Data Engineer - Training Pipelines & Inference

About the role

The Foundational Microscopy Image Analysis (MIA) project at HHMI aims to create a comprehensive, multimodal 3D/4D microscopy dataset and use it to power a vision foundation model capable of accelerating discovery across the life sciences. We are seeking a skilled Data Engineer to drive scientific innovation through robust data infrastructure, model training, and inference systems.

Responsibilities

• Design, develop, and optimize scalable data pipelines and build multi-node GPU training and inference pipelines for foundational models.

• Develop tools for ingesting, transforming, and integrating large, heterogeneous microscopy image datasets—including writing production-quality Python code to parse, validate, and transform microscopy data from published research papers, public databases, and internal repositories.

• Stay up to date with scientific literature to understand data context and processing requirements.

• Document data provenance and transformation steps comprehensively.

• Apply statistical tools and programming languages (e.g., Python, R) to analyze large datasets, develop custom functions, and extract actionable insights through effective visualization.

• Establish and maintain data standards, formats, workflows, and documentation to ensure data quality, accessibility, and reproducibility across projects.

• Collaborate with interdisciplinary teams, potentially mentor junior engineers, and direct or assist in directing the work of others to meet project goals while advising stakeholders on data strategies and best practices.

Requirements

• Bachelor’s degree in Computer Science, Data Science, Statistics, Applied Mathematics, or a related field with 3+ years of experience applying and customizing data mining, model training & inference methods and techniques.
• An equivalent combination of education and relevant experience will be considered.
• Experience with data formats such as Zarr, Parquet, HDF5, and efficient IO (e.g., webdataset).
• Experience with volumetric 3D/4D microscopy data analysis tools.
• Experience with high performance compute environments (cloud-based and slurm/lsf clusters) and model deployment platforms (e.g., Kubernetes, AWS SageMaker, Google Vertex AI, HF Inference).
• Experience with distributed data processing, Multi-node GPU processing and ML development frameworks such as PyTorch and/or JAX.
• Excellent technical documentation and communication skills.
• Experience in building scalable data solutions, working with big data technologies, and ensuring data quality and accessibility.
• Expertise in utilizing data visualization libraries and software (e.g., Matplotlib, R, Jupyter notebooks).
• Detail-oriented, creative, and organized team player with strong communication skills and a collaborative mindset.
• Able to effectively manage time, prioritize tasks, and clearly convey complex data concepts to technical and non-technical audiences.

Qualifications

• Remaining in a normal seated or standing position for extended periods of time;
• Reaching and grasping by extending hand(s) or arm(s);
• Dexterity to manipulate objects with fingers, for example using a keyboard;
• Communication skills using the spoken word;
• Ability to see and hear within normal parameters;
• Ability to move about workspace.

Skills

• Technical excellence in data engineering;
• Understanding of biological research contexts to ensure data integrity and scientific validity;
• Collaboration with multidisciplinary teams of computational and experimental scientists;
• Technical documentation and communication skills;
• Scalable data solutions;
• Data quality and accessibility;
• Data visualization;
• Time management and task prioritization;
• Complex data concept communication.

Benefits

A competitive compensation package, with comprehensive health and welfare benefits. A supportive team environment that promotes collaboration and knowledge sharing. The opportunity to engage with world-class researchers, software engineers and AI/ML experts, contribute to impactful science, and be part of a dynamic community committed to advancing humanity’s understanding of fundamental scientific questions. Amenities that enhance work-life balance such as on-site childcare, free gyms, available on-campus housing, social and dining spaces, and convenient shuttle bus service to Janelia from the Washington D.C. metro area. Opportunity to partner with frontier AI labs on scientific applications of AI (see here).

Pay

Data Engineer I: $86,181.60 (minimum) - $107,727.00 (midpoint) - $140,045.10 (maximum)
Data Engineer II: $98,039.20 (minimum) - $122,549.00 (midpoint) - $159,313.70 (maximum)
Data Engineer III: $112,629.60 (minimum) - $140,787.00 (midpoint) - $183,023.10 (maximum)

Schedule

Full-time, Monday through Friday.

Benefits

Our employees are compensated from a total rewards perspective in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our Benefits at HHMI site to learn more.

Equal Opportunity Employer

We use E-Verify to confirm the identity and employment eligibility of all new hires. HHMI is an Equal Opportunity Employer.