Founding ML Scientist, Molecular AI & MS

Novogaia; San Francisco (CA); On-site; USD 180,000 - 260,000; Full time

Benefits offered by this job

Visa sponsorship

Medical, dental, and 401(k)

Competitive salary and equity

Job summary

Novogaia is seeking a founding machine learning scientist to design and advance models that infer molecular structure and properties directly from mass spectrometry data. You will take ownership of Gaia-02, extending spectrum-to-structure reasoning and collaborating closely with computational biology and experimental teams.

This hands-on, fast-paced role sits in an early-stage company with significant autonomy and technical responsibility, offering competitive salary, early-stage equity, and

Qualifications

• Experience developing and training ML models in PyTorch or similar frameworks
• Experience designing novel modeling approaches and implementing the latest methods from the literature
• Ability to independently scope and execute research problems involving large, high-dimensional datasets, including handling noise and distributional shifts
• Experience training models at scale (cloud or HPC environments)
• Strong software engineering skills in Python, including writing clean, well-structured, production-quality code
• Experience with generative models (e.g., autoregressive, diffusion, flow) and geometric deep learning (e.g., GNNs, Deep sets, EGNNs)
• Experience working with molecular, chemical, or spectral datasets
• Familiarity with metabolomics or mass spectrometry workflows and computational models (e.g., MIST, DreaMS, ICEBERG)

Responsibilities

• Lead the development of the next generation of our molecular foundation model for mass spectrometry
• Design and train models for mass spectra to molecular structure inference
• Develop latent molecular representations from MS/MS and related data
• Extend structure predictions into downstream molecular reasoning (e.g., bioactivity, prioritization)

Job description

Novogaia is seeking a founding machine learning scientist to design and advance models that infer molecular structure and properties directly from mass spectrometry data. You will take ownership of Gaia-02, extending spectrum-to-structure reasoning and collaborating closely with computational biology and experimental teams.

This hands-on, fast-paced role sits in an early-stage company with significant autonomy and technical responsibility, offering competitive salary, early-stage equity, and