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Flagship Pioneering · 3 months ago

Associate Director / Director, AI & Machine Learning

Boston, MA USA

Full-time

Onsite

Senior Level, Lead/Staff, Director/Executive

7+ years exp

ProFound Therapeutics is pioneering the discovery of the expanded human proteome to unlock new potential therapeutics. They are seeking an experienced Associate Director / Director of AI & Machine Learning to shape and execute their AI/ML strategy while leading the development and implementation of advanced machine learning systems. This role will directly support the discovery of disease-driving proteins and pathways, advancing the mission to accelerate therapeutic development.

FinanceFinancial ServicesVenture Capital

H1B Sponsor Likely

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

Qualification

AI/ML strategyTransformer architecturesCausal inferencePythonGraph neural networksGenerative modelingMulti-omics dataCommunicationMentoringCross-functional collaboration

Required

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

Proven ability to balance strategic leadership with hands-on development and deployment of advanced ML models

Excellent communication skills, with the ability to convey complex technical insights to experimental biologists and drug discovery teams

Preferred

Experience working with multi-omics or high-dimensional biological data strongly preferred

Familiarity with knowledge graph technologies and graph databases is a plus

Experience with computational imaging or digital pathology data integration is a strong plus

Company

Flagship Pioneering

Glassdoor3.3

Flagship Pioneering is a venture capital firm that invests in life sciences and healthcare companies.

Founded in 2000

Cambridge, Massachusetts, USA

501-1000 employees

http://flagshippioneering.com

H1B Sponsorship

Flagship Pioneering has a track record of offering H1B sponsorships. Please note that this does not guarantee sponsorship for this specific role. Below presents additional info for your reference. (Data Powered by US Department of Labor)

Distribution of Different Job Fields Receiving Sponsorship

Represents job field similar to this job

Trends of Total Sponsorships

2025 (8)

2024 (4)

2023 (4)

2022 (4)

2021 (1)