Associate Director / Director, AI & Machine Learning job opportunity at Flagship Pioneering.

Home Jobs In United States Of America Tag: Machine Learning and AI Associate Director / Director, AI & Machine Learning position at Flagship Pioneering


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Flagship Pioneering Associate Director / Director, AI & Machine Learning
Experience: 8-years
Pattern: full-time
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Machine Learning and AI

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degreePhD
loacation Boston Massachusetts, United States Of America
loacation Boston Massach..........United States Of America

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.

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Associate Director / Director, AI & Machine Learning Applicants are expected to have a solid experience in handling Machine Learning and AI related tasks