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About This Role
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 a highly motivated Senior Machine Learning Engineer / Data Scientist to join our AI/ML team. This individual will play a central role in designing and implementing advanced AI/ML systems with a focus on Retrieval\-Augmented Generation (RAG), graph\-based RAG, large language models (LLMs), agentic orchestration, and conversational AI (chatbot) solutions. Working closely with the Head of AI/ML and cross\-functional partners, you will build and optimize LLM\-powered pipelines and multi\-agent systems that integrate knowledge graphs, multi\-omics data, and biological context to uncover disease\-driving proteins and pathways. The insights generated will directly support therapeutic discovery and development.
Key Responsibilities
- Architect and implement scalable RAG and LLM\-based systems that integrate multi\-modal data sources, including knowledge graphs, documents, and structured biological datasets.
- Design and deploy RAG and graph\-based RAG pipelines that leverage LLMs and knowledge graphs to retrieve, reason over, and synthesize complex biological information.
- Build and maintain agentic orchestration frameworks (multi\-agent systems) that coordinate LLM\-based agents for end\-to\-end scientific reasoning, data retrieval, and decision support.
- Collaborate with data engineering teams to design data pipelines that harmonize and prepare large\-scale omics datasets for model training.
- Develop and optimize conversational AI (chatbot) interfaces that enable scientists and stakeholders to query, explore, and interact with internal data and model outputs using natural language.
- Partner with experimental scientists to ensure model outputs are biologically interpretable and experimentally testable.
- Stay abreast of advances in LLMs, RAG architectures, agentic AI, and conversational AI; bring innovative ideas into the team.
Qualifications
- Ph.D. in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field with 1–3 years of industry experience (preferred); or M.S. in a related field with 4–6 years of industry experience.
- Proven track record in building LLM\-based applications, with hands\-on expertise in RAG, graph\-based RAG, agentic orchestration, and/or chatbot development.
- Proficiency in Python and LLM/ML frameworks such as LangChain, Hugging Face Transformers, PyTorch, or similar.
- Experience working with multi\-omics or high\-dimensional biological data is a plus
- Familiarity with probabilistic modeling, causal reasoning, or statistical inference is a plus.
- Strong experience with knowledge graph technologies, graph databases, and vector databases.
- Demonstrated ability to work in cross\-disciplinary teams, communicate complex ideas clearly, and deliver results in fast\-moving environments.
Why Join Us?
This role offers a unique opportunity to shape a next\-generation AI/ML platform at the intersection of computation and drug discovery. You will work in a collaborative environment with leaders in biology, computation, and therapeutics — helping to expand the boundaries of the proteome and accelerate the development of new medicines for patients.
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 at www.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.*
The salary range for this role is $96,000 \- $214,500\. 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.
Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI\-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [email protected].
Salary Context
This $96K-$214K range is below the median for Data Scientist roles in our dataset (median: $157K across 236 roles with salary data).
View full Data Scientist salary data →Role Details
About This Role
Data Scientists extract insights and build predictive models from data. In the AI era, many roles now include LLM-powered analytics, automated reporting, and integration with generative AI tools. The role has evolved from 'the person who runs SQL queries' to 'the person who builds AI-powered data products.'
Modern data science roles fall into two camps: analytics-focused (insights, dashboards, experimentation) and ML-focused (building predictive models, recommendation systems, NLP features). The best data scientists can operate in both modes. The AI shift means that even analytics-focused roles now involve building automated insight pipelines using LLMs, going well beyond one-off reports.
Across the 3,823 AI roles we're tracking, Data Scientist positions make up 8% of the market. At Flagship Pioneering, Inc., this role fits into their broader AI and engineering organization.
Data Scientist roles remain in high demand, though the definition keeps shifting. Companies increasingly want candidates who can bridge traditional statistics with modern ML and LLM capabilities. The 'pure insights' data scientist role is consolidating into analytics engineering, while the 'build models' data scientist role is merging with ML engineering.
What the Work Looks Like
A typical week includes: analyzing experiment results for a product feature launch, building a predictive model for customer churn, creating an automated reporting pipeline using LLM-powered summarization, presenting insights to stakeholders, and cleaning data (always cleaning data). The ratio of analysis to engineering varies by company, but expect both.
Data Scientist roles remain in high demand, though the definition keeps shifting. Companies increasingly want candidates who can bridge traditional statistics with modern ML and LLM capabilities. The 'pure insights' data scientist role is consolidating into analytics engineering, while the 'build models' data scientist role is merging with ML engineering.
Skills Required
Python, SQL, and statistical modeling are the foundation. Increasingly, roles want experience with LLMs for data analysis, automated insight generation, and building AI-powered data products. Familiarity with cloud data platforms (Snowflake, BigQuery, Databricks) and ML frameworks (scikit-learn, PyTorch) covers most job requirements.
Experimentation design and causal inference are underrated skills that separate strong candidates. Companies care about whether their product changes cause improvements, and can distinguish causation from correlation. A/B testing methodology, Bayesian statistics, and the ability to communicate uncertainty to non-technical stakeholders are high-value skills.
Good postings specify the data stack, the types of problems you'll work on, and the team structure. Look for companies that differentiate between analytics and ML data science. Vague 'data scientist' postings that list every skill under the sun usually mean the company doesn't know what they need.
