ProFound Therapeutics, Inc. | Boston, MA Associate Director / Director, AI & Machine Learning

Overview Boston, MA USA

About ProFound Therapeutics 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.

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 Flagship Pioneering is a biotechnology company that invents and builds platform 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 $90 billion in aggregate value. Many of the companies Flagship has founded 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 at www.flagshippioneering.com.

If your experience is close to what we're looking for, please consider applying. Experience comes in many forms, skills are transferable, and passion goes a long way. We know that diverse backgrounds and experiences make for the best problem-solving and creative thinking, which is why we're dedicated to adding new perspectives to the team and encourage everyone to apply. We look forward to learning more about you.

We are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

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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