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 to measure protein-protein interactions at scale with state-of-the-art machine learning to predict how proteins bind. We partner with leading pharmaceutical and biotechnology companies to enable the discovery of antibodies, molecular glues, and other protein interaction-related drugs. In parallel, we use our wet-lab and computational platforms to discover and develop an internal pipeline of biologics and molecular glues to improve human health.
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
Required
- 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.
Preferred
- 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, flexible time off, 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 a biotechnology company that leverages synthetic biology and machine learning to measure, predict, and engineer protein-protein interactions. Our AlphaSeq platform applies synthetic biology to experimentally measure millions of protein interaction affinities simultaneously. Protein binding data is incorporated into our AlphaBind platform to train machine learning models that predict binding from sequence. We use both platforms to discover and optimize high-impact therapeutics for our pipeline and in partnership with leading pharmaceutical and biotechnology companies.
In 2018, A-Alpha Bio spun out of the University of Washington’s Institute for Protein Design and Center for Synthetic Biology – both communities filled with brilliant and highly entrepreneurial scientists. Since the company’s inception, we have focused on an oncology-centered internal pipeline along with pharma and biotech partnerships to collaboratively train predictive machine learning models and discover and optimize drugs for therapeutic areas ranging from infectious disease to neurodegeneration. New members of the team should expect a fast-paced, highly dynamic, and interdisciplinary 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 custom designed lab and office 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. We are fortunate to be situated in a region that is renowned for its premier outdoor activities, including hiking, biking, climbing, skiing, kayaking, sailing, and more. 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!