Intern - Machine Learning Engineer

Vilya is a computational biotechnology company creating a novel class of medicines to precisely target disease biology. We believe computational approaches are an integral, if not foundational, component of drug discovery and development. Our platform is built on ground-breaking research in advanced computational approaches and taps into uncharted chemical space to design new molecular structures not found in nature.
We are harnessing the power of our platform to go after previously impossible targets in an array of indications. Vilya’s ultimate goal is to solve some of the most challenging unmet medical needs that exist today.
Our Vision: Harness a revolution in technology and biology to better human health
Our Mission: Build an independent, leading biotech company founded on intelligent drug design to cure the incurable
We think from atoms to bits – and everywhere in between; now, we are seeking a highly-motivated, creative, and knowledgeable Intern - Machine Learning Engineer to support Vilya's R&D efforts.
Vilya is a team-first organization, and we believe onsite work is essential to how we collaborate, move quickly, and build a strong culture. This is an onsite position in our Seattle office. Join us during the summer of 2026 to help us build a highly-scalable computational drug discovery platform!
RESPONSIBILITIES:

• Develop and maintain the infrastructure to support deep learning workflows for drug design at scale
• Implement and optimize algorithms for data processing, model training and model deployment
• Collaborate with and support the computational scientists at Vilya to help build a world-class computational macrocycle drug discovery pipeline
• Participate in the development and enhancement of our software platform to ensure that our codebase remains reliable, efficient, secure, and scalable
  

BASIC QUALIFICATIONS:

• Experience developing, deploying, and managing deep learning models and formatting large datasets for real-world problems
• Experience with modern deep learning frameworks, like PyTorch or JAX
• Experience with Python scientific computing tools, such as numpy, scipy, pandas, etc
• Understanding of general software development concepts, including git, containers, testing, cloud computing, etc
• Experience working within Linux environments
• Ability to effectively communicate with a team of diverse backgrounds
• Graduating with a B.S. or higher in Computer Science (or similar degree) in or before the spring of 2027
• Ability to work on site in our Seattle, WA office, no relocation costs will be provided through this internship
  

PREFERRED QUALIFICATIONS:

• A solid background in machine learning, including linear algebra, statistics, and calculus
• Experience with modern generative modeling frameworks, such as flow matching and diffusion
• Familiarity with techniques for modeling point-clouds or graphs (GNNs, equivariant transformers, etc.)
• Familiarity with basic cheminformatics libraries and tools (RDKit, OpenBabel, PyMol, etc.)
• An interest in drug discovery and working with biochemical data
  

VILYA INTERN COMPENSATION AND BENEFITS:

• Wage: $25/hour - $45/hour, based on a combination of education and experience
• Opportunity to work in a disruptive startup with a talented, experienced, and dedicated team
• Monthly commuter stipend