Principal ML Scientist, Multimodal Biological Reasoning at Flagship Pioneering, Inc.
About the role Flagship Pioneering is seeking a highly skilled Principal ML Scientist to take a leadership role in developing cutting-edge polyintelligent AI systems tailored for biological research and discovery. This position involves spearheading initiatives that combine human expertise, machine learning, and biological insights to build advanced reasoning engines. The successful candidate will work at the intersection of AI and biology, creating cutting-edge solutions that can autonomously analyze complex biological data, generate hypotheses, and support scientific decision-making. The role offers an exciting opportunity to influence the future of scientific discovery by integrating state-of-the‐art AI technologies into biological applications, ultimately enabling new insights and breakthroughs in health and medicine.
Key facts Location: Cambridge, MA USA Engagement: Full‐time Team: Pioneering Intelligence
What you'll do
Lead the design, development, and deployment of AI systems focused on biological data analysis, reasoning, and autonomous scientific exploration.
Architect and oversee the technical framework for biological AI applications, ensuring systems can process, interpret, and analyze diverse biological datasets effectively.
Convert complex biological challenges into precise model requirements, establishing clear specifications that guide development and validation processes.
Build and refine reasoning engines to be integrated into the AI Scientist platform, enabling autonomous hypothesis generation, experimental design, and data interpretation.
Collaborate closely with internal teams, including scientists, engineers, and product managers, to identify high‐value use cases, gather relevant biological data, and define success metrics.
Maintain ongoing communication of scientific insights, technological advancements, and project progress with stakeholders, including leadership and external partners.
Drive innovation by incorporating emerging AI methodologies such as large language models, biological foundation models, protein language models, genomic foundation models, and scientific agents into the platform.
Mentor and guide multidisciplinary technical teams working on multimodal AI projects, fostering a culture of scientific rigor, creativity, and continuous learning.
Establish best practices for model development, validation,



and interpretability, ensuring the AI systems are scientifically credible and reliable.
Evaluate and incorporate new AI techniques to improve the system's ability to reason about biological mechanisms, targets, and perturbations.
Support the integration of AI solutions into broader biological workflows, including drug discovery, target identification, and therapeutic development.
Engage with external scientific communities, conferences, and publications to share insights, promote collaboration, and stay at the forefront of AI and biology research.
Requirements
PhD, MS, or equivalent experience in computational biology, machine learning, bioengineering, computer science, systems biology, quantitative biology, translational science, or related disciplines.
Proven experience working within biotech, pharmaceutical, or AI‐driven scientific organizations, supporting or leading projects in AI applications for biology or drug discovery.
Demonstrated success in implementing AI/ML solutions within large‐scale biological or scientific workflows, with a focus on reasoning, data analysis, or autonomous systems.
Familiarity with large language models, biological foundation models, protein language models, genomic foundation models, scientific agents, or AI discovery platforms.
Experience working collaboratively with diverse teams, including scientists, engineers, data scientists, and external partners, to translate scientific questions into technical solutions.
Strong problem‐solving skills, with the ability to translate complex biological challenges into effective AI models and systems.
Ability to communicate technical concepts clearly to non‐technical stakeholders, including leadership and venture creation teams.
Experience with project management, leading initiatives from conception through deployment, and ensuring alignment with scientific and business goals.
Knowledge of regulatory considerations, including handling of sensitive biological data and compliance with relevant regulations.




Familiarity with ITAR regulations and the management of protected or classified biological information is a plus.
Nice to have
Experience with scientific discovery platforms and AI‐enabled drug discovery tools.
Knowledge of representation learning, multimodal modeling, and techniques for model fine‐tuning, post‐training, and benchmarking.
Prior leadership experience managing high‐caliber technical teams working on complex scientific challenges.
Background in translational science, target discovery, perturbation biology, or mechanism‐of‐action reasoning.
Familiarity with the latest advances in AI interpretability, model robustness, and scientific credibility assessments.
Skills & tools
Expertise in large language models, multimodal AI, representation learning, and benchmarking techniques.
Deep understanding of computational biology, AI for biology, and scientific discovery platforms.
Strong communication skills to effectively liaise with researchers, data engineers, scientists, executives, and venture teams.
Ability to evaluate scientific credibility, interpretability, and the mechanistic reasoning capabilities of AI models.
Experience leading technical teams through complex scientific and engineering challenges, fostering innovation and collaboration.
Proficiency in programming languages and frameworks relevant to AI development, such as Python, TensorFlow, PyTorch, or similar tools.
Practical notes
The salary range for this position is between $216,000 and $297,000.
Compensation will be determined based on the candidate's experience, skills, and qualifications.
Flagship Pioneering offers comprehensive healthcare coverage, an annual incentive program, retirement benefits, and various additional perks.
The provided salary and benefits information are estimates as of the publication date and may be subject to change.
The company is committed to equal opportunity employment and encourages applicants from diverse backgrounds to apply.
All qualified candidates will be considered without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.
Even if candidates do not meet every listed requirement, they are encouraged to apply, as the company values diverse and inclusive teams that bring different perspectives and experiences to scientific innovation.
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📌 Principal Ml Scientist, Multimodal Biological Reasoning (Western Australia)
🏢 Flagship Pioneering
📍 Western Australia