Biotech ML Data Scientist (Molecular Data)

Output Biosciences; San Francisco (CA); On-site; USD 140,000 - 220,000; Full time

Job summary

Output Biosciences is seeking a PhD-level computational biologist to own the data that our models learn from, moving beyond surface patterns to genuine molecular understanding. You will curate, source and transform diverse biological datasets, grounding them in first-principles biology to improve model reasoning.

In this role you will design benchmarks, create new training signals where data is sparse, and collaborate with model researchers to align data with learning objectives across scales

Qualifications

• PhD in computational biology, biophysics, structural biology, chemistry or related field with 2+ years of post-doctoral or industry research experience, or equivalent depth through combined biology and computational background.
• Deep understanding of molecular interactions, protein structure, and biological data at the molecular level, grounded in first principles.
• Experience working with large-scale biological or molecular datasets, including sourcing, cleaning, integrating, and analyzing heterogeneous data.
• Strong programming skills in Python and building computational pipelines for data processing at scale.
• Understanding of what ML models require from training data: coverage, quality, balance and evaluation rigor.
• Data construction as a research problem, considering signal, meaning and gaps.

Responsibilities

• Construct training datasets capturing protein and molecule interactions from diverse sources.
• Develop methods to expand training data beyond public databases where data is sparse or absent.
• Design benchmarks grounded in real molecular phenomena to test model learning.
• Collaborate with model researchers to determine data needs and learning priorities across modalities.
• Integrate data across scales and modalities to create coherent training signals.
• Design robust data splitting/evaluation to ensure generalization to real biological problems.
• Keep current with biological data sources, experimental methods, and molecular databases.

Skills

Computational biology

Biophysics knowledge

Python programming

Large-scale data analysis

Data integration

ML data requirements

Molecular interactions understanding

Education

PhD in computational biology or related field

Job description

Output Biosciences is seeking a PhD-level computational biologist to own the data that our models learn from, moving beyond surface patterns to genuine molecular understanding. You will curate, source and transform diverse biological datasets, grounding them in first-principles biology to improve model reasoning.

In this role you will design benchmarks, create new training signals where data is sparse, and collaborate with model researchers to align data with learning objectives across scales