Staff Software Engineer for AI-Driven Drug Discovery

Aqemia; Paris; Hybrid; EUR 75,000 - 105,000; Full time

Job summary

Aqemia is seeking a Staff Software Engineer for its Compute team based in Paris. The role focuses on creating scalable computing systems that power cutting-edge drug discovery processes. Ideal candidates will bring over 10 years of experience in software engineering, with expertise in production systems, distributed systems, and Python. The position offers collaboration with multidisciplinary teams and the chance to shape innovative scientific developments. Join us to make a real impact in healthcare.

Qualifications

• 10+ years of experience in software engineering with demonstrated impact at the staff level or equivalent.
• Strong experience building and operating production systems at scale.
• Deep expertise in distributed systems or compute-heavy environments.

Responsibilities

• Design, build, and operate scalable compute systems supporting training, inference, and scientific workloads.
• Improve the reliability, robustness, and performance of production systems used across research and platform teams.
• Develop internal tooling to streamline model and workflow lifecycle.

Skills

Software engineering

Production systems

Distributed systems

System architecture

Python

Tools

AWS

Postgres

SnowFlake

PyTorch

Kubernetes

Job description

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 isQEMI, 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 inventingnever-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 currentlyin 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, visitAQEMIA.com,ourWTTJ Page, and ourLinkedIn.

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 Engineering Department

The Engineering team (~12 people) builds and scales the technical foundations that power Aqemia’s drug discovery engine.

Bringing together expertise across software engineering, cloud infrastructure, data engineering, site reliability engineering (SRE), and scientific computing, the team designs and operates robust, secure, and high-performance platforms that enable Aqemia’s scientific and AI teams to experiment, train, deploy, and run models at scale.

Their work spans data infrastructure, scientific compute systems, cloud operations, orchestration, observability, CI/CD, developer tooling, and platform scalability. By transforming cutting-edge research into reliable and scalable systems, the team accelerates the discovery of new medicines while ensuring operational excellence and an outstanding developer experience.

Responsibilities

• Design, build, and operate scalable compute systems supporting training, inference, and scientific workloads

• Improve the reliability, robustness, and performance of production systems used across research and platform teams

• Develop internal tooling to streamline model and workflow lifecycle (build, test, deploy, run).

• Drive architectural decisions across compute and data systems in collaboration with engineering and research teams

• Improve developer experience for scientists by reducing friction in running and scaling experiments

• Establish and promote best practices in system design, observability, and AI-assisted / spec-driven development

• Contribute to raising the engineering bar across teams through mentorship and technical leadership

Qualifications

• 10+ years of experience in software engineering with demonstrated impact at the staff level or equivalent

• Strong experience building and operating production systems at scale

• Deep expertise in distributed systems or compute-heavy environments

• Strong hands-on experience in system architecture and design

• Fluent in Python and across the AWS / Postgres / SnowFlake / orchestration stack; comfortable on both sides of the code/infra boundary

• Serious hands-on experience with LLM-assisted engineering and spec-driven development - you’ve gone past tooling and built workflow and team practice around it

• Strong ownership mindset with the ability to operate across teams and communicate effectively

Nice‑to‑Have

• Experience with large-scale compute platforms or infrastructure

• Exposure to ML infrastructure or model execution environments

• Experience with PyTorch, CUDA, or running custom models in production

• Experience designing or operating workflow orchestration systems

• Track record of optimizing systems for cost-efficiency at scale

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 theFrench Tech 40andFrance 2030, highlighting our role as a key player in Europe’s DeepTech ecosystem.

Prime Location with Flexibility: Our offices are located in the heart ofParisandLondon (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