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 , our WTTJ Page, 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.

About our 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 across Artificial Intelligence and Machine Learning (both research and applications), data science, statistical physics and molecular simulations, computational chemistry (CADD), and other scientific disciplines. Together, they develop predictive models, physics-based simulations, and robust scientific pipelines that power AQEMIA's discovery platform.

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 Principal AI Research Scientist, you’ll join Aqemia’s Drug Discovery Platform Teams, leading the development of cutting-edge AI algorithms for modelling protein-ligand systems. You’ll collaborate closely with AI researchers, computational chemists, and drug discovery experts to integrate your innovations directly into our platform and accelerate the discovery of novel therapeutics.

At Aqemia, a Principal AI Research Scientist is a senior technical leader - a hands-on expert who drives AI innovation and ensures it is effectively embedded into the Drug Discovery Platform.

Responsibilities

Contribute to defining and driving the AI research strategy for molecular modelling, shaping the technical roadmap alongside scientific and executive leadership.
Lead ambitious, department-level research initiatives to develop novel AI models for protein-ligand interactions, molecular property prediction and molecular generation, from early research through to production.
Drive the development of advanced machine learning approaches, including deep learning, generative models, graph neural networks and physics-informed AI, while staying hands-on in the most critical technical work.
Partner with computational chemists, physicists and medicinal chemists to embed AI-driven solutions in our drug discovery pipelines and programmes.
Ensure models scale to real-world use, improving efficiency, interpretability and generalisation to unseen chemical space.
Mentor and develop researchers and engineers at all levels, raising the technical bar and building a culture of scientific excellence.

Qualifications

PhD or equivalent practical experience in AI/ML, Mathematics, Physics, Computational Chemistry or a related field.
Strong problem-solving skills, autonomy and a collaborative mindset.
A track record of pushing the state of the art: you’ve developed ML models from scratch and led state-of-the-art research initiatives end to end.
Expert programming skills in Python and deep learning frameworks (e.g. PyTorch, JAX, TensorFlow).
Experience leading cross-team projects autonomously and mentoring others.
Impact-driven: you turn research into something used in production.
Clear communication with both technical and non-technical stakeholders.

Nice‑to‑Have

Exposure applying AI to drug discovery on the chemistry side (protein modelling, small molecules, protein–ligand), with an open mind to new approaches.
Hands-on experience with scientific computing and molecular modelling libraries (e.g. RDKit, OpenMM).
Experience with Bayesian optimisation or uncertainty quantification.
Proficiency productionising models and working closely with engineering teams.

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

Principal AI Research Scientist