Pioneering Intelligence | Cambridge, MA Principal ML Scientist, Multimodal Biological Reasoning

Flagship Pioneering; Cambridge (MA); On-site; USD 216,000 - 297,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering in Cambridge, MA is seeking a Principal ML Scientist to lead groundbreaking efforts in building AI systems that unify human expertise and biological signals for biology. The role involves innovative model development for high-value use cases and integrating reasoning engines into scientific workflows.

The ideal candidate will possess strong expertise in modern LLMs, computational biology, and demonstrated ability to guide technical design and communication within interdisciplinary teams.

Qualifications

• Industry-leading expertise in modern LLMs, multimodal modeling, and ML systems.
• Deep experience in computational biology and AI-enabled drug discovery.
• Ability to work with scientists to define and translate discovery needs into technical plans.

Responsibilities

• Own the project roadmap from architecture to model readiness.
• Guide technical architecture through biological lens.
• Build and integrate reasoning engines into the AI Scientist platform.

Skills

Modern LLMs

Multimodal modeling

Computational biology

AI-enabled drug discovery

Biological data modalities

Education

PhD, MS in relevant fields

Tools

Machine Learning systems

LLMs

Job description

Principal ML Scientist, Multimodal Biological Reasoning

Cambridge, MA USA

The Role

Pioneering Intelligence is seeking a Lead for Flagship's ambitious efforts to build polyintelligent AI systems that unify human scientific expertise, machine intelligence, and nature’s biological signals into multi-modal, multi-scale reasoning engines for biology.

As Lead, you will have the unique opportunity to shape our biological reasoning efforts on both the technical and application levels. You will be a hands‑on lead for a team of talented machine learning scientists innovating on model architectures that will create best‑in‑class biological reasoning engines. You will be responsible for sourcing high-value use cases across Flagship and its portfolio companies and translating these into requirements to develop the model towards optimal performance on the unconventional life sciences problems that Flagship tackles. You will work with teams in Pioneering Intelligence and Flagship‑at‑large to apply our reasoning engines to discover new biology and engineer new biological solutions through massively parallel in‑silico reasoning. You will have the opportunity to originate and lead multiple projects in this space over time.

Key Responsibilities

• Own the roadmap: lead the project from architecture and data exploration through model readiness, benchmarking, refinement, and agentic integration.
• Guide technical architecture through a biological lens: guide multi‑modal, multi‑scale model design and ensure the system can ingest and reason over modalities relevant to mechanism‑of‑action reasoning, target discovery, perturbation biology, pathway reasoning, protein function, and autonomous discovery workflows.
• Translate biology into model and evaluation requirements: ensure model development is driven by biological relevance that enables real scientific workflows, not just benchmark performance or technical elegance.
• Build the engine for a novel science platform: develop and integrate reasoning engines into Pioneering Intelligence's AI Scientist platform for autonomous science.
• Source and shape portfolio use cases: interface with Flagship teams and portfolio company end‑users to identify use cases, source data assets, define success criteria, and create end‑user feedback loops for reasoning engines that are scientifically meaningful, tractable, and answer high‑value questions with real world application.
• Communicate the impact: disseminate strategic direction and scientific results to Flagship stakeholders and in public forums.

Qualifications

• 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.
• Demonstrated ability to work with scientists or biotech teams to scope high‑value use cases, identify data assets, define success criteria, and translate discovery needs into technical execution plans.
• Working knowledge of biological data modalities such as genomics, transcriptomics, perturbation data, protein sequence, protein structure, pathways, imaging, pathology, or time‑series biological data.
• Strong judgment around mechanism‑of‑action reasoning, target discovery, perturbation biology, scientific credibility, model limitations, hallucination risk, interpretability, and validation.
• Experience leading small, high‑caliber technical teams through ambiguous scientific or product problems.
• Ability to communicate clearly with ML researchers, data engineers, portfolio‑company scientists, executives, and venture creation leaders.
• Comfort operating in an entrepreneurial environment where the goal is not only to build a model, but to create a new capability that can reshape company creation and scientific discovery.

Requirements

• PhD, MS, or equivalent experience in computational biology, machine learning, bioengineering, computer science, systems biology, quantitative biology, translational science, or a related field.
• Experience in biotech, pharma, AI‑for‑science, AI drug discovery, venture creation, or a platform organization serving multiple scientific programs.
• Experience deploying AI/ML for biology systems into scientific workflows at enterprise scale.
• Experience with LLMs, biological foundation models, protein language models, genomic foundation models, scientific agents, or AI discovery platforms.
• Experience working across multiple internal and external customers, therapeutic programs, or discovery teams.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

The salary range for this role is $216,000 - $297,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.