Scientific Software Engineer | Kumar Lab

The Jackson Laboratory; Bar Harbor (ME); On-site; USD 86,000 - 144,000; Full time

Job summary

The Jackson Laboratory in Bar Harbor, ME is seeking a Scientific Software Engineer to advance ML and computer vision for digital behavioral measures in mice. You will design, train, and deploy production-quality models and pipelines, contribute to publications, and mentor team members while following robust MLOps practices and scalable software engineering.

A master's degree in CS/ML or equivalent experience, about three years of hands-on ML work, and strong communication are expected to join a

Qualifications

• Master's degree in CS/ML or related field with hands-on ML experience.
• Typically 3+ years of hands-on ML/deep learning work.
• Experience deploying ML models and following MLOps practices.
• Ability to explain complex technical trade-offs to scientists and stakeholders.
• Ability to mentor trainees and contribute to publications.

Responsibilities

• Design, train, and deploy computer vision and ML models and pipelines from concept to production.
• Evaluate models across strains, rigs, and sites; compare architectures and report results.
• Collaborate with lab members, review code, document work, and pursue technical growth.

Skills

Machine learning proficiency

Communication skills

Collaborative teamwork

Mentor trainees

Education

Master's degree in computer science / machine learning / related field

BS/BA with equivalent demonstrated experience

Tools

Python

PyTorch

ffmpeg

C++

Cython

SQLite

PostgreSQL

SLURM

Bash

Go

Kubernetes

GCP

AWS

Job description

Job Summary The Kumar Lab studies the genetic and neurological basis of behavior with the goal of therapeutic and mechanistic discovery. We leverage machine learning and computer vision methods to model human diseases by transforming videos of mice into quantitative behavioral traits. Technology developed by our lab has been deployed in the JAX Envision System, a home cage monitoring platform. Envision streams continuous petabyte-scale video from animal housing into a cloud archive and operates on it in close to real time using multi-task algorithms. Segmentation, pose estimation, and instance assignment are all used for action recognition, action localization tasks using supervised and unsupervised approaches to quantify complex animal behaviors representative of health and disease. As a Scientific Software Engineer, you will collaboratively shape the machine learning and computer vision engineering behind digital measures, harden pre-existing algorithms, and leverage robust MLOps principles. You will follow technical direction, mentor trainees, and drive publications and model releases that come out of the work. A successful candidate will be independently motivated, work collaboratively, and contribute meaningfully to the development of therapeutics for neurodevelopmental and neuropsychiatric disorders.

The Challenges

Mice are inherently difficult to study because they tend to avoid detection. As highly flexible, deformable animals, they are primarily active in low-light conditions and occupy small, confined spaces. These behaviors create significant challenges for computer vision tasks such as segmentation, pose estimation, instance tracking and identity tracking. Human Annotation is Expensive. Expert behaviorists’ time is limited, so creating a system that enables quick, high impact, scalable annotation is a must. Occlusion Complicates Behavior Annotation. Group-housed mice huddle and occlude each other. Models Must Generalize. Measures must perform across a diversity of genetic backgrounds, environments, coat colors, and sites, and across an archive too large to easily reprocess. Continual learning, edge-case mining, and efficient deployment are critical. You will be working with messy real-world data.

Key Responsibilities and Essential Functions

• 70% - Design, train, and deploy computer vision and machine learning models and the pipelines around them, from stated aims through production, working with direction from project sponsors/PIs and senior team members. Write code other people can read, run, and extend. Contribute to the publications and open-source releases that come out of these projects.
• 20% - Evaluate models: quantify how measures hold up across strain, rig, and site. Assess new methods and architectures against our problems and report what actually survives the comparison.
• 10% - Collaborate with lab members, review code, document what you build, and invest in your own technical growth.

What You're Good At

Depth in machine learning. A master's degree in computer science, machine learning, or a related field is preferred; a BS or BA with equivalent demonstrated experience is considered. Either way we expect roughly three years of hands‑on work and the ability to judge whether a method applies to our problem, implement it, and explain its performance.

Proficiency leveraging LLM-based coding assistants (e.g., GitHub Copilot, Claude Code) to accelerate development, while maintaining rigorous standards for code quality, correctness, and maintainability.

Production machine learning. PyTorch, training and evaluation infrastructure, model versioning, and deployment — including quantization and runtime optimization for edge inference — plus the data plumbing that carries video at volume (object storage, containers, Kubernetes, SLURM, Go, Bash). Working familiarity with technologies such as Python, PyTorch, ffmpeg, C++, Cython, SQLite, PostgreSQL, SLURM, Bash, as well as cloud providers and technologies like GCP, AWS.

