Software Engineer II, Machine Learning

Software Engineer II, Machine Learning

Molariti, Inc. | Cambridge, MA 02139 | Full-time, on-site | Job ID: MOL-2026-003

Molariti, Inc. is seeking a Software Engineer II, Machine Learning to develop the algorithms and data pipelines that turn raw sensor signal into reliable analytical results. This is a hands-on engineering role based on-site at The Engine, 750 Main St, Cambridge, MA, working closely with molecular biologists, hardware engineers, and software engineers. We are looking for a capable engineer with experience at the intersection of machine learning, software engineering, and instrumentation, who enjoys building new capabilities, solving challenging technical problems, working in interdisciplinary environments, and making an impact on healthcare in a fast-paced startup.

Key Responsibilities

Machine Learning & Signal Analysis

• Design, develop, and optimize machine learning and deep learning models for signal classification and quantification, from initial concept through deployment.
• Build and maintain the data pipelines that move sensor data from instrument to analysis to result.
• Work with scientists to define labels, training sets, and performance metrics for measurements that have no established reference model.
• Characterize model performance against analytical metrics, including detection limits, precision, and accuracy across the measurement range.
• Identify failure modes and characterize how models behave on inputs unlike the training data.

Software Engineering

• Develop and maintain software components in Python and C/C supporting model development, testing, and deployment.
• Implement unit testing, CI/CD pipelines, and automated quality practices appropriate to software that produces analytical results.
• Optimize models to run on the instrument within its compute, memory, and latency limits, and build cloud services supporting training and data management.
• Participate in code reviews and design discussions, and contribute to architecture decisions.
• Maintain documentation and internal tooling so that analysis workflows are reproducible by others.
• Contribute to adjacent areas of the stack as needed, including infrastructure, platform, and instrument-facing software; the primary focus of the role is robust, well-characterized models.

Cross-Functional Collaboration

• Work closely with molecular biology, hardware, and product teams to translate experimental needs into software requirements.
• Communicate model behavior, assumptions, and limitations clearly to colleagues without a machine learning background.

Qualifications

Required

• Bachelor’s, Master’s, or PhD degree in computer science, engineering, or a related field; equivalent experience considered
• 3 years of industry experience developing, testing, and deploying machine learning or deep learning models in production
• Strong proficiency in Python, and working proficiency in at least one systems language such as C/C or Rust
• Experience with time-series, signal, or other sequential data
• Experience with Linux, shell scripting, and debugging in Unix-like environments
• Experience with at least one major cloud provider (AWS, GCP, or Azure)
• Experience with version control, unit testing, test automation, and CI/CD pipelines
• Ability to work on-site in Cambridge, MA

Preferred

• Experience applying machine learning to instrument or sensor data
• Experience training and optimizing models on NVIDIA GPUs
• Experience deploying models to edge or embedded hardware
• Exposure to bioinformatics, scientific computing, or nucleic acid data
• Experience with containerization (Docker) and orchestration (Kubernetes)
• Experience with API development (REST or gRPC)
• Familiarity with embedded software or software running close to instrument hardware
• Experience working under software quality or validation requirements
• Startup experience

What We Offer

• Opportunity to build the analytical software layer of a novel measurement platform from the ground up
• Close collaboration with scientists and hardware engineers to turn a new measurement into a working analytical product
• Career growth pathways as part of an early-stage company
• Equity participation with meaningful upside

How to Apply

Apply through LinkedIn or send a CV to jobs@molariti.com with the subject line “MOL-2026-003 Software Engineer II, Machine Learning.” Please include:

• A brief note on why this role is a good fit for you
• Whether you are legally authorized to work in the United States
• Whether you are able to work on-site in Cambridge, MA, five days per week
• Whether you are in the Boston area or would relocate
• Your earliest available start date
• A link to your LinkedIn, Google Scholar, or personal site

Direct applicants only. We are not accepting candidates from staffing agencies, recruiters, or third-party firms. We kindly ask agencies not to submit unsolicited resumes or candidate materials, as Molariti will not be responsible for any fees related to unsolicited submissions, regardless of any subsequent engagement with the candidate.

Molariti, Inc. is an equal opportunity employer.