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Senior Machine Learning Scientist

Flagship Pioneering, Inc.Cambridge, UKArtificial Intelligence
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Salary
Not listed
Job type
Full-time
Experience
Senior
Posted
6 Oct 2026
Status
Open · checked 7d ago

About this role

Senior Machine Learning Scientist is a hybrid position located in Cambridge, UK, that suits professionals looking to build predictive models and agentic workflows for drug target discovery. The role involves developing machine learning systems to analyze somatic mutation data and connect genomic findings to protein function.

Role Overview

Quotient Therapeutics is hiring a Senior Machine Learning Scientist to design models and AI agents that convert somatic mutation data into actionable evidence for target discovery. The professional in this position will investigate how specific mutations alter protein behavior and affect cell selection in diseased tissue. Working on a cross-functional team, the scientist writes tested code and collaborates closely with computational scientists, biologists, and engineers. This hybrid role requires a minimum of three days per week in the Cambridge office.

Key Responsibilities

Build and evaluate predictive models regarding how coding and non-coding variants influence protein stability, function, interactions, and pathway activity through structure-based methods and protein language models.
Interpret somatic selection signals using variant-effect predictions to categorize mutations as gain-of-function, loss-of-function, or neutral, and identify their clusters in protein structures.
Design, construct, and evaluate AI agents and agentic workflows that gather evidence, execute analyses, and assist with hypothesis testing and target assessment.
Train, fine-tune, or adapt representation-learning methods, language models, and foundation models focused on target discovery.
Employ AI coding assistants to accelerate development while ensuring the final code remains readable, tested, and reproducible.
Function as a core team member on cross-functional projects, sharing responsibility for team objectives and contributing to shared codebases and reviews.
Present technical results clearly to scientists and leadership, detailing model assumptions, limitations, and subsequent steps.

Requirements

PhD in machine learning, computer science, bioinformatics, computational biology, statistics, genomics, engineering, or a related discipline, or an MSc accompanied by equivalent experience.
Strong proficiency in Python alongside practical experience building deep learning systems using frameworks such as PyTorch or JAX.
Direct background in applying, training, or evaluating machine learning models on complex biological data from the real world.
Familiarity with the ways genetic variants modify protein structure and function, alongside experience utilizing variant-effect prediction tools like ESM or AlphaMissense.
Frequent utilization of LLM-based workflows, AI coding assistants, or agentic development tools in daily operations.
Demonstrated specialization in areas such as biomedical foundation models, AI agents, single-cell genomics, causal inference, perturbation modelling, or large-scale biological datasets.
Demonstrated ability to operate within cross-functional teams and explain technical findings to non-specialists.
Proven technical depth supported by thesis work, academic papers, open-source contributions, or industry projects.

Skills and Tools

Python
PyTorch
JAX
Protein language models (e.g., ESM)
Structure-based models
AlphaMissense
AI coding assistants and LLM-based workflows
Single-cell genomics and Perturb-seq

About the Company

Quotient Therapeutics is a privately held, early-stage biopharma enterprise leveraging natural somatic genetic diversity to create breakthrough medicines. The organization utilizes high-accuracy sequencing to identify rare somatic mutations in non-cancerous diseased human tissue to nominate and assess therapeutic targets. Quotient is a Flagship Pioneering company, part of an innovation enterprise that has founded over one hundred life sciences organizations over the past twenty years to address critical needs in human health and sustainability.

How to Apply

Interested candidates should apply on the official company careers page.

Skills and tech stack

PythonPyTorchJAXESMAlphaMissenseLLMDeep LearningMachine Learning

Questions candidates ask

Where is the Senior Machine Learning Scientist position located?

The role is based in Cambridge, UK, and operates on a hybrid schedule with a minimum of three days per week required in the office.

What qualifications are required for the role?

Candidates must hold a PhD in machine learning, computer science, computational biology, genomics, bioinformatics, statistics, engineering, or a related field, or an MSc with equivalent experience.

What programming languages and frameworks are used?

The position requires strong Python skills and practical experience with deep learning frameworks such as PyTorch or JAX.

What is the primary focus of the machine learning work?

The work centers on building predictive models of variant effects on protein function and developing agentic AI workflows to turn somatic mutation data into evidence for drug target discovery.

Who operates Quotient Therapeutics?

Quotient Therapeutics is a Flagship Pioneering company that focuses on somatic genomics for drug target discovery.

Ready to apply?

The application is on the official Flagship Pioneering, Inc. careers page.

Apply on company site