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Senior Scientist, Machine Learning

A-Alpha Bio

A-Alpha Bio

Software Engineering
Seattle, WA, USA
Posted on Saturday, March 16, 2024

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 United States.

Starting Salary Range: $166,000 to $208,000 per year

Exemption Status: Exempt

Location Expectations: Remote-Eligible

Role Description

At A-Alpha Bio, we’re on a mission to improve human health by unlocking the potential of protein-protein interactions – and we’re now seeking a Senior Scientist to join our Machine Learning Research team in researching and developing cutting-edge machine learning models trained on proprietary protein-protein interaction (PPI) data for the optimization of biologics.

  • As an ML scientist, you’ll research state-of-the-art AI algorithms protein language models, generative AI, and geometric deep learning that unravel the intricacies of protein-protein interactions to advance our technology and power our in-house drug discovery pipeline.
  • As an ML engineer, you’ll develop a robust and extensible code base, advocate for software best practices, ensure data integrity, and deploy scalable models in cloud computing environments.
  • As a mentor, you’ll closely collaborate and serve as a role model for a team of world-class ML scientists, helping to raise the bar for research and increase team-wide technical expertise.

Key Responsibilities

  • Design and implement novel machine learning approaches for prediction and engineering of protein-protein interactions; use these approaches to solve challenges in drug discovery and optimization.
  • Generate deliverables (e.g., new code features, research reports, presentations, and data sets) to a high level of quality suitable for broad consumption within the company, as well as in accordance with assigned timelines.
  • Regularly and expertly contribute to the company codebase, authoring and reviewing merge requests and ensuring that new capabilities are effectively rolled out to the rest of the team.
  • Enthusiastically collaborate with the Machine Learning team, providing coaching, mentorship, and subject matter expertise to members of the broader Data Science department.
  • Perform other duties as assigned.

Qualifications & Experience


  • Bachelor’s degree in a related field with 6+ years of professional experience in machine learning, including 3+ years of direct experience with machine learning using biological sequence or protein structure data; or an equivalent combination of education and experience.
  • Extensive experience with deep learning, spanning use of modern software frameworks (PyTorch, TensorFlow, PyG); adapting, modifying, or originally developing model architectures (CNNs, VAEs, Transformers, graph neural networks); as well as familiarity with state-of-the-art generative AI approaches (diffusion, language models)
  • Deep understanding of underlying theory and mathematics for machine learning and ability to translate and implement it into code.
  • Strong expertise in data science and experience with manipulating/transforming data, model selection, model training, cross-validation, and deployment at scale.
  • Familiarity with scientific concepts in biochemistry, physical chemistry, molecular physics, and biology.
  • Excellent skills in communicating research results with both technical and non-technical audiences.


  • PhD in a related field.
  • Domain expertise with Python and Amazon Web Services (or other cloud provider, such as Azure, GCP).
  • Familiarity with developing, deploying, and maintaining machine learning engineering systems for model training and inference, including aspects of CI/CD, MLOps, distributed computing, and/or data engineering.
  • Familiarity with the state of the art in antibody engineering, protein engineering, synthetic biology, or other high-throughput biology environments.
  • A record of scientific research publications and/or presentations in top-tier journals and conferences.

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. At this time, A-Alpha Bio is unable to offer visa sponsorship in any form.

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.