Senior Applied ML Engineer

Ellkay, Llc; United States; Hybrid; USD 140,000 - 190,000; Full time

Benefits offered by this job

Medical, Dental, and Vision benefits

Employer-paid Life and LTD

401k w/ matching – once eligibility is

Work/life balance

Generous FTO

Remote work options

Employee Discounts

Gym membership / Exercise class stipen

On site in HQ Free daily lunches

Job summary

ELLKAY is seeking an accomplished ML/NLP Engineer to develop applied capabilities for understanding healthcare data, extracting content, and retrieving archive evidence. You will collaborate with clinical analysts and DME teams to define labels, train models, and preserve clinical meaning across production-ready solutions.

You will own domain-model quality, prototype search, and experiments from problem definition through deployment, balancing rules, embeddings, and LLMs while ensuring source

Qualifications

• 5+ years in applied ML/NLP or equivalent production engineering.
• Strong Python and SQL, applied statistics, experimental design, supervised learning, information retrieval, and NLP using modern ML frameworks.
• Hands-on experience with healthcare datasets, HL7 v2 or FHIR, and clinical terminology.
• Experience curating labels, building representative evaluation datasets, analyzing error severity, and preventing leakage across customers or source families.
• Ability to combine clinical rules, embeddings, trained models, and LLMs, and measure confidence and abstention.
• Ability to work directly with clinical SMEs and communicate model behavior to product and engineering teams.

Responsibilities

• Develop schema and document discovery, clinical entity extraction, semantic classification, terminology recommendations, and data-quality anomaly detection.
• Define clinical relevance labels and benchmarks for source-to-ELLKAY's canonical data model and FHIR mappings, archive retrieval, and interoperability recommendations.
• Combine domain rules, embeddings, supervised models, and LLMs. Preserve patient context, units, dates, negation, and source references.
• Prototype archive search and cited answers. Specify abstention and SME review when evidence is incomplete or clinical meaning is ambiguous.
• Design pilot experiments and analyze reviewer acceptance, error severity, task time, and performance across source-system families.
• Train and adapt models where labeled data and evaluation justify it. Compare against simple baselines, and retain source evidence for extracted facts and recommendations.

Skills

5+ years in applied ML/NLP

Python

SQL

Statistics

Experimental design

Supervised learning

NLP

Information retrieval

Healthcare datasets

HL7/FHIR

Clinical terminology

PyTorch

scikit-learn

Transformers

Education

Relevant degree or equivalent practical experience

Tools

PyTorch

scikit-learn

Transformers

Job description

If you are unable to complete this application due to a disability, contact this employer to ask for an accommodation or an alternative application process.

Engineering Shared Services Full Time US

ELLKAY started out providing connectivity solutions to laboratories and within a few years, grew to also provide data management solutions to ambulatory organizations. ELLKAY is now a trusted data management partner in five healthcare segments. ELLKAY’s solutions continue to serve laboratories and ambulatory practices and have expanded to empower hospitals and health systems, healthcare IT vendors, ambulatory practices, health plans, and other healthcare organizations with cutting-edge technologies and solutions that drive their growth and interoperability strategies. Today, ELLKAY remains true to our core values, building strong partner relationships and offering unparalleled service and support while providing innovative, scalable solutions to the challenges our customers face in today’s data-rich world. ELLKAY's experience, customer-focused approach, and reputation for innovation, speed, and accuracy differentiate ELLKAY as a premier partner for your interoperability needs and data management strategy.

Job Description:

Develop applied ML and NLP capabilities that help ELLKAY understand healthcare data, discover migration scope, extract document content, and retrieve relevant archive evidence. The engineer will work with clinical analysts and DME teams to define labels, train and evaluate models, and preserve clinical meaning. The role owns domain-model quality and experiments from problem definition through production adoption.

