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.
Trans- fer learning enables predictions in network biology.Nature, 618 (7965):616–624
6 Pith papers cite this work. Polarity classification is still indexing.
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OPD-Evolver uses on-policy self-distillation in fast interaction and slow attribution loops to build agents with holistic memory competence, outperforming prior systems by up to 11.5% and allowing a 9B model to compete with much larger ones.
MEDAL distills manifold embeddings into autoencoders to enable out-of-sample extension and held-out validation of dimension reduction methods.
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.
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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OPD-Evolver: Cultivating Holistic Agent Evolver via On-Policy Distillation
OPD-Evolver uses on-policy self-distillation in fast interaction and slow attribution loops to build agents with holistic memory competence, outperforming prior systems by up to 11.5% and allowing a 9B model to compete with much larger ones.
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MEDAL: Manifold Embedding Distillation via Autoencoder Learning
MEDAL distills manifold embeddings into autoencoders to enable out-of-sample extension and held-out validation of dimension reduction methods.
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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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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.