Machine Learning Engineer

Job Description

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 Machine Learning Engineer to help us build a highly-scalable computational drug discovery platform.

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 and help make a difference for patients!

RESPONSIBILITIES:

Develop and maintain the infrastructure to support machine learning workflows for drug discovery 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 is reliable, efficient, secure, and scalable.

BASIC QUALIFICATIONS:

1+ year of experience developing and maintaining ML pipelines

Understanding of general software development concepts, including git, containers, testing, cloud computing, etc.

Experience with modern deep learning frameworks, like PyTorch or JAX

Experience with Python scientific computing tools, such as numpy, scipy, pandas, etc.

Experience working with big data pipelines

Experience working within Linux environments

Ability to effectively communicate with a team of diverse backgrounds

B.S. in computer science (or equivalent industry experience)

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 BENEFITS:

Opportunity to work in a disruptive startup with a talented, experienced, and dedicated team

401(k) plan with employer matching for contributions

Stock options

Excellent medical, dental, and vision coverage

Open, flexible vacation policy

Support to attend professional conferences meaningful to your career growth

Monthly cell phone and internet stipend

Monthly wellness and commuter stipend

#LI-Onsite

Salary range for Seattle, WA

$154,000—$174,000 USD

Full-time