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Director of Machine Learning Research

A-Alpha Bio

A-Alpha Bio

Software Engineering
Seattle, WA, USA
Posted on Thursday, March 30, 2023

A-Alpha Bio is an early-stage and rapidly-growing drug discovery company headquartered in Seattle, WA. We are enabling the next generation of high-impact therapeutics by combining high-throughput synthetic biology with state-of-the-art machine learning. We partner with leading pharma and biotech companies to enable the discovery of antibodies, molecular glues, and other protein interaction-related drugs. In parallel, we use our AlphaSeq technology internally to build a Biologics Pipeline for clinical development and/or asset licensing opportunities.

Candidates local to Seattle are preferred, but remote applicants are welcome to apply. Candidates must reside in the US.

Starting Salary Range: $223,000 - $279,000 per year

Exemption Status: Exempt

Location Expectations: Remote-Eligible (travel to Seattle required once quarterly, on average)

Role Description

A-Alpha Bio is seeking an experienced and highly motivated Director of Machine Learning Research to lead a team of ML Scientists and Engineers responsible for the development and deployment of cutting-edge machine learning models trained on proprietary AlphaSeq data to design and optimize biologics. The Director will be responsible for the development, prioritization, and management of complex internal research initiatives involving synthetic biology, antibody engineering, and machine learning. The role will also work closely with the Project Management and Business Development teams to determine feasibility, bandwidth constraints, ownership, and execution of external partnerships and collaborations involving machine learning. Success in this position requires the ability to prioritize based on key strategic objectives, synthesize complex issues into actionable solutions, and effectively and persuasively communicate to diverse stakeholders, including the executive team. The ideal candidate will have significant management experience in a highly technical environment, and must be passionate about being a strong advocate for their team. This position will report to the VP of Data Science.


  • Grow and manage a high-performing team of researchers and engineers working on machine learning for protein design and optimization.
  • Build systems and tools that enable scientists to rapidly design, test, and iterate on ML models at scale.
  • Set the direction for engineering practices related to data and model management, model assessment and benchmarking workflows, collection of data and metadata from wet-lab experiments, and design and execution of wet-lab experiments to support ML research goals.
  • Work closely with scientists leading A-Alpha’s external partnerships and internal programs to maximize the impact of machine learning for ongoing drug discovery and optimization campaigns.
  • Participate in the publication of research papers and filing of patents.



  • PhD in Computer Science, Machine Learning, Computational Biology, or a similar field; or an equivalent combination of education and experience.
  • 10+ years of industry experience and 5+ years of management
  • Direct experience in the application of deep learning to high-throughput biological sequence data.
  • Familiarity with state-of-the-art ML techniques in at least one of the following areas: antibody or protein engineering, drug discovery, NGS-based assays, and/or synthetic biology.
  • Proven leadership in recruiting and managing high-performing teams of scientists and engineers in a cross-functional and fast-paced environment, with a history of maximizing and growing internal talent.
  • Ability and desire to contribute to ML research as an expert individual contributor in addition to management duties.
  • Impressive technical track record at leading technology or pharma/biotech.
  • Strong interpersonal and verbal/written communication.
  • Strong problem-solving skills and creativity.


  • Experience with the development and deployment of ML models for design of biologics.
  • Experience with the application of NLP techniques to high-throughput biological sequence data at scale.
  • Experience creating and maintaining deployment pipelines with CI/CD tools.
  • Expertise with Python, Pandas, Pytorch, and AWS.

We offer competitive compensation, including benefits and equity in a fast-growing start-up. Applicants must have legal authorization to work in the United States.

About A-Alpha Bio

A-Alpha Bio is an early-stage biotechnology company combining synthetic biology and machine learning to dramatically improve the discovery of high-impact therapeutics. We believe that abundant high-quality data is critical for understanding biology and curing disease – and synthetic biology is our catalyst. Our proprietary AlphaSeq platform uses genetically engineered cells to quantitatively measure millions of protein interactions – from which we generate high-resolution models of biology.

In 2018, we spun out of the University of Washington’s Institute for Protein Design and Center for Synthetic Biology – both fantastic communities of brilliant and highly entrepreneurial scientists. Since the company’s inception, we have focused on partnering with pharmaceutical companies to discover and optimize drugs for therapeutic areas ranging from infectious disease to cancer. We are growing rapidly, and new members of the team should expect a fast-paced and highly dynamic work environment. We are building a diverse, meritocratic, and supportive team that shares our values of speaking the truth, shooting for the moon, taking the reins, playing for the team, and improving the world.

A-Alpha Bio is headquartered in a brand-new combined office/lab space in downtown Seattle's Belltown neighborhood. While the startup lifestyle occasionally requires grueling hours, we strongly value the need for a work-life balance and time out of the lab/office. We are fortunate to be situated in a region that is renowned for its premier outdoor activities, including hiking, biking, climbing, skiing, kayaking, and sailing. At A-Alpha, you’ll find many who love the outdoors, but also gamers, amateur chefs, explorers, sports fans, bakers, crafters, photographers, brewers, jetsetters, animal lovers, and artists. Whatever your passions, you belong at A-Alpha Bio.