Senior Machine Learning Researcher

Hlx Life Sciences; Boston (MA); On-site; USD 120,000 - 160,000; Full time

Benefits offered by this job

High-ownership position

Significant scope for career growth

Collaboration with world-class experts

Job summary

Hlx Life Sciences in Boston seeks a Senior Machine Learning Researcher to contribute to foundational models in single-cell biology. The role focuses on designing innovative architectures, conducting independent research, and building core modeling infrastructure.

Applicants should have 6+ years of machine learning experience, a Master's or higher degree, and strong Python and deep learning skills. The position offers a collaborative environment with opportunities for substantial scientific contributions.

Qualifications

• 6+ years of experience in machine learning with focus on transformer-based architectures.
• Strong proficiency in Python and deep learning frameworks.
• Proven track record of end-to-end model development.

Responsibilities

• Design, train, and optimise foundation models for single-cell RNA sequencing.
• Develop novel deep learning architectures for structured biological data.
• Build scalable training and inference pipelines for large datasets.

Skills

Machine learning

Transformer-based architectures

Python

Deep learning frameworks (PyTorch, TensorFlow)

Biological modelling

Education

Master's degree or higher in Computer Science, Artificial Intelligence, Computational Biology

Tools

PyTorch

TensorFlow

Job description

Senior Machine Learning Researcher – Biological Foundation Models

About the Company

A well-funded, AI-native biotech company based in Boston working at the intersection of large-scale machine learning and cellular biology. The company is building foundation models to understand and predict cellular behaviour, with the long-term goal of making biology programmable and predictable rather than empirical.

The founding team combines deep expertise in AI, machine learning research, and biology, with strong academic and entrepreneurial pedigree. The company is backed by leading life science and deep tech investors and is in a period of rapid team growth.

The company generates proprietary biological data at scale using novel experimental approaches, and trains large-scale models designed to generalise broadly across biological contexts — underpinning applications in drug discovery, disease modelling, and cell therapy.

The Role

As a Senior Machine Learning Researcher, you will be a core contributor to the development of foundation models for single-cell biology. Working alongside machine learning researchers and computational biologists, you will design novel architectures, drive independent research, and help build the core modelling infrastructure of the platform.

This is a methods-focused, research-heavy role. The team is looking for someone who builds from first principles and wants to operate at the scientific frontier — not someone running existing pipelines.

Responsibilities

• Design, train, and optimise foundation models for single-cell RNA sequencing and other high-dimensional omics data
• Develop novel deep learning architectures tailored to structured biological data
• Build scalable, distributed training and inference pipelines for large-scale biological datasets
• Work closely with computational biologists to ensure models produce biologically meaningful and interpretable outputs
• Engage with the underlying biology — contributing to scientific thinking and research direction, not just the ML
• Mentor and provide technical guidance to colleagues across the research team

Required Qualifications

• 6+ years of experience in machine learning with a strong focus on transformer-based architectures and large-scale model development
• Master's degree or higher in Computer Science, Artificial Intelligence, Computational Biology, or a related field
• Strong proficiency in Python and deep learning frameworks such as PyTorch or TensorFlow
• Proven track record of end-to-end model development, from prototyping through to production
• Experience working independently and driving research with minimal direction
• Genuine interest in applying ML to biological problems

Preferred Qualifications

• PhD with a strong publication record in top ML and/or computational biology venues — strongly preferred
• Hands-on experience with single-cell RNA sequencing data and biological modelling — strongly preferred
• Familiarity with reinforcement learning, diffusion models, or multimodal architectures applied to high-dimensional data
• Experience working in a startup or fast-paced research environment

Why This Role

• Work on foundational research with genuine therapeutic relevance across drug discovery and cell therapy
• High-ownership position with significant scope for scientific contribution and career growth
• Collaborate with a team that brings together world-class ML and biology expertise
• Join at a pivotal stage of company growth, with strong investor backing

Interested or know someone who might be? Get in touch.