Engineer I, Machine Learning

About Alltrna

Flagship Pioneering has conceived of and created 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.

Alltrna is the world’s first tRNA platform company to decipher tRNA biology and pioneer tRNA therapeutics to treat thousands of diseases. Alltrna unlocks tRNA biology to correct disease. The company's platform incorporates AI/ML tools to learn the tRNA language and deliver diverse programmable molecules with broad therapeutic potential. Alltrna has an unprecedented opportunity to advance a single tRNA medicine to unify treatment across a wide range of diseases with the same underlying genetic mutation. Alltrna was founded in 2018 by Flagship Pioneering. For more info, visit www.alltrna.com.

About The Role 

At Alltrna, we pair high throughput experimental approaches with predictive models to drive and accelerate the development of novel RNA-based therapeutics. We are seeking an innovative, collaborative, and highly motivated ML engineer to join our experienced team in expanding our drug design platform. As a engineer in our Computational & Molecular Biology team, you will work closely with fellow data scientists and molecular biologists to develop and hone sequence-to-function models that leverage in-house assay data. This is a great opportunity for an early career computer scientist, data scientist, or computational biologist to gain end-to-end industry experience in the blooming field of RNA drug discovery ­­­­­­­­­­­­­­­­­­­− from developing and benchmarking algorithms, to training models on in vitro data, and ending in production models that can be used to explore novel compounds.

Core Responsibilities

• Developing machine learning models on in vitro sequence-activity measurements
• Perform hyperparameter optimization and benchmarking on in-house datasets to evaluate model performance
• Support explanatory analyses that promote understanding of model features and design strategies.
• Communicate results within and outside Alltrna’s Computational Biology team and participate in scientific discussions

Qualifications and skills

• Currently pursuing a graduate degree in Computer Science, Computational Biology, Bioinformatics, Statistics, Mathematics, Physics, or another quantitative field (MS or PhD)
• Fluent in Python (+ Pandas, Numpy) and at least one common ML library (TensorFlow/Keras, PyTorch, scikit-learn, etc.)
• Familiar with code management (version control/Git, unit tests, Jupyter notebooks, docstrings)
• Good verbal, communication, and collaboration skills

       Preferred Qualifications:

• Experience with one or more of the following deep learning architectures: Transformers, GNNs, VAEs, or GANs
• Comfortable working in a cloud-computing environment (AWS, GCP).
• Prior experience with hyperparameter optimization and evaluation of machine learning algorithms
• Prior model development experience in a research setting, such as a conference publication, thesis work, or previous engineer.

What We’ll Offer You

• Comprehensive, competitive healthcare and dental coverage through Blue Cross Blue Shield, vision coverage through VSP, family leave, paid time off, 401k retirement plan, disability and life insurance, and fully covered parking/commuter benefits.
• A dynamic early-stage work environment and highly interdisciplinary, talented, and collaborative team.
• Participation in an unprecedented opportunity to advance a single tRNA medicine to restore disrupted protein production, regardless of target, for thousands of diseases with the same underlying genetic mutation.
• Professional growth opportunities through mentoring, training, immersion in cross-functional projects, and opportunities to learn and try new things.

Our Core Values 

1. PATIENTS DESERVE BETTER. We are transforming medicine, boldly building a new future for patients.
2. CURIOSITY SPARKS DISCOVERY. We ardently explore the unknown, catalyzing new scientific