OmicsLM integrates continuous omics embeddings into LLMs for multi-sample biological reasoning, matching specialized models on profile tasks while outperforming them and general LLMs on language-guided QA over real expression data.
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
6 Pith papers cite this work. Polarity classification is still indexing.
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2026 6verdicts
UNVERDICTED 6representative citing papers
ORBIT uses an intervention-consistent self-supervised objective in a transformer to infer asymmetric gene program influences from observational scRNA-seq data, recovering Alzheimer's vulnerability patterns and achieving 0.984 macro F1 cell-type classification from 220 pathway scores.
Shesha quantifies directional coherence of single-cell CRISPR responses, correlates strongly with effect magnitude, distinguishes pleiotropic from lineage-specific regulators, and predicts chaperone activation after magnitude correction.
Geometric stability, defined as the directional coherence of cellular responses to perturbation, provides a framework for assessing whether resulting cellular states are stable beyond conventional metrics of intervention success.
RAG-GNN augments GNNs with retrieved literature knowledge via gated fusion to improve functional clustering of 379 proteins in cancer signaling networks, raising silhouette score by 0.093.
Two new methods distill implicit regulatory knowledge from single-cell foundation models to enable generalizable gene regulatory network inference on unseen data.
citing papers explorer
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OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning
OmicsLM integrates continuous omics embeddings into LLMs for multi-sample biological reasoning, matching specialized models on profile tasks while outperforming them and general LLMs on language-guided QA over real expression data.
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ORBIT: Learning Gene Program Co-Activation Structure for Cell-Type-Stratified Pathway Rewiring Analysis in Single-Cell Transcriptomics
ORBIT uses an intervention-consistent self-supervised objective in a transformer to infer asymmetric gene program influences from observational scRNA-seq data, recovering Alzheimer's vulnerability patterns and achieving 0.984 macro F1 cell-type classification from 220 pathway scores.
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Geometric coherence of single-cell CRISPR perturbations reveals regulatory architecture and predicts cellular stress
Shesha quantifies directional coherence of single-cell CRISPR responses, correlates strongly with effect magnitude, distinguishes pleiotropic from lineage-specific regulators, and predicts chaperone activation after magnitude correction.
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From Syntax to Semantics: Geometric Stability as the Missing Axis of Perturbation Biology
Geometric stability, defined as the directional coherence of cellular responses to perturbation, provides a framework for assessing whether resulting cellular states are stable beyond conventional metrics of intervention success.
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RAG-GNN: Integrating Retrieved Knowledge with Graph Neural Networks for Precision Medicine
RAG-GNN augments GNNs with retrieved literature knowledge via gated fusion to improve functional clustering of 379 proteins in cancer signaling networks, raising silhouette score by 0.093.
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Towards Universal Gene Regulatory Network Inference: Unlocking Generalizable Regulatory Knowledge in Single-cell Foundation Models
Two new methods distill implicit regulatory knowledge from single-cell foundation models to enable generalizable gene regulatory network inference on unseen data.