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