Paper List
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A Theoretical Framework for the Formation of Large Animal Groups: Topological Coordination, Subgroup Merging, and Velocity Inheritance
This paper addresses the core problem of how large, coordinated animal groups form in nature, challenging the classical view of gradual aggregation by...
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CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design
This paper addresses the critical limitation of current protein structure prediction models (like AlphaFold3) where high-confidence scores (pLDDT) can...
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Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A
This paper addresses the critical bottleneck in therapeutic peptide design: how to efficiently optimize lead peptides with geometric constraints while...
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Pharmacophore-based design by learning on voxel grids
This paper addresses the computational bottleneck and limited novelty in conventional pharmacophore-based virtual screening by introducing a voxel cap...
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Human-Centred Evaluation of Text-to-Image Generation Models for Self-expression of Mental Distress: A Dataset Based on GPT-4o
This paper addresses the critical gap in evaluating how AI-generated images can effectively support cross-cultural mental distress communication, part...
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ANNE Apnea Paper
This paper addresses the core challenge of achieving accurate, event-level sleep apnea detection and characterization using a non-intrusive, multimoda...
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DeeDeeExperiment: Building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor
This paper addresses the critical bottleneck of managing and organizing the growing volume of differential expression and functional enrichment analys...
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Cross-Species Antimicrobial Resistance Prediction from Genomic Foundation Models
This paper addresses the core challenge of predicting antimicrobial resistance across phylogenetically distinct bacterial species, where traditional m...
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.