HOWARD HUGHES MEDICAL INSTITUTE HHMI

AI Engineer - AI+CryoET

Janelia Research Campus, USA · Principal

Sponsorship not specifiedDetected 1 hour ago

PythonGitLinuxMachine LearningDeep LearningPyTorchHRISStructural AnalysisMicroscopyExperimental DesignCommunicationCollaboration

About the role

This role is part of the AI+CryoET project within AI@HHMI, a multi-institutional project at the intersection of cryo-electron tomography (cryoET), molecular dynamics simulation, and machine learning.
(2) identifying the arrangement and connectivity of nucleosomes in chromatin that give rise to chromosome structure in cell nuclei and biochemical reconstitutions.
Success in this role requires close collaboration with cryoET experts, structural biologists, and computer scientists to ensure models work in challenging real-world scenarios of a biologically not yet fully understood system.

Develop methods to leverage gold nanoparticle detections to improve tomogram reconstruction, addressing challenges in tilt-series alignment, deformations, and low signal-to-noise conditions.
Design and execute rigorous AI model training and evaluation pipelines, including proper handling of missing wedge artifacts, CTF effects, and sim-to-real transfer from MD-derived synthetic training data.
Identify where additional human annotation and proofreading will be most helpful and design and guide annotation efforts.
Contribute to scientific publications, present findings at conferences, and maintain a well-documented codebase enabling seamless reproduction and extension of results.
Collaborate with interdisciplinary teams across multiple institutions.
AI@HHMI: HHMI is investing $500 million over the next 10 years to support AI-driven projects and to embed AI systems throughout every stage of the scientific process in labs across HHMI.
The project aims to develop AI methods for mesoscale structural biology, understanding how cellular macromolecules organize into higher-order structures.
Opportunity to partner with frontier AI labs on scientific applications of AI.

The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).
ability to see and hear within normal parameters
ability to move about workspace.
Master's or PhD in Computer Science, Applied Mathematics, Physics, Computational Chemistry, or a related field, or equivalent combination of education and experience.
3+ years training and evaluating deep learning models, particularly on 3D or volumetric image data. Experience with detection, segmentation, or inverse problems in imaging is strongly preferred.
Strong Python skills, and proficiency in PyTorch and/or JAX. Ability to reason about neural network behavior from first principles: how architectural choices, regularization, and training procedures affect model behavior.
Rigorous experimental design: model comparisons, ablation studies, reproducibility.
Commitment to open science.
Experience with scalable GPU-based computing environments on Linux HPC clusters and high-throughput processing for large-scale data.
Excellent communication skills and keen interest in working in a truly interdisciplinary environment.
Ways to stand out:
Experience with cryo-EM/ET data processing, tomographic reconstruction, or related inverse problems in imaging.
Familiarity with molecular dynamics simulations (e.g., OpenMM, LAMMPS) and/or synthetic data generation for training ML models.

Current HHMI Employees, click here to apply via your Workday account.
Please include a cover letter with your application.
Cryo-EM/ET and computational structural biology projects are especially relevant.
Discuss results, limitations, and challenges encountered.
If the project was collaborative, describe your specific contributions.
Include links to relevant code repositories and your GitHub/Gitlab profile, personal website, or similar evidence.
Experience with detection, segmentation, or inverse problems in imaging is strongly preferred.

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.
AI Engineer I: $96,325.60 (minimum) - $120,407.00 (midpoint) - $156,529.10 (maximum)
AI Engineer II: $123,125.60 (minimum) - $153,907.00 (midpoint) - $200,079.10 (maximum)
AI Engineer III: $149,515.20 (minimum) - $186,894.00 (midpoint) - $242,962.20 (maximum)
AI Engineer IV: $184,453.60 (minimum) - $230,567.00 (midpoint) - $299,737.10 (maximum)
HHMI's salary structure is developed based on relevant job market data.

A competitive compensation package with comprehensive health and welfare benefits.
See https://www.anthropic.com/news/anthropic-partners-with-allen-institute-and-howard-hughes-medical-institute
HHMI considers a candidate's education, previous experiences, knowledge, skills and abilities, as well as internal consistency when making job offers.
Compensation and Benefits

This listing is sourced directly from HOWARD HUGHES MEDICAL INSTITUTE HHMI's careers page and normalized into a canonical job model.