Paper List
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Translating Measures onto Mechanisms: The Cognitive Relevance of Higher-Order Information
This review addresses the core challenge of translating abstract higher-order information theory metrics (e.g., synergy, redundancy) into defensible, ...
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Emergent Bayesian Behaviour and Optimal Cue Combination in LLMs
This paper addresses the critical gap in understanding whether LLMs spontaneously develop human-like Bayesian strategies for processing uncertain info...
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Vessel Network Topology in Molecular Communication: Insights from Experiments and Theory
This work addresses the critical lack of experimentally validated channel models for molecular communication within complex vessel networks, which is ...
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Modulation of DNA rheology by a transcription factor that forms aging microgels
This work addresses the fundamental question of how the transcription factor NANOG, essential for embryonic stem cell pluripotency, physically regulat...
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Imperfect molecular detection renormalizes apparent kinetic rates in stochastic gene regulatory networks
This paper addresses the core challenge of distinguishing genuine stochastic dynamics of gene regulatory networks from artifacts introduced by imperfe...
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PanFoMa: A Lightweight Foundation Model and Benchmark for Pan-Cancer
This paper addresses the dual challenge of achieving computational efficiency without sacrificing accuracy in whole-transcriptome single-cell represen...
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Beyond Bayesian Inference: The Correlation Integral Likelihood Framework and Gradient Flow Methods for Deterministic Sampling
This paper addresses the core challenge of calibrating complex biological models (e.g., PDEs, agent-based models) with incomplete, noisy, or heterogen...
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Contrastive Deep Learning for Variant Detection in Wastewater Genomic Sequencing
This paper addresses the core challenge of detecting viral variants in wastewater sequencing data without reference genomes or labeled annotations, ov...
Hierarchical pp-Adic Framework for Gene Regulatory Networks: Theory and Stability Analysis
SECIHTI-CIMAT, Unidad Mérida, Mérida, Yucatán, México | Universidad Autónoma del Estado de Hidalgo, Pachuca, Hidalgo, México
30秒速读
IN SHORT: This paper addresses the core challenge of mathematically capturing the inherent hierarchical organization and multi-scale stability of gene regulatory networks (GRNs) using a novel p-adic ultrametric framework.
核心创新
- Methodology Introduces a stability measure μ that quantifies how dynamics contract or expand across hierarchical resolution levels, computed solely from discrete network data (transition map and gene ordering).
- Methodology Proposes a ball-level classification of fixed points (contracting, expanding, isometric) within the p-adic framework, extending the classical point-wise attracting/repelling/indifferent trichotomy to hierarchical sets.
- Biology Defines an optimal regulatory hierarchy by minimizing μ over all N! gene orderings, which, in the A. thaliana floral network (N=13), successfully places known master regulators (UFO, EMF1, LFY, TFL1) in leading positions without prior biological knowledge.
主要结论
- The p-adic ultrametric provides a natural fractal framework (self-similar nested-ball structure) for embedding discrete GRN dynamics and modeling hierarchical organization across scales.
- The stability measure μ and ball-level fixed-point classification are fully determined by the discrete network data (f, ι), making them computationally accessible despite their foundation in the analytical field ℂp.
- Application to the A. thaliana floral development network (N=13, p=2) demonstrates that minimizing μ recovers a biologically meaningful hierarchy, placing master regulators (UFO, EMF1, LFY, TFL1) in leading positions and distinguishing floral organ attractors (e.g., IEAA vs. IEEE patterns).
摘要: Gene regulatory networks exhibit hierarchical organization across scales; capturing this structure mathematically requires a metric that distinguishes regulatory influence at each level. We show that the ultrametric of the p-adic integers ℤp—whose self-similar nested-ball structure is a natural fractal encoding of multi-scale organization—provides such a framework. Embedding the N-gene state space into ℤp and working over the complete, algebraically closed field ℂp, we prove the existence of rational functions that interpret the discrete dynamics and construct hierarchical approximations at each resolution level. These constructions yield a stability measure μ—aggregating how the dynamics contracts or expands across resolution levels—and a ball-level classification of fixed points—contracting, expanding, or isometric—extending the attracting/repelling/indifferent trichotomy of non-Archimedean dynamics from points to balls. A key result is that μ and the classification, although their definition and dynamical meaning require the analytical tools of ℂp, are fully determined by the discrete data. Minimizing μ over all N! gene orderings defines an optimal regulatory hierarchy; for the Arabidopsis thaliana floral development network (N=13, p=2), a μ-minimizing ordering places known master regulators—UFO, EMF1, LFY, TFL1—in the leading positions and recovers the accepted developmental hierarchy without biological input beyond the transition map.