ELISA: An Interpretable Hybrid Generative AI Agent for Expression-Grounded Discovery in Single-Cell Genomics

arXiv:2603.11872 · q-bio.GN, cs.AI · Submitted 2026-03-12 · Read on arXiv

q-bio.GN, cs.AI

Submitted: 2026-03-12

Updated: 2026-07-31

Code: https://github.com/omaruno/ELISA-An-AI-Agent-for-Expression-Grounded-Discovery-in-Single-Cell-Genomics

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Ontology — 71× in this paper · explained in 2 episodes
• Embeddings — 35× in this paper · explained in 2 episodes
• Alignment — 28× in this paper · explained in 1 episode
• Cystic Fibrosis — 25× in this paper
• Consistency — 15× in this paper · explained in 3 episodes
• Foundation Model — 14× in this paper · explained in 3 episodes
• Benchmark — 13× in this paper · explained in 2 episodes
• Differential Expression — 10× in this paper
• Immune Checkpoint Blockade — 9× in this paper
• Benchmarking — 7× in this paper · explained in 3 episodes
• Foundation Models — 7× in this paper · explained in 7 episodes
• Generative AI — 6× in this paper · explained in 2 episodes
• Mean Reciprocal Rank — 6× in this paper
• Cosine Similarity — 5× in this paper · explained in 3 episodes
• Grounding — 5× in this paper · explained in 3 episodes
• AI Agents — 4× in this paper · explained in 2 episodes
• Accuracy — 4× in this paper · explained in 1 episode
• Agentic AI — 4× in this paper · explained in 1 episode
• Clustering — 4× in this paper · explained in 2 episodes
• Embedding-Linked Interactive Single-cell Agent — 4× in this paper
• Gene Ontology — 3× in this paper
• Hallucination — 3× in this paper · explained in 3 episodes
• Provenance — 3× in this paper · explained in 4 episodes
• alpha — 3× in this paper · explained in 1 episode
• Agentic AI systems — 2× in this paper · explained in 1 episode
• Agentic System — 2× in this paper · explained in 2 episodes
• Generalization — 2× in this paper · explained in 13 episodes
• Interpretability — 2× in this paper · explained in 15 episodes
• RAG — 2× in this paper · explained in 3 episodes
• Verification — 2× in this paper · explained in 2 episodes
• Abundance — 1× in this paper · explained in 1 episode
• Action Space — 1× in this paper · explained in 1 episode
• Aggregation — 1× in this paper · explained in 1 episode
• Core — 1× in this paper · explained in 2 episodes
• Fidelity — 1× in this paper · explained in 2 episodes
• Generalizability — 1× in this paper · explained in 6 episodes
• Graph Construction — 1× in this paper · explained in 3 episodes
• Introspection — 1× in this paper · explained in 2 episodes
• Large Language Model (LLM) — 1× in this paper · explained in 3 episodes
• Latent Representation — 1× in this paper · explained in 2 episodes
• Latent Representations — 1× in this paper · explained in 3 episodes
• Latent Space — 1× in this paper · explained in 7 episodes
• Multi-Agent Framework — 1× in this paper · explained in 3 episodes
• Multimodal Learning — 1× in this paper · explained in 2 episodes
• Score Function — 1× in this paper · explained in 4 episodes
• Trace — 1× in this paper · explained in 2 episodes

Sources

• Accelerating scientific discovery with Co-Scientist
• CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis
• Tokensome: Towards a Genetic Vision-Language GPT for Explainable and Cognitive Karyotyping
• The Llama 3 Herd of Models
• GPT-4 Technical Report
• Gemini: A Family of Highly Capable Multimodal Models
• UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

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