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: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. 16053v1 Announce Type: cross Abstract: Gene regulatory networks (GRNs) link transcription factor (TF) proteins to their target genes, yet reconstructing these networks from genome-wide data remains challenging under practical and methodological constraints.
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:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.
arXiv:2407. 07357v3 Announce Type: replace Abstract: Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing.
arXiv:2606. 24940v1 Announce Type: cross Abstract: Predicting transcriptional responses to genetic perturbations could reduce the experimental burden of functional genomics, but extrapolation to genes that were never perturbed during training remains difficult.
arXiv:2607. 04527v1 Announce Type: cross Abstract: Biological systems exhibit a hierarchical structure, characterised by directed flow from upstream regulators to downstream effects.
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.
LapDDPM is a conditional Graph Diffusion Probabilistic Model that generates high‑fidelity, biologically plausible single‑cell RNA sequencing data. It incorporates graph‑based inductive biases and a spectral adversarial perturbation mechanism to enforce robustness against structural noise, effectively acting as a Distributionally Robust Optimization framework. The model extends to spatial transcriptomics and multi‑modal data, and experimental results on datasets such as PBMC3K, Dentate Gyrus, HLCA, Visium, and 10x Multiome show it outperforms state‑of‑the‑art baselines in distribution matching, manifold preservation, and downstream utility.
Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics.
Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence.
arXiv:2608. 05928v1 Announce Type: new Abstract: Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes.