Data Science Fellow - AI/NLP

Role Description

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
• 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
• Natural-language interfaces over structured biological knowledge

Responsibilities include:

• 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.

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.

Benefits

• 100% Medical, Dental & Vision Coverage for Employees
• Paid Time Off and Paid Holidays
• 401K match up to 5%
• Educational Benefits for Career Growth
• Employee Referral Bonus
• Flexible Spending Accounts:
• Healthcare (FSA)
• Parking Reimbursement Account (PRK)
• Dependent Care Assistant Program (DCAP)
• Transportation Reimbursement Account (TRN)

Salary Range

$90,000 - $100,000 USD