Senior ML Software Engineer

About Aqemia

Aqemia is a next-generation pharmatech reinventing drug discovery with quantum-inspired physics and generative AI. Our mission: design innovative small-molecule drug candidates for dozens of critical diseases, faster and smarter, without relying on experimental data. Unlike traditional approaches, Aqemia starts drug discovery purely in silico. By combining physics-based models with large language models trained on proprietary data, we identify promising molecules with high accuracy before synthesis. We’ve already delivered multiple preclinical successes and secured strategic partnership. Our internal pipeline is growing fast, with several programs in in vivo optimization. We’re a team of 65+ based in Paris and London, we bring together chemists, physicists, engineers, and machine learning experts to push the boundaries of what’s possible in early-stage drug discovery.

The Role

As a Senior ML Software Engineer in the DH Team, you will focus on building and scaling the platform-facing product that manages the full lifecycle of Aqemia’s predictive models, our core scientific assets. You’ll scale and industrialize ML/deep learning models developed by research scientists, so they can be efficiently served to our Drug Hunter community. You will play a critical role in the development, deployment, and maintenance of single predictors, ensuring they are robust, reproducible, and seamlessly integrated into the platform that drives our drug discovery engine. This role is deeply technical and foundational to our platform’s performance, reliability, and scalability.

What you’ll do

• Design and implement ML product and infrastructure to support the training, evaluation, deployment, and versioning of predictive models
• Industrialize and optimize ML/deep learning models developed by scientists, making them scalable and cost-efficient in production
• Collaborate closely with scientists to integrate diverse predictors (physics-based, AI-based, hybrid) into the platform
• Ensure reproducibility, traceability, and performance of model pipelines across the full lifecycle
• Develop APIs and tools that expose predictors as scalable services to other teams
• Contribute to software engineering best practices across the ML stack (testing, CI/CD, observability)
• Partner with platform engineers and product stakeholders to ensure technical alignment and delivery

What we’re looking for

• 6+ years of experience in software engineering with strong focus on machine learning systems
• Deep proficiency in Python and ML ecosystem (e.g. PyTorch, scikit-learn, MLFlow)
• Solid understanding of data and model lifecycle management, versioning, and deployment
• Experience building ML infrastructure and model-serving pipelines in production environments
• Familiarity with cloud-based architecture (AWS preferred), containerization (Docker), and orchestration tools
• Ability to work autonomously and lead initiatives with high technical ownership
• Strong communication skills and ability to work closely with scientists and engineers alike

Preferred mindset

• You care about building solid foundations for ML at scale
• You combine scientific curiosity with software engineering rigor
• You enjoy tackling complexity and finding elegant, maintainable solutions
• You thrive in a cross-functional, fast-moving environment where models meet production

Why Join Us

At Aqemia, engineers don’t just build software, they help discover real drugs. You’ll work at the intersection of AI, physics and chemistry, transforming bold scientific ideas into robust, production-grade tools that accelerate discovery.

• DeepTech Mission: Build the platform that powers AI-driven drug discovery, combining quantum-inspired physics with generative models
• Real-World Impact: Every feature shipped helps scientists prioritize molecules and design better candidates, faster
• Modern Stack & Challenges: Python, FastAPI, Airflow, Snowflake, Kubernetes, ML workflows, scientific infra, data engineering at scale
• High Ownership, High Impact: Engineers contribute to architecture, tooling, and scientific decision-making
• Interdisciplinary Team: Collaborate with chemists, physicists, ML researchers, and product teams
• Prime Locations: Central Paris or London offices, with 2 remote days/week
• Strategic Traction: Backed by $100M in funding and a $140M partnership with Sanofi

Join us if you’re excited to shape the future of AI-driven drug discovery, and want your code to change the course of real diseases.