Compensation Benchmarks
Data Scientist roles pay a median of $198,000 based on 808 positions with disclosed compensation. Senior-level AI roles across all categories have a median of $227,400. This role's midpoint ($155K) sits 22% below the category median. Disclosed range: $96K to $214K.
Across all AI roles, the market median is $200,100. Top-quartile compensation starts at $253,500. The 90th percentile reaches $307,500. For comparison, the highest-paying categories include AI Engineering Manager ($275,000) and AI Safety ($274,200). By seniority level: Entry: $97,880; Mid: $165,000; Senior: $227,400; Director: $247,800; VP: $250,000.
Flagship Pioneering, Inc. AI Hiring
Flagship Pioneering, Inc. has 1 open AI role right now. They're hiring across Data Scientist. Based in Cambridge, MA, US. Compensation range: $214K - $214K.
Location Context
Across all AI roles, 15% (590 positions) offer remote work, while 3,217 require on-site attendance. Top AI hiring metros: New York (2,643 roles, $211,000 median); San Francisco (2,168 roles, $253,000 median); Los Angeles (1,792 roles, $191,580 median).
Career Path
Common paths into Data Scientist roles include Data Analyst, Statistician, Quantitative Researcher.
From here, career progression typically leads toward Senior Data Scientist, ML Engineer, AI Product Manager.
Start with statistics and SQL. Build a real analysis project on public data that demonstrates insight generation alongside model building. The market values data scientists who can communicate findings clearly to business stakeholders. If you want to move toward ML engineering, invest in software engineering fundamentals and production deployment skills.
What to Expect in Interviews
Interviews combine statistics, coding, and business acumen. SQL is almost always tested, often with complex joins and window functions. Expect a case study round where you're given a business problem and asked to design an analysis plan. Coding rounds focus on pandas, statistical modeling, and visualization. The strongest differentiator is how well you communicate insights to non-technical stakeholders during presentation rounds.
When evaluating opportunities: Good postings specify the data stack, the types of problems you'll work on, and the team structure. Look for companies that differentiate between analytics and ML data science. Vague 'data scientist' postings that list every skill under the sun usually mean the company doesn't know what they need.
AI Hiring Overview
The AI job market has 3,823 open positions tracked in our dataset. By seniority: 112 entry-level, 1,798 mid-level, 1,516 senior, and 397 leadership roles (Director, VP, C-Level). Remote roles make up 15% of the market (590 positions). The remaining 3,217 roles require on-site or hybrid attendance.
The market median for AI roles is $200,100. Top-quartile compensation starts at $253,500. The 90th percentile reaches $307,500. Highest-paying categories: AI Engineering Manager ($275,000 median, 41 roles); AI Safety ($274,200 median, 55 roles); Research Engineer ($260,000 median, 434 roles).
Data Scientist roles remain in high demand, though the definition keeps shifting. Companies increasingly want candidates who can bridge traditional statistics with modern ML and LLM capabilities. The 'pure insights' data scientist role is consolidating into analytics engineering, while the 'build models' data scientist role is merging with ML engineering.
The AI Job Market Today
The AI job market spans 3,823 open positions across 15 role categories. The largest categories by volume: AI/ML Engineer (2,629), Data Scientist (322), AI Software Engineer (279). These three account for the majority of open positions, though smaller categories often have higher per-role compensation because of specialized skill requirements.
The seniority mix tells a story about where AI teams are in their maturity. Entry-level roles (112) are outnumbered by mid-level (1,798) and senior (1,516) positions, reflecting that most companies are past the 'build a team from scratch' phase and need experienced engineers who can ship production systems. Leadership roles (Director, VP, C-Level) total 397 positions, representing the bottleneck between technical execution and organizational strategy.
Remote work availability sits at 15% of all AI roles (590 positions), with 3,217 requiring on-site or hybrid attendance. The remote share has stabilized after the post-pandemic correction. Senior and specialized roles (Research Scientist, ML Architect) are more likely to be remote-eligible than entry-level positions, partly because experienced hires have more negotiating power and partly because these roles require less hands-on mentorship.
AI compensation is structured in clear tiers. The market median sits at $200,100. Top-quartile roles start at $253,500, and the 90th percentile reaches $307,500. These figures include base salary with disclosed compensation. Total compensation (including equity, bonuses, and sign-on) runs 20-40% higher at companies that offer those components.
Category matters for compensation. AI Engineering Manager roles lead at $275,000 median, while Prompt Engineer roles sit at $140,000. The spread between highest and lowest-paying categories reflects the premium on specialized technical skills versus broader analytical roles.
The most in-demand skills across all AI postings: Python (1,979 postings), Aws (1,190 postings), Azure (899 postings), Rag (839 postings), Gcp (726 postings), Pytorch (595 postings), Prompt Engineering (595 postings), Claude (540 postings). Python dominates, appearing in the vast majority of role descriptions regardless of category. Cloud platform experience (AWS, GCP, Azure) is the second most common requirement. The newer entrants to the top skills list (RAG, vector databases, LLM APIs) reflect the shift from traditional ML toward generative AI applications.
Frequently Asked Questions
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