment.
Humility – Open to feedback and different perspectives, always striving for improvement.
Why Join Us ?
At AQEMIA, we work for a mission: joining us means having your own impact on changing the way drugs are discovered, and helping to shape the direction of our fast-growing company and team.
Expanding Drug Discovery Pipeline: Focused on critical therapeutic areas like Oncology, CNS, Immuno-inflammation... with in vivo proof of concept/patent stage programs. Collaborations with top Pharma, including a $140M Sanofi deal.
World-Class Interdisciplinary Team: work alongside exceptional talent at the intersection of technology and life sciences. Our teams combine deep expertise in AI, physics-based modeling, biology, and medicinal chemistry to push the boundaries of innovation.
DeepTech Recognition: AQEMIA is proud to be part of the French Tech 120 and France 2030, highlighting our role as a key player in Europe’s DeepTech ecosystem.
Prime Location with Flexibility: Our offices are located in the heart of Paris and London (King’s Cross), with flexible work arrangements including up to two remote days per week.
Strong Financial Backing: $100M raised from leading European and International investors
We may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses. These tools assist our recruitment team but do not replace human judgment. Final hiring decisions are ultimately made by humans. If you would like more information about how your data is processed, please contact us.
