Flagship Labs 117: Generative Chemistry Co-Op

Location: Cambridge, MA USA Department: Co-Ops & Internships

This position is open exclusively to current Northeastern University Co-Op students.

Work Period: January 2027 to June 2027. This is a full - time, 40 hours per week position with 5 days in office.

About Flagship Labs 117

Flagship Labs 117 (FL 117) is a Flagship-backed, stealth-stage AI x Bio startup pioneering the next generation of multi-modal generative models for biomolecular design. We are building the architectures, training pipelines, and computational frameworks that will power the future of intelligent drug discovery. We are looking for extraordinary computational scientists and engineers. You will collaborate closely with an interdisciplinary team of ML researchers, computational biologists, and biophysicists to push the limits of molecular representation and generative modeling.

About Flagship Pioneering

Flagship Labs 117 was founded by Flagship Pioneering's venture creation engine 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 company’s 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.

Flagship Pioneering Co-Op Program

Welcome to Flagship Pioneering Co-Op Program for the cohort dreaming big and taking courageous leaps. You'll join fellow peers across our ecosystem of companies and learning firsthand how we build first-in-category companies. You’ll have access to enrichment sessions, a dedicated professional development track, and a mentor that help guide you toward your next step. By the end, you will carry on a meaningful project outcome, a genuine network, and a front-row view of how Flagship pioneer new ventures that change the world.

About the Role

Our Co-ops will work on cutting-edge problems at the intersection of machine learning, biology, and chemistry, helping advance our molecular design platform.

We use techniques such as

Multimodal generative models: diffusion, flow matching, and language models (ex: for proteins)

Data-driven biophysical modeling to link molecular structure and function.

Key Responsibilities

Work with an interdisciplinary team of scientists to build models and deploy models

Curate and organize data from multiple publicly and proprietary sources

Experiment with diverse datasets and novel techniques

Communicate your work to a multi-disciplinary audience

Basic Requirements

Fluency in Python and experience implementing ML methods with standard tools and packages (e.g., PyTorch, JAX).

Readiness to deep dive into the biology/physics/chemistry of the platform companies we build

Preferred Requirements

Experience working with RDKit, BioPython, Rosetta, OpenMM, PySCF, etc

Publications or experience in CS, ML, Computational Chemistry/Biology or a similar computational field.

Experience with generative models, natural language processing, graphical neural networks, reinforcement learning, or similar.

Familiarity with software development, including git and public cloud computing resources (e.g. AWS, GCP, Azure).

What We Offer

Build alongside founders. You’ll work inside the same hypothesis-driven process Flagship uses to conceive and launch first-in-category companies.

This can be the start of a longer story. Strong co-ops are considered for future opportunities across Flagship and its portfolio companies, not just for this one role.

Work alongside people who left the safe path. Your colleagues are scientists, engineers, and operators who chose to build something new rather than join something already established.

Take on real ownership. You're contributing to ventures that are still being defined. Your work can shape real decisions, not just support them.

Be paid like the contributor you are. Compensation reflects the real work you take on.

Flagship Pioneering is 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.

The pay range for this role is $25 - $35 per hour. This role is a short-term engagement that is not eligible for health and welfare benefits. Retirement benefits may be available after completing a set number of hours. Compensation and benefits information is based on Flagship Labs 117'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, 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 ques