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Senior Machine Learning Engineer, Molecular Modeling

Rockville, Maryland
Job Type
14 Jul 2022

Axle Informatics is a scientific research and information technology company that offers innovative computer services, informatics, and bioresearch solutions to research centers and healthcare organizations around the globe. With expertise in software engineering, bioinformatics, molecular research, and program management, we focus on developing and applying technological tools and scientific techniques to empower the world of research. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH).

Job Description

We are looking for a Senior Machine Learning Engineer, Molecular Modeling to support projects at the NIH. The position will be based in North Bethesda, Maryland. We are looking for a skilled and motivated engineer with expertise in molecular modeling, representation and active learning, and software engineering. The successful applicant will be involved with developing a next-generation open source molecular modeling platform to facilitate high throughput screening, drug discovery, and other molecular modeling efforts across the NIH. Axle is offering this position as in-person, fully remote, or hybrid.

The engineer will contribute to the design and creation of tools and interfaces which enable the automation and execution of large-scale drug discovery pipelines on our integrated computational platform. This involves leveraging representation and active learning techniques to efficiently traverse vast chemical spaces to help accelerate preclinical drug discovery projects. The new libraries will be part of a rapid decision-making platform to advance lead molecules to the clinic and facilitate high-throughput screening to help scientists study unexplored biologically active chemical space.

The ideal candidate will be an expert in state-of-the-art representation learning methods and have some experience in a modern computational chemistry domain as well as significant software engineering craft. They will work with the molecular modeling team and other domain experts to translate their needs into requirements for the platform. They will participate in software design and documentation; stay current with scientific and technical literature; stay informed about new approaches and technologies, including participation in conferences, and/or workshops; and independently locate and utilize scientific resources.

  • Participate in scientific-related needs assessment, as well as facilitate the development of the molecular modeling platform.
  • Lead the design and implementation of low-dimensional chemical space representations and active learning workflows built on top of the molecular modeling platform.
  • Create and maintain APIs and plugins which integrate machine learning applications and molecular modeling packages.
  • Act as an expert technical and scientific resource for software development staff in all phases of the development and implementation process
  • Containerize and deploy developed software on internal cloud computing platforms.

The ideal candidate will have:
  • A Master's degree or equivalent in computer science, computer engineering, bioengineering, statistics, chemical engineering, life sciences, or related STEM fields. Or equivalent practical experience.
  • Demonstrable expertise in representation learning, deep learning, and active learning methods.
  • Advanced programming skills with intricate knowledge of at least Python and/or modern C++.
  • Demonstrated ability to write high-quality, production-ready code (readable, well-tested, with well-designed APIs).
  • Familiarity with cheminformatic and bioinformatic tools and libraries such as RDKit and PubChem.
  • Familiarity with cloud computing services (AWS, GCP, or Azure).
  • Experience implementing systems and supporting non-technical scientific staff.
  • A high level of attention to detail.
  • A strong work ethic, and the ability to design projects within diverse research areas and datasets.
  • Excellent oral and written communication skills in English, and record keeping skills.

    • 100% Medical, Dental & Vision premium coverage for Employees
    • Paid Time Off (Including Holidays)
    • Employee Referral Bonus
    • 401K Match
    • Tuition reimbursement and professional development opportunities
    • Flexible Spending Accounts:
      • Healthcare (FSA)
      • Parking Reimbursement Account (PRK)
      • Dependent Care Assistant Program (DCAP)
      • Transportation Reimbursement Account (TRN)
The diversity of Axles employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.

Accessibility: If you need an accommodation as part of the employment process please contact: Email:

Disclaimer: The above description is meant to illustrate the general nature of work and level of effort being performed by individuals assigned to this position or job description. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description or responsibilities as needed.

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  • Job Reference: 658157592-2
  • Date Posted: 14 July 2022
  • Recruiter: Axle Informatics
  • Location: Rockville, Maryland
  • Salary: On Application
  • Sector: Manufacturing Operations
  • Job Type: Permanent