Paper List
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Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
This work addresses the core challenge of extracting reusable, interpretable, and high-performance biological algorithms from the opaque internal repr...
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MS2MetGAN: Latent-space adversarial training for metabolite–spectrum matching in MS/MS database search
This paper addresses the critical bottleneck in metabolite identification: the generation of high-quality negative training samples that are structura...
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Toward Robust, Reproducible, and Widely Accessible Intracranial Language Brain-Computer Interfaces: A Comprehensive Review of Neural Mechanisms, Hardware, Algorithms, Evaluation, Clinical Pathways and Future Directions
This review addresses the core challenge of fragmented and heterogeneous evidence that hinders the clinical translation of intracranial language BCIs,...
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Less Is More in Chemotherapy of Breast Cancer
通过纳入细胞周期时滞和竞争项,解决了现有肿瘤-免疫模型的过度简化问题,以定量比较化疗方案。
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Fold-CP: A Context Parallelism Framework for Biomolecular Modeling
This paper addresses the critical bottleneck of GPU memory limitations that restrict AlphaFold 3-like models to processing only a few thousand residue...
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Open Biomedical Knowledge Graphs at Scale: Construction, Federation, and AI Agent Access with Samyama Graph Database
This paper addresses the core pain point of fragmented biomedical data by constructing and federating large-scale, open knowledge graphs to enable sea...
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Predictive Analytics for Foot Ulcers Using Time-Series Temperature and Pressure Data
This paper addresses the critical need for continuous, real-time monitoring of diabetic foot health by developing an unsupervised anomaly detection fr...
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Hypothesis-Based Particle Detection for Accurate Nanoparticle Counting and Digital Diagnostics
This paper addresses the core challenge of achieving accurate, interpretable, and training-free nanoparticle counting in digital diagnostic assays, wh...
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.