Machine Learning Intern

Job Description

About Generate Biomedicines

Generate:Biomedicines is a pioneering therapeutics company operating at the intersection of machine learning, biological engineering, and medicine. They lead the field of Generative Biology™ to create breakthrough medicines by computationally generating novel therapeutics instead of traditional discovery methods. The company has developed a powerful machine learning-powered biomedicines platform capable of generating new drugs across a wide range of biologic modalities, representing a potential fundamental shift in biotherapeutic development.

Driven by an audacious vision, Generate:Biomedicines believes in the revolutionary power of generative biology to transform lives. Founded in 2018 by Flagship Pioneering, the company has secured over $700 million in funding, enabling rapid scaling. They employ 300+ employees across offices in Somerville and Andover, Massachusetts.

The Role: Machine Learning Intern (Summer 2026)

The Machine Learning team at Generate:Biomedicines is dedicated to developing new technologies for protein generative modeling and therapeutic discovery. We are seeking creative and motivated graduate student interns for a summer research program.

Interns will work closely with a mentor to develop a project exploring novel ML modeling approaches for proteins. These projects will address foundational problems in biochemistry, molecular biology, and immunology, leveraging cutting-edge advancements in ML for language, vision, geometry, and uncertainty.

Interns will gain broad exposure to platform technologies through cross-functional interactions with the wet lab, alongside social and educational programming designed to connect them with industry scientists and provide insights into translating research into medicines for patients.

Internship Projects for Summer 2026 are available within:

• Machine Learning
• Data Science
• Computational Structure Determination
• Computational Protein Generation groups

Here’s how you will contribute:

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

Examples of past mentor/mentee projects 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 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, 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.

Compensation:

• The hourly pay range provided reflects our current estimate for this non-exempt position. Your actual hourly rate will be based on factors including job-related skills, experience, internal equity, relevant education/training, and market dynamics.
• Per Hour Pay Range: $55.29 — $71.88 USD

Diversity & Inclusion:

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. Exceptions to this policy will be made if required by applicable law, or for requests due to a medical reason, a sincerely held religious belief, or any other exemptions recognized by applicable law.

Recruitment & Staffing Agencies Disclaimer:

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.