arXiv:2607. 18602v1 Announce Type: new Abstract: Cooperative gene regulation often depends on groups of regulators acting jointly, but most gene regulatory network (GRN) inference methods output pairwise regulator-target rankings.
arXiv:2606. 14734v1 Announce Type: cross Abstract: Motivation: Gene regulatory network inference from single-cell RNA sequencing (scRNA-seq) data is important for uncovering cell-state-specific transcriptional programs.
arXiv:2607. 17671v1 Announce Type: new Abstract: Large-scale single-cell perturbation atlases make it possible to ask an inverse question: given an observed transcriptional response, which annotated targets and compounds in a fixed library are most consistent with that response?
arXiv:2608. 00985v1 Announce Type: new Abstract: The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values.
arXiv:2607. 17345v1 Announce Type: new Abstract: Background: Untargeted LC-MS metabolomics requires a long chain of preprocessing decisions, each with several equally defensible options.
arXiv:2608. 05359v1 Announce Type: new Abstract: CASCADE is an agentic framework that predicts downstream transcriptional effects of gene perturbation from precomputed ARACNe regulatory networks, exposed via MCP.
arXiv:2607. 13120v1 Announce Type: cross Abstract: Inferring gene regulatory networks (GRNs) from single-cell transcriptomic data is crucial for biological discovery, yet existing approaches suffer from a fundamental misalignment with real-world needs.
arXiv:2604. 11305v3 Announce Type: replace Abstract: Conformal selection (CS) uses calibration data to identify test inputs whose unobserved outcomes are likely to satisfy a pre-specified minimal quality requirement, while controlling the false discovery rate (FDR).
arXiv:2607. 19426v1 Announce Type: cross Abstract: Single-cell datasets are increasingly costly to store, audit, and reuse for model training.
arXiv:2607. 14097v1 Announce Type: new Abstract: We introduce RegNetAgents, an AI-oriented multi-agent framework for structured, query-driven regulatory candidate identification across heterogeneous gene regulatory networks.
arXiv:2607. 19426v2 Announce Type: replace-cross Abstract: Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training.
arXiv:2606. 00685v1 Announce Type: new Abstract: Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease.
arXiv:2606. 23880v1 Announce Type: new Abstract: From climate teleconnections to gene regulation, modern time-series datasets encompass tens or hundreds of interacting variables, making causal discovery increasingly challenging.