Rong Fu

Rong Fu, Yongtai Liu, Xiaowen Ma et al.

Longitudinal T cell receptor repertoires contain signals of clonal expansion, contraction, disappearance, and reappearance after immune perturbation. Static repertoire language models usually summarize a sample as a bag of sequences, so the sampling interval, sequencing depth, and clone presence pattern are only weakly represented. This paper presents DynImmune-BERT, a continuous time repertoire model for patient level immune status prediction. The method combines depth adaptive centered log ratio initialization, clone presence gated Neural ordinary differential equation dynamics, bounded neighborhood self attention, event based state restart, and a hybrid transport objective that supervises dominant and rare clone mass. A low rank meta adapter initializes reappearing clonotypes while keeping the parameter count independent of the number of observed clones. The evaluation separates literature reported baselines from internally controlled temporal comparisons, reports uncertainty for small external cohorts, adds calibration and threshold diagnostics, and visualizes latent clone trajectories and attention neighborhoods. The results indicate that event aware temporal modeling can complement strong static encoders when longitudinal repertoire structure is available, while small external cohorts and protocol differences require cautious interpretation.

Rong Fu, Yongtai Liu, Xiaowen Ma et al.

We study degeneracy guided list compression for greedy graph coloring when graph structure is available before colors are sampled. Our exposure calibrated ordering framework assigns each vertex an independent uniform list according to its backward neighborhood in a color independent order. Its certified instantiation, Profiled Structure Aware Asymmetric Palette Sparsification, or P-SAPST, reverses a minimum degree removal sequence and obtains every backward exposure from the removal profile. For each fixed profile, we characterize the exact local budget required by independent uniform lists under history robust greedy recovery. The profile yields linear list volume on high degree forests and on a core fringe family where reciprocal rank allocation requires Theta(n log^2 n) sampled colors. Exact conflict expectation, concentration, and a dense exposure barrier complete the theoretical description. The evaluation contains 40,320 runs over SAPBench and two SNAP networks. At the theorem scale, P-SAPST reduces mean list size by 47.6 percent relative to calibrated APST while attaining 99.8 percent observed greedy success. P-SAPST Lite replaces peeling with a degree order and provides a lower latency order choice within the same framework. On stress graphs with 250,000 vertices and up to 1,251,868 edges, Lite obtains a payload ratio of 0.865, while calibrated APST obtains 7.886. On email Enron, the corresponding ratios are 0.193 and 5.814. Compression is strongest on hub dominated and power law graphs and disappears near the dense exposure barrier. The method complements edge oblivious streaming APST by addressing an offline regime in which structural plans can be reused.