• Develop schema and document discovery, clinical entity extraction, semantic classification, terminology recommendations, and data-quality anomaly detection.
• Define clinical relevance labels and benchmarks for source-to-ELLKAY's canonical data model and FHIR mappings, archive retrieval, and interoperability recommendations.
• Combine domain rules, embeddings, supervised models, and LLMs. Preserve patient context, units, dates, negation, and source references.
• Prototype archive search and cited answers. Specify abstention and SME review when evidence is incomplete or clinical meaning is ambiguous.
• Design pilot experiments and analyze reviewer acceptance, error severity, task time, and performance across source-system families.
• Train and adapt models where labeled data and evaluation justify it. Compare against simple baselines, and retain source evidence for extracted facts and recommendations.

Collaboration and ownership

Partner with Data Platform and product engineers, clinical/data SMEs, DME/QA, and security teams. Build reusable services for ELLKAY products and preserve source evidence, approved data-use rights, and tenant isolation. Model or agent proposals follow established human approval and platform release workflows.

Qualifications:

Required qualifications:

• 5+ years in applied ML, NLP, or equivalent production engineering experience, including model development and evaluation.
• Strong Python and SQL, applied statistics, experimental design, supervised learning, information retrieval, and NLP using modern ML frameworks.
• Hands-on experience with healthcare datasets, EHR/lab workflows, HL7 v2 or FHIR, and clinical terminology.
• Experience curating labels, building representative evaluation datasets, analyzing error severity, and preventing leakage across customers or source families.
• Ability to combine clinical rules, embeddings, trained models, and LLMs, and measure confidence and abstention.
• Ability to work directly with clinical SMEs and communicate model behavior to product and engineering teams. A relevant degree or equivalent practical experience is acceptable.

Preferred qualifications:

LOINC, SNOMED CT, ICD-10, RxNorm, OCR/document extraction, clinical negation and temporal reasoning, learning-to-rank, and migration/archive experience. Familiarity with PyTorch, scikit-learn, transformer models, or equivalent tools.

Expected outcomes

• First 90 days: define the selected healthcare use case, produce an SME-reviewed benchmark with error severity labels, and establish manual/rules/model baselines.
• By six months: deliver a discovery, extraction, or retrieval pilot that meets agreed clinical quality thresholds and reports precision/recall, evidence relevance, coverage, and abstention.
• By 12 months: target 30% less analyst discovery/review time on comparable pilot tasks, with no increase in critical errors. Demonstrate performance across two source families and preserve provenance for all exposed clinical facts.
• Quality, performance, and business-impact targets will be calibrated to the selected use cases and their initial baselines. Delivery depends on the corresponding platform capabilities and approved customer pilot scope.

ELLKAY offers a comprehensive and competitive benefit package that starts day one!

Including:

• Medical, Dental, and Vision benefits
• Employer-paid Life and LTD
• 401k w/ matching – once eligibility is met
• Work/life balance
• Generous FTO
• Remote work options
• Employee Discounts
• Gym membership / Exercise class stipends

Our awesome culture includes:

• Working with talented, collaborative, and friendly people who love what they do
• Professional growth within
• Innovation environment
• On site in HQ Free daily lunches

Awards:

• 2025 Top Workplaces Employee Appreciation
• 2025 Top Workplaces Employee Well-Being
• 2025 Top Workplaces Professional Development
• 2026 NJ Top Workplaces

Additional information

At ELLKAY, we are committed to operating as a hybrid workplace, offering employees flexibility in how they structure their time between in-office and remote work. We recognize the significance of fostering connections, collaboration, and creativity within our office culture and its positive impact on our business. Our philosophy of operating as a hybrid workplace underscores our dedication to enabling employees to tailor work-life balance to their individual preferences. For those who do not live within 40 miles of one of our offices, we are open to considering remote work for candidates whose skills and experience strongly align with the role. While we prioritize a hybrid work environment for most roles, we understand the importance of flexibility and are open to remote work for specific positions and specialized skill sets.

For more information on our company, visit www.ELLKAY.com.

ELLKAY LLC is a Smoke-Free Workplace.

ELLKAY, LLC provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.