Associate Director, Portfolio Modeling & Simulation

Who We Are

Flagship Pioneering is a bioplatform innovation 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.

Position Summary

We are seeking an Associate Director, Portfolio Modeling & Simulation to join the Strategic Operations and Analytics team to collaborate with Pioneering Intelligence (PI), a Flagship initiative dedicated to developing AI/ML-powered platforms for transformative applications in life sciences and related fields, to build a state-of-the-art computational capabilities for strategic portfolio modeling. Flagship Pioneering increasingly leverages data and systems to create novel insights that drive some of the most important decisions made across the Flagship enterprise. The Strategic Operations and Analytics team works closely with Flagship’s CEO, Managing Partners, and most teams across Flagship in support of driving value throughout the organization and across our companies. In this role, you will lead the design and implementation of quantitative models that guide portfolio strategy across a complex pipeline. You will advance the science and ship decision tools that translate research into strategic resourcing and allocation choices for high-impact decisions across the Flagship ecosystem by building proprietary models and leveraging state-of-the-art computational methods. 

Responsibilities

• Formulate and solve multi-objective portfolio optimization problems using modern optimization libraries and state-of-the-art statistical methods; generate Pareto trade-offs and scenario recommendations.
• Develop and validate PTRS models; calibrate against internal/external benchmarks and quantify uncertainty.
• Build portfolio simulations (e.g., Monte Carlo, scenario/sensitivity, discrete-event) to quantify risk-adjusted value, timelines, and resource needs
• Incorporate asset interdependencies (correlated technical risk, shared resources, indication overlap) and real-world constraints into models
• Design decision frameworks to inform asset selection, staging, and go/no-go decisions
• Build and maintain data pipelines; ensure data quality and documentation
• Create visualizations for translating complex results into key insights 
• Collaborate cross-functionally to develop, validate, and refine models
• Present progress in regular research meetings, prepare reports, and present findings for stakeholders and leadership
• Stay up to date on advances in Bayesian modeling, stochastic/robust optimization, and portfolio analytics; propose and prototype improvements

Qualifications

• PhD in a highly quantitative field (Statistics, Applied Math, Operations Research, Computer Science, Econometrics, Biostatistics, or similar).
• Deep proficiency in probabilistic/Bayesian modeling and uncertainty quantification (hierarchical models, survival/time-to-event, calibration, posterior predictive checks).
• Hands-on simulation experience (Monte Carlo, scenario/stress testing, discrete-event) plus sensitivity/uncertainty analysis.
• Decision/valuation modeling for R&D portfolios (risk-adjusted NPV, VOI/EVSI, real options); ability to translate business questions into quantitative experiments.
• Fluency in Python and standard statistical analysis packages
• Demonstrated ability to collaborate in interdisciplinary teams and communicate complex technical concepts effectively
• Ability to take initiative and work independently
• Excellent analytical and problem-solving skills tailored to innovative computational research

Preferred

• Prior industry experience (3+ years)
• Experience analyzing large-scale pharma/biotech or healthcare datasets and deriving strategic insights
• Prior use of specialized competitive intelligence databases (e.g. Clarivate Cortellis, EvaluatePharma, Citeline, GlobalData, etc.)
• Experience with version control software (e.g. Git) and AWS cloud computing
• Experience building PTRS models and familiarity with the PTRS literature and benchmarks.
• Biotech/pharma domain experience: development stage gates, clinical success rates, indication correlations, and trial timeline/resource modeling.
• Experience with experiment tracking and model governance (MLflow/W&B/DVC), and lightweight Python-based data pipelines.

Flagship Pioneering and our ecosystem companies 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. 

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

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 $150,000 - $185,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering’s good faith estimate as of the date of publication and may be modified in the future.