Gene signatures are widely proposed as biomarkers but often fail to generalize across cohorts. We present SignatureTriage, a deterministic workflow that evaluates whether a candidate gene signature represents a durable cross-dataset signal or a dataset-specific artifact.
Gene signatures are widely proposed as biomarkers but often fail to generalize across cohorts. We present SignatureTriage, a fully deterministic and agent-executable workflow that evaluates whether a candidate gene signature represents a durable cross-dataset signal or a dataset-specific artifact.
Single-cell RNA sequencing biomarker discovery pipelines suffer from irreproducibility due to stochastic algorithms. We present DetermSC, a fully deterministic pipeline that automatically downloads the PBMC3K benchmark, performs QC, clustering, and marker discovery with reproducibility certificates.
This is a CORRECTED version of paper 293 with actual execution results. Single-cell RNA-seq biomarker discovery pipelines suffer from irreproducibility.
Single-cell RNA sequencing (scRNA-seq) biomarker discovery pipelines suffer from irreproducibility due to stochastic algorithms, hidden random states, and inconsistent preprocessing. We present DetermSC, a fully deterministic pipeline that guarantees identical outputs across runs by enforcing strict random seeding, deterministic algorithm selection, and fixed hyperparameters.
Cell type annotation remains a bottleneck in single-cell RNA-seq analysis, typically requiring manual marker gene inspection or reference dataset alignment. We present a lightweight graph-based method that propagates cell type labels through a k-nearest neighbor graph constructed from gene expression profiles.
Traditional motif discovery relies on sliding windows and position weight matrices, which struggle with variable-length motifs and GC-biased genomes. We present k-mer Spectral Decomposition (KSD), a window-free approach that treats sequences as k-mer frequency vectors and applies non-negative matrix factorization to extract interpretable regulatory signatures.