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Principal ML Scientist, Multimodal Biological Reasoning

3 weeks, 1 day ago
United States
Full-time
Lead
AI Research Scientist
Data Science and Analytics
LLM Machine Learning
Apply Now
Flagship Pioneering

Flagship Pioneering

Flagship Pioneering is a biotechnology firm that invents and develops innovative life science platforms and companies aimed at transforming human health and promoting sustainability.

Biotechnology
251-1K
Founded 1999
View All Jobs 12

Description

  • Own the roadmap from architecture and data exploration through model readiness, benchmarking, refinement, and agentic integration.
  • Guide multi-modal, multi-scale model design through a biological lens for reasoning over mechanism of action, target discovery, perturbation biology, pathway reasoning, protein function, and autonomous discovery workflows.
  • Translate biological needs into model and evaluation requirements that support real scientific workflows and not just benchmark performance.
  • Develop and integrate reasoning engines into Pioneering Intelligence’s AI Scientist platform for autonomous science.
  • Source, evaluate, and shape high-value use cases with Flagship teams and portfolio company end users.
  • Identify data assets, define success criteria, and build feedback loops for scientifically meaningful applications.
  • Apply reasoning engines with internal teams to discover new biology and engineer new biological solutions through in-silico reasoning.
  • Communicate strategic direction and scientific results to Flagship stakeholders and public audiences.
  • Lead and mentor a small, high-caliber technical team through ambiguous scientific and product problems.

Requirements

  • PhD, MS, or equivalent experience in computational biology, machine learning, bioengineering, computer science, systems biology, quantitative biology, translational science, or a related field.
  • Industry-leading expertise in modern LLMs, multimodal modeling, representation learning, fine-tuning, post-training, benchmarking, and ML systems.
  • Deep experience in computational biology, AI-for-biology, AI-enabled drug discovery, translational data science, biological foundation models, or scientific discovery platforms.
  • Experience deploying AI/ML systems for biology into scientific workflows at enterprise scale.
  • Experience with LLMs, biological foundation models, protein language models, genomic foundation models, scientific agents, or AI discovery platforms.
  • Working knowledge of biological data modalities such as genomics, transcriptomics, perturbation data, protein sequence, protein structure, pathways, imaging, pathology, or time-series biological data.
  • Demonstrated ability to scope high-value use cases with scientists or biotech teams and translate them into technical execution plans.
  • Strong judgment around mechanism-of-action reasoning, target discovery, perturbation biology, scientific credibility, model limitations, hallucination risk, interpretability, and validation.
  • Experience leading small technical teams through ambiguous scientific or product problems.
  • Experience in biotech, pharma, AI-for-science, AI drug discovery, venture creation, or a platform organization serving multiple scientific programs.
  • Experience working across multiple internal and external customers, therapeutic programs, or discovery teams.
  • Ability to communicate clearly with ML researchers, data engineers, portfolio-company scientists, executives, and venture creation leaders.
  • Comfort operating in an entrepreneurial environment focused on creating new capabilities for company creation and scientific discovery.

Benefits

  • Salary range of $216,000 - $297,000.
  • Healthcare coverage.
  • Annual incentive program.
  • Retirement benefits.
  • Broad range of additional benefits.
  • Equal opportunity employer commitment.
  • Consideration for candidates who do not meet every qualification, with encouragement to apply anyway.

Interested in this position?

Apply directly on the company website

Apply Now

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