(ID: 2026-2316)
Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques to empower decision-making and accelerate research discoveries. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH).
We are seeking a postdoctoral researcher to develop AI/NLP and knowledge engineering methods that transform biomedical literature, experimental protocols, and source evidence into structured, quarriable, and evidence-grounded knowledge for organoid protocol standardization and optimization.
The postdoc will work at the intersection of large language models, biomedical NLP, scientific document understanding, knowledge graphs, ontology grounding, computational biology, and human-in-the-loop curation. Potential projects include LLM-based protocol extraction, retrieval-augmented literature mining, curated knowledge graph construction, ontology and entity normalization, protocol comparison, consensus protocol derivation, benchmark design, and natural-language interfaces over structured biological knowledge.
Responsibilities
Design and implement AI/NLP methods for biomedical literature mining and structured protocol knowledge extraction.
Develop benchmark datasets, annotation guidelines, and evaluation pipelines for scientific information extraction.
Build and evaluate RAG, in-context learning, fine-tuning, graph matching, entity normalization, and KG query workflows.
Analyze extraction errors, model behavior, retrieval failures, grounding quality, and biological ambiguity.
Collaborate with software engineers to integrate research methods into usable tools and reproducible pipelines.
Collaborate with organoid biologists and domain experts to translate biological protocol knowledge into computable representations.
Prepare manuscripts, conference abstracts, technical reports, design documents, and open-source research artifacts.
Help define research milestones, evaluation criteria, and publication strategy for protocol intelligence work.
Required Qualifications
PhD in computer science, computational biology, bioinformatics, biomedical informatics, NLP, machine learning, data science, or a related field.
Strong Python programming skills.
Demonstrated research experience with NLP, information extraction, LLMs, RAG, transformers, structured prediction, or scientific text mining.
Ability to design controlled computational experiments, create benchmark datasets, and analyze results rigorously.
Familiarity with biological, biomedical, or scientific data.
Strong written communication skills and interest in publishing methods-oriented research.
Comfort working with complex, evolving research codebases and interdisciplinary teams.
Preferred Qualifications
Experience with scientific document processing, PDF parsing, biomedical literature mining, or methods-section extraction.
Experience with knowledge graphs, ontologies, graph databases, graph algorithms, or semantic data modeling.
Hands-on experience with fine-tuning LLMs, LoRA/QLoRA, Hugging Face, PyTorch, or API-based model evaluation.
Hands-on experience with prompt engineering, structured JSON extraction, schema validation, tool use, or agentic LLM workflows.
Hands-on experience with RAG systems, vector search, graph-augmented retrieval, or natural-language query over structured data.
Exposure to bioinformatics concepts (e.g., sequence alignment, clustering, or phylogenetic analysis) that can inform protocol comparison and similarity methods.
Background in stem cell biology, organoids, developmental biology, wet-lab protocols, or biological assays, enabling more effective collaboration with domain experts.
Disclaimer: The above description is meant to illustrate the general nature of work and level of effort being performed by individuals assigned to this position or job description. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description or responsibilities as needed.
The diversity of Axle's employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based on age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.
Accessibility: If you need an accommodation as part of the employment process please contact: [email protected]
This role has a market-competitive salary with an anticipated base compensation range listed below. Actual salaries will vary depending on a candidate's experience, qualifications, skills, and location.
