---
title: 'Machine Learning Scientist, Pretraining at Profluent'
canonical: 'https://feeny.ai/job/machine-learning-scientist-pretraining-profluent-emeryville-rj16p67r3h9c'
type: 'job'
last_seen: '2026-09-06'
---

# Machine Learning Scientist, Pretraining at Profluent

- **Company:** Profluent
- **Location:** Emeryville, CA
- **Compensation:** $200k–$330k
- **Work type:** hybrid
- **Posted:** 2026-08-03
- **Last confirmed live:** 2026-09-06
- **Apply:** https://job-boards.greenhouse.io/profluent/jobs/5375801008

## Job description

Profluent is the frontier AI lab for biology. Profluent builds powerful foundation models for all of life's molecules, unlocking solutions that transform medicine, agriculture, and beyond. Founded in 2022 and headquartered in Emeryville, CA, Profluent is backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures and has 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

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.

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

## About Profluent

## Company Overview
- **One-liner**: Profluent is an AI-first protein design company that develops deep generative models to design and validate novel, functional proteins for biomedicine, agriculture, and other industries.
- **Entity Type**: Private (Series B; total funding $150M)
- **Headquarters**: Emeryville, California, United States
- **Founded**: 2022
- **Founders**: Ali Madani (CEO), Alexander Meeske

## Core Business
- **Primary industries**: Biotechnology, Artificial Intelligence, Genetic Medicine
- **Target customers**: B2B – pharmaceutical companies, biotech firms, agricultural companies, and research institutions
- **Mission statement**: "Decode the language of life with AI" – using AI to author new biology and create solutions that transform medicine, agriculture, and beyond.

## Products & Services
- **OpenCRISPR**: The world's first AI-designed gene editor, made open-source to accelerate genome editing research. Based on a novel nuclease generated by Profluent's generative AI.
- **AI Protein Design Platform**: A proprietary platform that writes proteins from scratch or by reimagining natural scaffolds, enabling rapid design of proteins for therapeutic, industrial, and agricultural applications.
- **Partnerships (e.g., Eli Lilly)**: Collaborations to develop AI-designed recombinases for genetic medicine, with deal value up to $2.25 billion.

## Market Standing
- **Valuation / Market Cap**: Not publicly available
- **Key Metric (Total Funding)**: $150M raised across multiple rounds (Seed $9M in 2022, Venture Round $35M in 2024, Series B $106M in 2025)
- **Notable Investors**: Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, Convergent Ventures
- **Growth Signals**: 
  - Headcount grew 78.4% YoY (53 employees as of mid-2026)
  - Published generative AI research in Nature (July 2025)
  - Secured a landmark partnership with Eli Lilly (up to $2.25B in milestones)
  - LinkedIn followers grew 67.8% in the past year (11,906 followers)

## Competitive Advantages
- **Pioneering AI-first protein design**: One of the few companies translating large language models (LLMs) to biology, with demonstrated ability to create functional gene editors from scratch.
- **Open-source gene editing**: OpenCRISPR-1 provides a freely available AI-designed nuclease, establishing thought leadership and potential ecosystem lock-in.
- **Cross-disciplinary team**: Combines top ML talent (from Salesforce, Meta, Amazon) with leading biologists (from CRISPR pioneers, UCSF, Harvard, Arc Institute).
- **Published in top journals**: Nature publication validates the scientific rigor of their approach.

## Strategic Focus
- Advance AI-designed recombinases for in vivo gene editing through the Lilly partnership
- Expand platform to design enzymes, antibodies, and industrial proteins
- Continue open-source releases to drive adoption and attract top research talent
- Scale headcount across ML, biology, and bioinformatics functions

## Why Work Here
- **Culture & Mission**: Opportunity to work at the frontier of AI and biology, authoring new proteins that can transform medicine and agriculture. Team culture emphasizes curiosity, societal impact, and breakthrough science.
- **Work Policy**: Hybrid – most roles require 2-3 days on-site at the Emeryville, CA headquarters. Some lab-based roles (e.g., in vivo pharmacology, LNP formulation) are fully on-site.
- **Team mix**: Diverse backgrounds spanning ML science, structural biology, software engineering, and drug discovery. Flat structure with direct access to founders and top domain experts.
- **Notable perks**: Backed by top-tier investors; highly collaborative environment; opportunities to publish and release open-source work.
- **Growth trajectory**: Fast-growing company (78% headcount increase in last year) with substantial funding runway and a high-profile pharma partnership, offering strong career progression.

## Sources
1. [profluent.bio](https://www.profluent.bio/)
2. [Greenhouse Jobs at Profluent](http://job-boards.greenhouse.io/profluent)
3. [LinkedIn Company Page](https://www.linkedin.com/company/profluent-bio)
4. [CB Insights Profile](https://www.cbinsights.com/company/profluent-bio)

## Other roles at Profluent

- [Software Engineer, Machine Learning Platform](https://feeny.ai/job/software-engineer-machine-learning-platform-profluent-emeryville-hywmbz47mnac) — Emeryville, CA
- [Controller](https://feeny.ai/job/controller-profluent-emeryville-5cn74bd9x1tp) — Emeryville, CA
- [Executive Director / Vice President, Biology & Translational Pharmacology](https://feeny.ai/job/executive-director-vice-president-biology-translational-pharmacology-profluent-rr9mkm28evx8) — Emeryville California, United States
- [Machine Learning Scientist, BioML](https://feeny.ai/job/machine-learning-scientist-bioml-profluent-emeryville-4q794vqye0e5) — Emeryville, CA
- [Associate Director - Director, In Vivo Pharmacology](https://feeny.ai/job/associate-director-director-in-vivo-pharmacology-profluent-emeryville-california-st6r3q5meyk1) — Emeryville California, United States
- [Machine Learning Scientist, Reinforcement Learning](https://feeny.ai/job/machine-learning-scientist-reinforcement-learning-profluent-emeryville-yheaagr10bes) — Emeryville, CA
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- [Senior Software Engineer, Data Platform](https://feeny.ai/job/senior-software-engineer-data-platform-profluent-emeryville-abqg7npe00ws) — Emeryville, CA
- [Machine Learning Research Engineer](https://feeny.ai/job/machine-learning-research-engineer-profluent-emeryville-apxa7hrr11cy) — Emeryville, CA
- [Lead Scientist / Associate Director, Bioinformatics and Data Science](https://feeny.ai/job/lead-scientist-associate-director-bioinformatics-and-data-science-profluent-vdkp2feygcje) — Emeryville, CA