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Preprint . 2026
License: CC BY
Data sources: Datacite
ZENODO
Preprint . 2026
License: CC BY
Data sources: Datacite
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Negative Result Note: Spectral "Collapse" Signals in Longitudinal Gene Coexpression Landscapes under Anti–PD-1 Therapy

Authors: Melegh, Janos Gabor;

Negative Result Note: Spectral "Collapse" Signals in Longitudinal Gene Coexpression Landscapes under Anti–PD-1 Therapy

Abstract

We explored whether longitudinal gene coexpression networks during anti–PD-1 therapy exhibit robust signatures consistent with a global spectral “collapse” or critical transition (e.g., proliferation of soft modes reflected in spectral entropy / effective rank changes). Using a patient-level pre-treatment vs on-treatment design and focusing on three immunology-motivated gene modules (CYTOLYTIC_CORE, IFNG_AP_CORE, CHECKPOINTS), we computed multiple threshold-swept (“landscape”) network metrics and tested responder vs non-responder differences via permutation and empirical nulls (random gene sets matched by size). We did not find stable, reproducible evidence for a global collapse narrative in this cohort. A modest module-specific signal appeared for a cytolytic module in a threshold/transition-like feature (Δτ*), but several curve-based spectral-window analyses proved numerically fragile (NaNs and overlap loss across patients). This note documents the workflow, observed limitations, and why the attempted “universal spectral collapse” framing is not currently well-supported here, aiming to help others avoid similar dead ends.

Keywords

spectral entropy, effective rank, soft modes, coexpression network, immunotherapy, anti–PD-1, longitudinal, negative results

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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