Associate Director / Director, AI & Machine Learning

ABOUT PROFOUND

ProFound Therapeutics is pioneering the discovery of the expanded human proteome to unlock a new universe of potential therapeutics. By integrating multi-omics, advanced computation, and translational biology, we aim to reveal and characterize thousands of previously uncharted proteins and systematically explore their role in health and disease.

THE ROLE

We are seeking an experienced Associate Director / Director of AI & Machine Learning to join our growing team. This individual will play a key leadership role in shaping and executing our AI/ML strategy while remaining actively involved in hands-on model development and implementation. Reporting directly to our CTO, the successful candidate will lead the design and deployment of advanced machine learning systems — including generative and transformer-based models (LLMs), graph neural networks, and causal inference methods — within a multi-agent causal AI framework. These efforts will directly support the discovery of disease-driving proteins and pathways, advancing ProFound’s mission to accelerate therapeutic development.

KEY RESPONSIBILITIES

• Provide technical leadership while remaining hands-on in developing, training, and deploying AI/ML models.
• Architect and implement scalable ML systems that integrate multi-modal data (genomics, transcriptomics, proteomics, imaging, digital pathology, perturbation data).
• Lead the development of graph-based, transformer-based, and generative models (including LLMs and multi-modal transformers for biological and imaging data) to capture biological relationships and simulate interventions.
• Drive the creation of a multi-agent causal AI framework that integrates causal graph learning, interventional simulation, and knowledge graph reasoning.
• Collaborate with data engineering teams to design robust pipelines that harmonize and prepare large-scale omics datasets for model training.
• Implement, evaluate, and optimize causal inference approaches (e.g., DAG learning, treatment-effect estimation, counterfactual modeling).
• Partner closely with experimental scientists to ensure model outputs are biologically interpretable and experimentally testable.
• Mentor and develop junior AI/ML team members, fostering technical excellence and cross-disciplinary collaboration.
• Stay current with emerging advances in AI/ML, causal modeling, and computational biology; proactively introduce new approaches that strengthen the platform.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS

• Ph.D. or M.S. in Computer Science, Computational Biology, Biostatistics, Applied Mathematics, or related field, with 7+ years of relevant post-graduate or industry experience (biotech, pharma, or AI/ML research).
• Demonstrated expertise in transformer architectures, LLMs, graph neural networks, and generative modeling.
• Strong background in causal inference and probabilistic modeling, with practical experience applying DAG-based or counterfactual methods.
• Proficiency in Python and ML frameworks such as PyTorch, TensorFlow, JAX, or PyTorch Geometric.
• Experience working with multi-omics or high-dimensional biological data strongly preferred.
• Proven ability to balance strategic leadership with hands-on development and deployment of advanced ML models.
• Familiarity with knowledge graph technologies and graph databases is a plus.
• Experience with computational imaging or digital pathology data integration is a strong plus.
• Excellent communication skills, with the ability to convey complex technical insights to experimental biologists and drug discovery teams.

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. The level of the role will be commensurate with the education and years of experience of the identified candidate.

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. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship atwww.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

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.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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The salary range for this role is $212,000 - $319,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. ProFound Therapeutics, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on ProFound Therapeutics, Inc.'s good faith estimate as of the date of publication and may be modified in the future.