Paper List
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Developing the PsyCogMetrics™ AI Lab to Evaluate Large Language Models and Advance Cognitive Science
This paper addresses the critical gap between sophisticated LLM evaluation needs and the lack of accessible, scientifically rigorous platforms that in...
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Equivalence of approximation by networks of single- and multi-spike neurons
This paper resolves the fundamental question of whether single-spike spiking neural networks (SNNs) are inherently less expressive than multi-spike SN...
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The neuroscience of transformers
提出了Transformer架构与皮层柱微环路之间的新颖计算映射,连接了现代AI与神经科学。
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Framing local structural identifiability and observability in terms of parameter-state symmetries
This paper addresses the core challenge of systematically determining which parameters and states in a mechanistic ODE model can be uniquely inferred ...
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Leveraging Phytolith Research using Artificial Intelligence
This paper addresses the critical bottleneck in phytolith research by automating the labor-intensive manual microscopy process through a multimodal AI...
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Neural network-based encoding in free-viewing fMRI with gaze-aware models
This paper addresses the core challenge of building computationally efficient and ecologically valid brain encoding models for naturalistic vision by ...
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Scalable DNA Ternary Full Adder Enabled by a Competitive Blocking Circuit
This paper addresses the core bottleneck of carry information attenuation and limited computational scale in DNA binary adders by introducing a scalab...
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ELISA: An Interpretable Hybrid Generative AI Agent for Expression-Grounded Discovery in Single-Cell Genomics
This paper addresses the critical bottleneck of translating high-dimensional single-cell transcriptomic data into interpretable biological hypotheses ...
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.