NEWS

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bioIOT 0.2.0

• New R core solver: soft_sinkhorn() (Anderson-accelerated semi-relaxed soft Sinkhorn), row_conditional(), make_cost(), row_ce_loss(), zscore_phi().
• New fitting: fit_iot() with exact implicit gradients, two-stage debias refit and multi-restart; print/summary methods for bioIOT_fit.
• New trajectory layer: transition_matrix(), pseudotime_from_transition(), build_state_features().
• New single-cell interfaces: runIOT() generic with matrix, SingleCellExperiment and Seurat methods.
• New visualisation (ggplot2): plot_transition_heatmap(), plot_transition_flow(), plot_theta(), plot_pathway_trend().
• New reproducible demo: simulate_iot_states() plus bundled dataset demo_iot_states.
• New vignette and expanded test suite (implicit-gradient vs finite differences, recovery, interfaces, plots).

bioIOT 0.1.0

• Initial release: pathway_markers, score_pathways, collapse_probes, gsm_id, has_cel_file, find_platform_file.