Machine Learning Intern

About Generate Biomedicines

Generate:Biomedicines is a new kind of therapeutics company – existing at the intersection of machine learning, biological engineering, and medicine – pioneering Generative Biology™ to create breakthrough medicines where novel therapeutics are computationally generated, instead of being discovered. The Company has built a machine learning-powered biomedicines platform with the potential to generate new drugs across a wide range of biologic modalities. This platform represents a potentially fundamental shift in what is possible in the field of biotherapeutic development.

We pursue this audacious vision because we believe in the unique and revolutionary power of generative biology to radically transform the lives of billions, with an outsized opportunity for patients in need. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Generate:Biomedicines was founded in 2018 by Flagship Pioneering and has received over $700 million in funding, providing the resources to rapidly scale the organization. The Company has offices in Somerville and Andover, Massachusetts with 300+ employees.

The Role:

The Machine Learning team at Generate:Biomedicines develops new technologies for protein generative modeling and therapeutic discovery, and we are looking for creative and motivated graduate student interns to join us for a summer of research. During this time, interns will work with a mentor to develop a project exploring new kinds of ML modeling approaches for proteins, which can address foundational problems in biochemistry, molecular biology, and immunology while leveraging advances at the forefront of ML for language, vision, geometry, and uncertainty. Interns will have broad exposure to the technologies across the platform through cross functional interactions with the wet lab as well as social and educational programming to get to know scientists working in industry and to learn more about how research can translate into making medicines for patients. 

Internship projects for the summer of 2026 are available within the machine learning, data science, computational structure determination, and computational protein generation groups at Generate:Biomedicines. 

Here's how you will contribute:

• Contribute to ML research advancing the state of art in machine learning of sequence, structure, and function, its application to therapeutic generation, and its acceleration with agentic approaches to science 
• Work with a mentor to advance a summer research project while collaborating and developing high-quality code in a cross-functional team 

Examples of past projects developed between mentor and mentee include: 

• Building generative models of protein sequence and structure
• Modeling protein interactions using generative models
• Building and evaluating models that predict biophysical properties or drug like properties
• Learning new representations for proteins
• Leveraging Generate’s high-throughput functional data to advance protein design
• Application of generative models to design molecules for real-world drug programs 

Key Experiences during the internship will include: 

• Exploring ideas and innovations with your mentor and team
• Presenting your research to the Computational Sciences team, and learning from experienced team members  
• A capstone presentation of your project at the Machine Learning Intern Summer Symposium, where you’ll present your work to the entire company
• Several events with your mentors and teammates 

The Ideal Candidate will have:

• Current PhD Student in Applied Math, Computer Science, Computational Biology, Statistics, or a related field is required for this internship
• Experience with conceiving of, implementing, and developing novel Machine Learning methodology with generative modeling and/or LLM-based workflows
• Experience with modern deep learning frameworks such as Pytorch, JAX, or Tensorflow
• Proficiency in Python and experience analyzing data with Numpy/Scipy, R, or similar 
• Experience working with protein sequence and/or structure data is a plus
• Experience with developing agentic applications that orchestrate LLMs with tools (APIs, databases, code execution) is a plus

Timeline: 3 months, June-August in Summer 2026

Location: Onsite Monday-Friday at our location in Somerville, Massachusetts 

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Generate:Biomedicines 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.

COVID Safety:

Generate:Biomedicines enforces a mandatory vaccination policy for COVID-19. All employees must be fully vaccinated and have received a booster.  The purpose of this policy is to safeguard the health of our employees, their families, and the community at large from infectious disease that may be reduced by vaccinations.  The Company will make exceptions to this policy if required by applicable law and will consider requests for an exemption from this policy due to a medical reason, or because of a sincerely held religious belief, or any other exemptions that may be recognized by applicable.

Recruitment & Staffing Agencies: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.