Machine Learning Co-Op

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Metaphore Biotechnologies is harnessing the power of mimicry to make previously intractable drug targets accessible and unlock breakthroughs that outperform today's drugs for maximum patient impact. The company's MIMiC™ platform is a computationally driven bioplatform designing new therapeutics where function, specificity, and selectivity are programmable.

Metaphore Biotechnologies is a product of Flagship Pioneering's venture creation engine, which has also given rise to companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally 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.

Role Overview

Metaphore Biotechnologies is seeking an enthusiastic Machine Learning Co-op to join our machine learning-guided therapeutic discovery and development engine for a 6-month graduate internship. In this role, you will work closely with our machine learning scientists to expand our in silico screening capabilities by identifying, implementing, and evaluating state-of-the-art protein developability models. Your work will directly support our efforts to improve the success rate of de novo protein designs by filtering out problematic designs and ranking candidate molecules for selection.  This role offers hands-on exposure to applying cutting-edge machine learning methods in a biotech company. The ideal candidate will have prior experience with machine learning applications to biomolecules and familiarity with protein biochemistry.  You will have the opportunity to work closely with members of our machine learning group as well as Metaphore’s preclinical and platform teams to generate and experimentally evaluate model predictions. This position offers the chance to join a dynamic team and an environment that encourages development and discussion around new ideas to unlock the potential of molecular mimicry for therapeutics development.

Key Responsibilities

• Identify, implement, and evaluate externally published state-of-the-art protein property prediction models
• Incorporate validated models into existing in silico screening pipelines for producibility, improving selection and prioritization of de novo protein designs
• Develop reproducible and documented code
• Collaborate with machine learning, platform, and preclinical teams to interpret results and guide experimental testing
• Contribute to discussions around new ideas and approaches in machine learning-driven protein design and property prediction

Qualifications

• Undergraduate or graduate student in computational biology, machine learning, bioinformatics, biophysics, or a related field
• Strong programming skills in Python and experience with PyTorch
• Prior experience applying protein design or structure prediction models, such as ProteinMPNN, AlphaFold, Boltz, RFdiffusion, or related tools
• Experience evaluating or benchmarking machine learning models on real biological datasets is a plus
• Solid understanding of molecular biochemistry and biophysics, particularly as related to protein folding and stability.  Familiarity with issues related to protein expression, stability, or manufacturability is a plus.
• Ability to work independently while collaborating effectively in a multidisciplinary team environment

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.

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 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 Metaphore Biotechnologies, Inc.'s good faith estimate as of the date of publication and may be modified in the future.