Specialized expertise in machine learning and machine learning frameworks and tools.

Judgment about prioritization

This role demands that an individual balance competing priorities across scientific, engineering, and deadline driven requirements.

Excellent oral and written communication

You will explain complex technical trade-offs to biologists, to institutional stakeholders, and to external collaborators, and you will contribute to manuscripts. You proactively elicit feedback, are comfortable explaining your work to scientists, and encourage discussion.

Engagement with your work and a track record of productivity

Background in biological sciences, or a real appetite to learn the domain.

Pay Range: $85,987 - $143,962, pay is determined by years of experience.

About JAX

The Jackson Laboratory is an independent, nonprofit biomedical research institution with a National Cancer Institute-designated Cancer Center and nearly 3,000 employees in locations across the United States (Maine, Connecticut, California), Japan and China. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health. Founded in 1929, JAX applies over nine decades of expertise in genetics to increase understanding of human disease, advancing treatments and cures for cancer, neurological and immune disorders, diabetes, aging and heart disease. It models and interprets genomic complexity, integrates basic research with clinical application, educates current and future scientists, and provides critical data, tools and services to the global biomedical community. For more information, please visit www.jax.org.

EEO Statement

The Jackson Laboratory provides equal employment opportunities to all employees and applicants for employment in all job classifications without regard to race, color, religion, age, mental disability, physical disability, medical condition, gender, sexual orientation, genetic information, ancestry, marital status, national origin, veteran status, and other classifications protected by applicable state and local non-discrimination laws.

Bar Harbor

The Jackson Laboratory's 43-acre scenic Bar Harbor campus is nestled between the Gulf of Maine and the mountains of Acadia National Park. Some of the best hiking and biking in the world (over 50 square miles of mountains, lakes, views, and dramatic coastline) is accessible from our campus. We are one mile from downtown Bar Harbor, which offers a vibrant downtown district with a plethora of restaurants, shops, museums, and galleries.

Ellsworth

The Charles E. Hewett Center in Ellsworth, Maine, is a state‑of‑the‑art facility that serves researchers world wide. The facility represents the culmination of nine decades of unmatched experience and leadership in breeding and caring for laboratory mice. Ellsworth, Maine, is one of Maine’s fastest growing cities. With a growth rate of nearly 20%, Ellsworth is a bustling year‑round community and acts as a hub for surrounding towns. It is located nearby Acadia National Park and hosts numerous special events, concerts and festivals each year. Residents have access to fabulous shopping, recreation, museums, galleries, and dining at a variety of independent restaurants.

Farmington

JAX Genomic Medicine is transforming medicine by improving patient care, lowering costs, and increasing life span and health span. JAX Genomic Medicine’s research focuses on the complex genetic causes of disease and on the development of genomic solutions tailored to each person's unique genetic makeup. JAX Genomic Medicine sits on a 17-acre site on the campus of the University of Connecticut Health Center. The 183,500-square-foot facility opened in the fall of 2014. Now, it houses over 300 biomedical researchers, technicians, and support staff in state‑of‑the‑art computing facilities and laboratories. In Connecticut, JAX resides in the scenic town of Farmington, in the state’s capitol region. The Hartford region, which offers some of the best public schools in the country, is made up of both bigger cities and smaller, charming historic New England towns. JAX Genomic Medicine is also geographically located within 2 hours of Boston and New York and is close to multiple transportation systems, including bus lines, highways, railroads and international airports.

Sacramento

The JAX® Mice, Clinical and Research Services facility is located in Sacramento, the state capital of California. Sacramento is less than a two-hour drive from San Francisco, Napa Valley, and scenic Lake Tahoe, and a short flight to both Los Angeles and Orange County. Sacramento is the birthplace of the nation’s Farm to Fork movement, and offers excellent restaurants, gastro-pubs, wineries, theaters, and museums. Outdoor activities are plentiful: Boating, white water rafting, and riding the scenic bicycle trails are popular. Housing and other costs of living are more affordable in Sacramento and its surrounding suburbs than in most other neighboring areas in the North Bay, making Sacramento one of the hottest housing markets in the country year after year.

Augusta

JAX’s Maine Cancer Genomics Initiative (MCGI) is located in Augusta, Maine, in the Harold Alfond Center for Cancer Care (HACCC), at Maine General Hospital. It began operations in 2016 with three overarching goals: to provide cancer genomic testing for Maine cancer patients; to develop and deliver physician education about clinical genomic cancer diagnostics; and to build a network in Maine of oncology practices conducting studies in genomic medicine.