Senior Machine Learning Scientist, Cheminformatics



Software Engineering
San Francisco, CA, USA · Remote · San Francisco Bay Area, CA, USA
Posted on Saturday, May 13, 2023

Senior Machine Learning Scientist, Cheminformatics

Atomwise is a technology-enabled pharmaceutical company leveraging the power of AI to revolutionize small molecule drug discovery. The Atomwise team invented the use of deep learning for structure-based drug design; this technology underpins Atomwise’s best-in-class AI discovery engine, which is differentiated by its ability to find and optimize novel chemical matter. Atomwise has extensively validated its discovery engine, delivering success in over 185 projects to-date including a wide-variety of protein types and numerous “hard-to-drug” targets. Atomwise is building a wholly owned pipeline of small-molecule drug candidates, with three programs in lead-optimization and over 30 programs in discovery. The company has raised over $174 million from leading venture capital firms to advance its mission to make better medicines, faster.

The Atomwise Machine Learning Research & Cheminformatics group works on solving challenging machine learning problems for small-molecule drug discovery and development. We have a dynamic and stimulating work environment that encourages creativity, innovation, and problem-solving. We believe that our success is driven by the quality of our team, and we are committed to providing a supportive and inclusive workplace where all employees can thrive.

About the role

We are seeking a highly skilled Machine Learning Scientist with expertise in structure-based drug discovery and cheminformatics. The successful candidate will have a deep understanding of modern machine learning and deep learning techniques and be able to apply them to large, complex data sets to extract meaningful insights. Working closely with our team of biologists, chemists, software engineers, and other cheminformatics scientists, the Machine Learning Scientist will communicate complex concepts clearly and effectively.


  • Implement and apply machine learning algorithms that drive our internal pipeline in early discovery and for partner projects.
  • Analyze and interpret large and complex data sets using machine learning techniques to extract insights and improve our internal decision-making processes.
  • Keep up to date with the latest developments in machine learning, cheminformatics and related fields such as bioinformatics to identify opportunities and apply these techniques to our work.
  • Present research findings at conferences and communicate results and insights to stakeholders in a clear and concise manner.


  • PhD in Computer Science, Statistics, Mathematics, Cheminformatics, Bioinformatics, or a related field
  • Strong background in machine learning and statistical modeling techniques
  • Proficiency in Python and experience with machine learning libraries such as Scikit-Learn, TensorFlow, and PyTorch
  • Familiarity with deep learning techniques, e.g. Graph Neural Networks (GNNs) or transformers. Experience with active learning is a plus.
  • Experience handling large-scale and complex real-world data. Preference with experience curating, compiling, and utilizing datasets with at least millions of data points.
  • 3+ years of experience of developing or applying predictive models in a corporate environment.
  • Hands-on experience with structure-based drug discovery
  • Excellent communication and collaboration skills
  • Strong problem-solving skills and attention to detail

Preferred qualifications:

  • Domain expertise and hands-on experience developing and applying deep learning models to address open challenges in drug discovery.
  • Familiarity with cloud computing platforms such as AWS or GCP.
  • A strong track record of publications in top-tier academic journals and conferences. Candidates who have published AI-related research in the field of drug discovery or pharmaceuticals are highly desirable.

If you're excited about making a significant impact on the future of drug discovery, we encourage you to apply today!

Compensation & benefits

  • Competitive salary, commensurate with experience
  • Stock compensation plan – you’ll be an Atomwise 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
  • High performance culture
  • Great colleagues

Atomwise is an equal opportunity employer and strives to foster an inclusive workplace. Our mission is to develop better medicines faster, and we know that we need a diverse team to develop medicines that serve diverse populations. Accordingly, Atomwise 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.

*Pay range for this role is between $205,000 - $235,000*