Head of AI/ML Therapeutic Design

About this role

Company Description

Metaphore Biotechnologies is a Flagship Pioneering-founded company focused on creating a new class of functional biological therapeutics. We are pioneering the power of function-first AI drug design and high-throughput data assays to make previously intractable drug targets accessible and unlock breakthroughs that outperform today's drugs for maximum patient impact.

Our computationally driven MIMIC™ platform is the world's first structure-independent sequence-to-function platform for protein design. Inspired by nature, our mission is to transform patient lives by unlocking the power of biological therapeutics with a new mimic-discovery platform.

Role Summary

Metaphore is seeking an exceptional, execution-driven scientist and leader to serve as Head of AI/ML Therapeutic Design, driving the next frontier of AI-powered biologics. In this role, you will define the vision and long-term strategy for Metaphore’s AI/ML platform while leading a team of experts to build a scalable, high‑performance AI/ML engine. Working closely with cross-functional drug discovery teams, you and your team will translate advances in AI/ML into impactful therapies by delivering actionable molecule candidates. As a key member of the R&D leadership team, you will shape how AI/ML transforms every stage of our drug discovery process—from high-throughput assay design and novel therapeutic generation to lead optimization and candidate nomination. This role offers a unique opportunity to drive our integrated discovery platform end-to-end and help bring transformative therapeutics from concept to clinic.

Key Responsibilities

• Scientific & Technical Leadership: Deploy state-of-the-art generative models for de novo protein design, and molecule screening, and optimization, focusing on timely drug discovery impact. Architect and train new models with a clear path towards program impact and differentiation.

• Strategic Vision: Define the AI strategy and deployment for Metaphore. Oversee at-scale compute infrastructure and propose collaborative data acquisition strategies to continuously train, evaluate, and optimize our models while optimizing costs and program impact.

• Team Building & Mentorship: Recruit, mentor, and lead a multidisciplinary team of computational scientists. Foster a culture of engineering rigor, scientific curiosity, and bold, tech-first innovation. Act as a senior hands-on mentor to nurture and grow the team.

• Platform Operations & LDBT Loop: Partner deeply with our Discovery as well as Biologics & Enabling Technologies teams to seamlessly integrate high-throughput laboratory data into model training, accelerating the Learn-Design-Build-Test (LDBT) loop to an industrial scale. Consistently demonstrate rapid learning and iterative improvements to our AI/ML platform across stakeholders.

• Portfolio Impact: Drive the computational discovery of novel therapeutic candidates across multiple modalities, advancing our internal pipeline and strategic partnerships (such as our active pharma collaborations).

• External Engagement: Represent Metaphore’s AI/ML platform externally, clearly communicating differentiation and value. Cultivate partnerships with leading tech providers, cloud computing partners, and academic institutions. Publish breakthroughs in top-tier AI conferences and scientific journals.

Required Qualifications

• Advanced degree (PhD preferred) in Computer Science, Machine Learning, Computational Biology, Physics, Applied Mathematics, or related discipline.

• 15+ years of industry or rigorous academic experience, with a proven track record of developing and deploying novel deep learning architectures for molecular biology, protein design, or structural biology.

• Deep expertise in modern machine learning paradigms (Transformers, Diffusion, Equivariant architectures) and a strong command of state-of-the-art tools, including ML-ops.

• Demonstrated experience leveraging AI/ML, reproducibly and at scale, delivering impact in drug discovery contexts.

• Demonstrated experience with modern engineering architectures to facilitate rapid and scalable implementation and deployment of AI/ML capabilities.

• Demonstrated experience leveraging heterogeneous high- and small-throughput datasets to drive model development.

• Significant experience managing and scaling high-performing computational teams in a fast-paced, matrixed tech-bio or big tech environment.

• A strong publication record in top-tier AI/ML venues (e.g., NeurIPS, ICML, ICLR) and/or scientific journals (e.g., Nature, Science, Cell), or a track record of shipping impactful, widely used models/software in the biomolecular space.

Values and Behaviors

• We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort working in and contributing to a dynamic and cross-functional team environment.

• Ability to translate complex AI concepts to cross-functional stakeholders, seamlessly bridging the gap between cutting-edge computational research and wet-lab drug discovery.

• Act decisively and own end-to-end accountability, making timely, data-informed decisions, taking responsibility for results, and delivering commitments in dynamic environments.

• At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way.

About Flagship Pioneering Flagship Pioneering invents and builds bioplatform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $75 billion in aggregate value. The current Flagship ecosystem comprises 43 companies, including Moderna (NASDAQ: MRNA), Generate Biomedicines, Omega Therapeutics, Sana Biotechnology, and Tessera Therapeutics.

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