Senior Machine Learning Scientist

Most of the molecules driving human biology are invisible to us. Mass spectrometers already detect metabolites, lipids, and peptides, but the vast majority of those signals never get identified. A typical experiment names a small fraction of its features and discards the rest. We call this biology's dark matter. It’s signal-rich and mechanism-defining, yet almost entirely opaque.

Matterworks is building the foundation models that make that dark matter legible. Our Large Spectral Models do for biochemical biology what AlphaFold and ESM did for proteins: turning a library-bound discipline into something predictable and generative, and embedding it at every stage of R&D.

Come build the future of biological discovery with us.

Position Overview

As a Senior Machine Learning Scientist, you will be a core contributor to our deep learning systems, designing, building, and optimizing the neural network architectures that interpret complex mass spectrometry data. You will own significant model components and drive projects from experimentation through deployment. This role requires hands-on depth in deep learning and a passion for building high-quality, impactful models.

Key Responsibilities

• Model Development: Design, adapt, and optimize deep learning architectures for our scientific domains and data modalities, working within our Large Spectral Model framework.

• Project Execution: Own and deliver on complex ML projects, including experiment design, implementation, evaluation, and iteration based on results.

• High iteration velocity: Write clean, well-tested code in PyTorch and NumPy enabling a high experimentation rate.

• Research and Innovation: Stay current with deep learning research and its applications in chemistry and biology. Propose and prototype new ideas to enhance our modeling capabilities.

• Collaboration: Work closely with scientists and engineers across the team to integrate models into our product and infrastructure.

Qualifications

• Ph.D. M.S. in a quantitative field (Computer Science, Chemistry, Physics, or related), or equivalent experience.

• 3+ years of hands-on experience building and deploying deep learning models.

• Strong proficiency in Python, PyTorch, and NumPy.

• Demonstrated experience designing or adapting neural network architectures. Publications or a portfolio of relevant projects valued.

• Experience with spectral analysis, structure prediction, or molecular representation learning is a plus.

• Familiarity with scientific data formats (e.g., HDF5, mzML, Zarr) is a plus.

Given the cross-disciplinary and innovative nature of our work, effective collaboration and communication are critical to our progress. We operate in a flexible hybrid model that accommodates both fully remote team members and those who work full-time from our Somerville, MA office. While some positions may require regular in-person presence for hands-on work or local collaboration, many roles can be performed remotely with team members distributed across various locations.

Matterworks offers full-time employees a competitive base salary, stock options, and benefits (health & dental, vision, long- and short-term disability, life insurance, 401k with company match). Employees enjoy a flexible work & unlimited time away policy, commuter benefits and parking, regular team meals and outings, and company support for continued education/coursework and conference participation.

Matterworks, Inc. is an equal opportunity employer. All candidates for employment at Matterworks are considered without regard to race, color, religion, national origin, age, sex, marital status, ancestry, physical or mental disability, veteran status, gender identity, sexual orientation, or any other category protected by law.