Machine Learning Engineer Software Engineer Jobs in San Diego, CA

Machine Learning Engineer III

The Marlin Alliance, Inc. | San Diego, CA | Hybrid | Clearance Required

About The Marlin Alliance Incorporated in 2002, The Marlin Alliance is a digital transformation company dedicated to ensuring our clients compete and win in tomorrow's digital world. We specialize in creating technical solutions that allow for seamless execution of automated business processes and the generation of governed, machine-consumable data. From strategic planning to advanced analytics and cybersecurity, our team provides cutting-edge, cross-disciplinary solutions. We are seeking motivated professionals who share our agile, solution-oriented mindset and are ready to deliver the real, practical results relied upon by our clients.

Position Overview The Machine Learning Engineer III designs and implements sophisticated models and algorithms tailored for naval applications, leveraging expertise in modern machine learning methods and cloud-native development. This technical lead oversees the full lifecycle of AI solutions, from initial architectural design to deployment within distributed systems and operational Navy environments. By collaborating across multidisciplinary teams and applying rigorous software engineering standards, the role ensures the delivery of scalable, mission-critical intelligence that meets complex maritime requirements.

Location:

• San Diego, CA
• On site NAVWAR
• There will be some (15%) travel required to Arlington, VA; Colorado Springs, CO; Charleston, SC; Denver, CO; or other customer locations as needed.

Citizenship and Clearance requirements:

• US Citizenship is required
• No Dual Citizenship
• Active Secret clearance required; TS SCI clearance highly preferred

Responsibilities:

• Design, develop, and implement machine learning models and algorithms for naval applications.
• Develop and deploy algorithms, mathematical models, and machine learning models into real-world operational environments.
• Perform data preprocessing, feature engineering, model evaluation, and validation.
• Collaborate with engineers, data scientists, and mission stakeholders to align ML solutions with operational requirements.
• Develop cloud-native ML pipelines using AWS, Azure, Docker, Kubernetes, or equivalent platforms.
• Implement ML solutions using frameworks such as TensorFlow, PyTorch, and scikit-learn.
• Contribute to distributed computing and parallel processing approaches to optimize ML model performance.
• Participate in CI/CD pipeline development, automation, and DevSecOps workflows.
• Apply cybersecurity principles in the design and deployment of machine learning systems.
• Provide documentation, technical reports, and engineering artifacts consistent with PMAT and government standards.
• Stay current with advancements in machine learning, data science, and emerging technologies relevant to naval and DoD applications.

Required Skills and Experience:

• 10+ years of experience as a data scientist, data engineer, geospatial engineer, machine learning engineer, or software engineer.
• Proven experience developing and deploying algorithms, mathematical models, or machine learning models in real-world applications.
• Strong programming skills in Python.
• Familiarity with cloud platforms (e.g., AWS, Azure) or containerization technologies (e.g., Docker, Kubernetes).
• Familiarity with software engineering best practices, including Git.
• Experience with ML frameworks such as TensorFlow, PyTorch, or scikit-learn.
• Strong programming skills in Java, C++, Go, or Rust.
• Experience with distributed computing and parallel processing.
• Experience with CI/CD pipelines and automation tools (GitHub Actions, GitLab CI, Jenkins).
• Strong analytical, problem-solving, and communication skills.
• Ability to work effectively in a collaborative team environment.
• Previous experience supporting government agencies or military organizations.
• Ability to safely carry tools, equipment, and materials aboard ship, including ascending and descending shipboard ladders(stairwells) and navigating confined spaces while maintaining required points of contact. Tools and equipment will weigh no more than 50 lbs.
• Ability to perform required work aboard Navy vessels and in shipboard environments, including navigating narrow passageways, ascending, and descending ladders (stairwells), working on elevated platforms, and operating in variable sea conditions.
• Ability to perform activities on a reoccurring basis during shipboard operations or testing evolutions.
• Ability to comply with Navy safety requirements and wear required personal protective equipment (PPE).

Preferred Skills and Experience:

• Experience with cloud-native architecture and software API design.
• Experience integrating machine learning into operational DoD systems or edge computing environments.
• Familiarity with DoD AI strategies, MLOps, or data engineering in secure environments.
• Experience supporting NAVWAR, NIWC Pacific, or other Navy C2/ISR programs.

Education and Certification Requirements:

• Bachelor of Science degree in Artificial Intelligence, Data Science, Computer Science, Machine Learning, or Statistics.
• Advanced degrees (MS/PhD) in related fields are preferred but not required.
• Additional certifications in cloud, cybersecurity, AI/ML, or DevSecOps are a plus if required by contract.

Work Environment and Mental/Physical Demands:

The physical demands described here are representative of those that must be met by an employee to successfully perform the essential functions of this position. Reasonable accommodations may be made to enable individuals with disabilities to perform the functions.

• Typical office environment with no unusual hazards.
• The noise level in the work environment is usually moderate.
• Constant sitting while using the computer terminal.
• Constant use of sight abilities while reviewing documents.
• Constant use of speech/hearing abilities for communication.
• Occasional reaching, stooping, kneeling, or crouching may be required.
• Occasional lifting up to 20 pounds.
• Constant use of mental alertness.
• Frequent work under deadlines.

Compensation $140,000 – $195,000 annually, commensurate with experience.

Work Environment Typical professional office environment. Requires sustained focus, extended periods at a computer workstation, and occasional lifting up to 20 lbs. Reasonable accommodations will be made for individuals with disabilities.

Disclaimer:

This job description in no way states or implies that these are the only duties to be performed by the employee(s) incumbent in this position. Employees will be required to follow any other job-related instructions and to perform any other job-related duties requested by any person authorized to give instructions or assignments. All duties and responsibilities are essential functions and requirements and are subject to possible modification to reasonably accommodate individuals with disabilities.

To perform this job successfully, the incumbents will possess the skills, aptitudes, and abilities to perform each duty proficiently. Some requirements may exclude individuals who pose a direct threat or significant risk to the health or safety of themselves or others. The requirements listed in this document are the minimum levels of knowledge, skills, or abilities.

This document does not create an employment contract, implied or otherwise, other than an “at-will” relationship.

An Equal Opportunity Employer/Protected Veterans/Individuals with Disabilities.