Principal Machine Learning Engineer

Who You Are

The Altos Labs Scientific Computing & Data (SCD) group consists of software, data, and machine learning engineers implementing scalable data engineering solutions enabling Altos Labs' scientific mission. We are currently hiring a Principal Data Engineer, Knowledge Graphs, and Data Semantics to lead the development of knowledge graphs integrating data at multiple biological scales.

This role will be responsible for designing ontologies and information models capturing multimodal genomics, imaging, mass spectrometry, and clinical data generating unique insights on cell rejuvenation and health. The knowledge graph will be the engine to integrate internal and external experimental datasets, reference datasets, and ontologies, and provide the foundation to drive AI/ML research at Altos Labs. The Principal Data Engineer will drive standardization of the datasets being generated across Altos Labs using ontologies and controlled vocabularies, including Gene Ontology, Drug Target Ontology (DTO), BioAssay Ontology, and semantic models representing cells and cell lines. This role would own the strategy and implementation of knowledge graph and semantic data management across various modalities and use cases, working closely with researchers across Altos Science & Medical Institutes. As a Principal data engineer, you will shape the culture, strategy, and technology roadmap of the group.

Responsibilities

• Integrate multimodal genomics, imaging, mass spectrometry and clinical data to represent knowledge about proteins, genes, transcription factors, pathways to generate unique insights on cell rejuvenation and health.
• Building conceptual models for representing perturbations (single and combinational) and resultant response from cells and networks.
• Develop knowledge graph representing information at multiple biological scales, providing an integrated view of internal and external datasets,  enabling computational and data science research
• Integrate internal and external experimental datasets, reference datasets and ontologies
• Standardize datasets being generated across Altos and provide single source of truth
• Own the strategy and implementation of knowledge graph and semantic data management across various modalities and use cases, and work closely with stakeholders across global research organization
• Be a trusted partner for scientific teams in order to ideate and develop engineering solutions to support and accelerate research across various labs.
• Be a thought leader bridging Altos Labs Scientific Computing & Data group with other leading engineering organizations and academic institutions, and to promote Altos Labs as best place to work for top data engineering talent
• Engage extensively with major consortiums for medical R&D, large genomics research institutes, and leading startups leveraging latest system design and implementations to support Altos Labs mission

Requirements

• Masters or PhD in Computer Science, Bioinformatics with strong emphasis on data and knowledge modeling
• 8+ years of experience in academia and/or industry working with research data sets (genomics, imaging & microscopy)
• Hands-on experience in knowledge graph & ontology development, and programming in python, R or Java
• Experience in successfully bringing data products from inception, ideation, prototyping and implementation
• Experience or familiarity with biology, bioinformatics, or common biological data analysis methods and experience working with biologists or bioinformaticians
• Exposure to large language models within biomedical domain and beyond
• Ability to work in cross functional and cross location teams