Machine Learning Research Engineer, AI/ML for Drug Discovery

About Numerion Labs:

Numerion Labs (previously known as Atomwise) is an AI-native biotech company leveraging AI/ML to revolutionize small molecule drug discovery. The Numerion team invented the use of deep learning for structure-based drug design, which is a core technology of our best-in-class AI discovery and optimization engine, which is differentiated by its ability to find and optimize novel chemical matter. In multiple settings, structurally novel chemical matter has increased the likelihood of developing first-in-class and best-in-class medicines that have the potential to transform patient care.

Numerion has extensively tested its discovery and optimization engine, delivering hit ID success in over 230 academic and collaboration projects to date that cover a wide breadth of protein classes and numerous “hard-to-drug” targets. We work in collaborative partnerships with other companies, and we are building an internal pipeline of small-molecule drug candidates with first-in-class and best-in-class potential in immunology.

The Role:

We seek a highly motivated and creative Machine Learning Research Engineer to join our ML Platform team. You will be at the forefront of developing and applying advanced machine-learning models to accelerate the discovery of novel therapeutics. Your work will directly impact the development of innovative AI-driven drug discovery platforms. This role offers the opportunity to work on challenging problems at the intersection of machine learning, chemistry, and biology, with access to extensive datasets and state-of-the-art computational resources.

Responsibilities:

• Conduct original research in developing, implementing, and modifying model architectures, data representations, and tooling for virtual screening of ultra-large libraries and for optimization of hit compounds toward drug-like properties
• Perform in-depth analyses of model outputs and performance metrics to identify opportunities for improvement
• Design, execute, and communicate the results of experiments to evaluate and improve model performance
• Maintain and extend our scalable and efficient machine learning frameworks for at-scale use by drug discovery teams
• Collaborate with domain-expert model users and applications scientists
• Stay current with the latest literature in relevant domains and integrate cutting-edge advances into our ML models
• Share results with internal and external stakeholders, with varying levels of ML expertise, via presentations, publications, conferences, blog posts, etc.

Qualifications:

• Either a PhD in machine learning, computer science, statistics, computational chemistry, or a related field; OR documented exceptional experience in cutting-edge ML research in the form of high-impact publications and open-source projects
• 3+ years of experience in an industry setting (preferably 1+ years in a small startup)
• Hands-on experience with R&D in modern ML - for example in diffusion models, flow-matching, foundation model training methods, etc - including experience designing and implementing novel architectures and algorithms
• Experience with collaborative software engineering and developing high quality, maintainable, well-documented code, especially in Python and PyTorch
• Strong communications skills, particularly in communicating with domain experts applying and working with ML models, and with non-experts seeking to understand the impact of your discoveries (or models)

Preferred:

• Record of publications, conference presentations, open-source projects, etc.
• Experience with modern machine learning models of biological molecules and chemical systems
• Familiarity with molecular data and commonly used cheminformatics and bioinformatics tools, such as RDKit, PyMol, etc.
• Facility with the use of LLM coding tools is a plus
• Location in the San Francisco Bay Area commutable to our downtown SF office 1-3 days a week is preferred; location in our San Diego office or remote is possible for the right candidate

Compensation & Benefits:

• Competitive salary, commensurate with experience
• Stock compensation plan – you'll be a Numerion Labs co-owner
• Platinum health, dental, and vision benefits for you and your dependents
• 401(k) retirement plan with generous company match (up to 4%)
• Flexible paid time off (PTO), 13 paid holidays, and wellness breaks for employees to spend time with their loved ones and recharge
• Health Savings and Flexible Spending Account options to help save money on healthcare, daycare, and commuting
• Employee Assistance Program (EAP) and Pet Insurance
• Funding for professional development and conference attendance
• Flexible work schedule
• Generous paid parental leave

Numerion Labs is an equal opportunity employer and strives to foster an inclusive workplace. We are a TechBio company leveraging AI/ML to revolutionize small-molecule drug discovery, and we know that we need a diverse team to develop medicines that serve diverse populations. Accordingly, Numerion does not make any employment decisions (including but not limited to, hiring, compensation, and promotions) on the basis of race, religion, color, national origin, gender, gender identity, sexual orientation, age, veteran status, disability status, or any other characteristics protected by applicable federal, state, and local law.

We strongly encourage people of diverse backgrounds and perspectives to apply.

The base salary for this position is $175,000- $250,000. Pay is determined by multiple factors including, but not limited to, a candidate's geographical location, experience and skills.