Tianyang Xu

Tianyang Xu, Tianci Liu, Niraj Rayamajhi et al.

Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease. Reconstructing GRNs from paired single-cell transcriptomic and chromatin accessibility data is promising but challenging: scATAC is extremely sparse, and most methods rely on fixed peak-to-gene links and weak supervision. We present EpiAwareNet, a prior-guided multi-omic Transformer framework that reconstructs GRNs from paired single-cell data using only lightweight biological priors. In Stage 1, EpiAwareNet learns joint gene-peak representations with a gene-peak cross-attention module, enabling data-driven, gene-specific aggregation of accessibility signals rather than hard-coded peak-to-gene assignments. In Stage 2, EpiAwareNet incorporates a bulk-derived GRN prior as noisy positive edges to provide weak supervision under label scarcity, refining regulatory scores while remaining robust to prior noise. In our experiments, EpiAwareNet improves GRN reconstruction over representative single- and multi-omic baselines and yields GRNs with greater biological plausibility, such as improved recovery of known regulatory interactions, suggesting that lightweight biological priors from bulk data can effectively guide single-cell GRN inference when combined with adaptive cross-modal representation learning. Code and data will be available at https://github.com/tianyang-x/EpiAwareNet_pub.

Tianyang Xu, Dan Zhang, Kushan Mitra et al.

Large language model (LLM) agents are increasingly deployed to tackle complex tasks, often necessitating collaboration among multiple specialized agents. However, multi-agent collaboration introduces new challenges in planning, coordination, and verification. Execution failures frequently arise not from flawed reasoning alone, but from subtle misalignments in task interpretation, output format, or inter-agent handoffs. To address these challenges, we present VeriMAP, a framework for multi-agent collaboration with verification-aware planning. The VeriMAP planner decomposes tasks, models subtask dependencies, and encodes planner-defined passing criteria as subtask verification functions (VFs) in Python and natural language. We evaluate VeriMAP on diverse datasets, demonstrating that it outperforms both single- and multi-agent baselines while enhancing system robustness and interpretability. Our analysis highlights how verification-aware planning enables reliable coordination and iterative refinement in multi-agent systems, without relying on external labels or annotations.