Machine Learning Scientist, Pretraining

Profluent; Emeryville (CA); Hybrid; USD 200,000 - 330,000; Full time

Benefits offered by this job

Competitive compensation with equity

401(k) with employer match

Health/dental/vision insurance

Generous PTO

Professional development

Job summary

Profluent Bio, Inc. in Emeryville, CA is seeking a Machine Learning Scientist to drive research on pretraining large-scale models for protein design. You will prototype novel autoregressive, diffusion and representation learning methods and collaborate with biology and ML teams.

This early employee role offers equity, a strong compensation package, and comprehensive benefits as you help shape the scientific direction of the company.

Qualifications

• PhD (or equivalent industry experience) in Computer Science, Machine Learning, Natural Language Processing, Applied Math, Computational Biology, Statistics, or a related field.
• Experience with conceiving, implementing, and evaluating novel ML and pretraining large-scale LLMs in biomolecular domain.
• Publications at major ML conferences or frontier AI/ML labs experience.
• Experience with modern deep learning frameworks such as PyTorch or Jax.

Responsibilities

• Design and develop state-of-the-art autoregressive, diffusion and representation learning models for protein design.
• Collaborate across ML and protein design teams to apply, adapt and improve pretraining techniques from other domains to biomolecular DL models.
• Architect, implement, and optimize core infrastructure to support the pretraining of protein language models.
• Curate relevant datasets and design tasks for rigorous evaluation of generative models.
• Implement, analyze, and interpret multiple computational approaches and present results to colleagues in regular update meetings.
• Work within a collaborative, fast-paced, interdisciplinary team across biology and ML to shape scientific and strategic vision.

Skills

LLM pretraining in biology

PyTorch

JAX

Research prototyping

Education

PhD in CS/ML/biomolecular fields

Tools

PyTorch

Job description

Profluent is an AI-first protein design company. Founded in 2022, we develop deep generative models to design and validate novel, functional proteins to revolutionize biomedicine. Based in Emeryville, CA, we are backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures, and have raised over $150M to date.

The Role We're looking for a motivated and creative Machine Learning (ML) Scientist to drive research into pretraining large-scale deep learning models for biomolecular design. This position offers an opportunity to work at the forefront of generative modeling research across language processing, representation learning, and protein engineering. You should be a self-directed researcher who has the ability to rapidly prototype and evaluate new models and algorithms in the biomolecular domain. As an early employee, you will proactively shape the direction of our machine learning efforts and collaborate across diverse teams of computational and experimental scientists.

Responsibilities

• Design and develop state-of-the-art autoregressive, diffusion and representation learning models for protein design
• Collaborate across the machine learning and protein design teams to apply, adapt and improve pretraining techniques from other domains to biomolecular deep learning models
• Architect, implement, and optimize core infrastructure to support the pretraining of protein language models
• Curate relevant datasets and design tasks for rigorous evaluation of generative models
• Implement, analyze, and interpret multiple computational approaches and present results to colleagues in regular update meetings
• Work within a collaborative, fast-paced, interdisciplinary team across biology and machine learning to help shape the scientific and strategic vision of the company

Qualifications

• PhD (or equivalent industry experience) in Computer Science, Machine Learning, Natural Language Processing, Applied Math, Computational Biology, Statistics, or a related field
• Experience with conceiving of, implementing, and evaluating novel machine learning and pretraining large scale LLMs or other models in biomolecular domain
• Publications at major machine learning conferences (NeurIPS, ICML, ICLR) or scientific journals (Nature, Science, Nature Biotech, Nature Methods, PNAS) or experience pre-training LLMs at frontier AI/ML labs
• Experience with modern deep learning frameworks such as Pytorch or Jax

Preferences

• Familiarity with foundational biology of proteins and nucleic acids
• Experience developing machine learning models for proteins (language models, structure prediction, design)
• Experience with cloud compute platforms (GCP, AWS, Azure, OCI)
• Previous experience in data extraction and curation from bioinformatics data sources
• Familiarity with wet lab experimental assays and associated limitations

What We Offer

• High-growth opportunity with meaningful impact on the future of protein design
• Competitive compensation package with equity participation
• 401(k) with a strong employer match
• Comprehensive benefits including health/dental/vision insurance
• Generous PTO policy and commitment to work-life balance
• Professional development opportunities in a cutting-edge field at the intersection of AI and biology

Employment Eligibility Verification

Legal authorization to work in the United States is required. In compliance with federal law, all persons hired must verify their identity and work eligibility and complete the required employment verification form upon hire.

Profluent Bio, Inc is an equal opportunity employer promoting diversity and inclusion in the workspace. We do not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical conditions, veteran status, sexual orientation, gender (including gender identity and gender expression), sex (which includes pregnancy, childbirth, and breastfeeding), genetic information, taking or requesting statutorily protected leave, or any other basis protected by law.

Hiring Salary Range $200,000 — $330,000 USD