Paper List
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Formation of Artificial Neural Assemblies by Biologically Plausible Inhibition Mechanisms
This work addresses the core limitation of the Assembly Calculus model—its fixed-size, biologically implausible k-WTA selection process—by introducing...
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How to make the most of your masked language model for protein engineering
This paper addresses the critical bottleneck of efficiently sampling high-quality, diverse protein sequences from Masked Language Models (MLMs) for pr...
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Module control in youth symptom networks across COVID-19
This paper addresses the core challenge of distinguishing whether a prolonged societal stressor (COVID-19) fundamentally reorganizes the architecture ...
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JEDI: Jointly Embedded Inference of Neural Dynamics
This paper addresses the core challenge of inferring context-dependent neural dynamics from noisy, high-dimensional recordings using a single unified ...
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ATP Level and Phosphorylation Free Energy Regulate Trigger-Wave Speed and Critical Nucleus Size in Cellular Biochemical Systems
This work addresses the core challenge of quantitatively predicting how the cellular energy state (ATP level and phosphorylation free energy) governs ...
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Packaging Jupyter notebooks as installable desktop apps using LabConstrictor
This paper addresses the core pain point of ensuring Jupyter notebook reproducibility and accessibility across different computing environments, parti...
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SNPgen: Phenotype-Supervised Genotype Representation and Synthetic Data Generation via Latent Diffusion
This paper addresses the core challenge of generating privacy-preserving synthetic genotype data that maintains both statistical fidelity and downstre...
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Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements
This paper addresses the challenge of efficiently generating novel, cell-type-specific regulatory DNA sequences with high predicted activity while min...
Geometric framework for biological evolution
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30秒速读
IN SHORT: This paper addresses the fundamental challenge of developing a coordinate-independent, geometric description of evolutionary dynamics that bridges genotype and phenotype spaces, revealing evolution as a learning process.
核心创新
- Methodology Establishes a generally covariant framework for evolutionary dynamics that operates consistently across genotype and phenotype spaces, enabling coordinate-independent analysis.
- Theory Demonstrates through maximum entropy principle that the inverse metric tensor equals the covariance matrix, transforming the Lande equation into a covariant gradient ascent equation.
- Methodology Models evolution as a learning process where the specific optimization algorithm is determined by the functional relationship g(κ) between metric tensor and noise covariance.
主要结论
- The maximum entropy principle yields fundamental identification: g^{αr,βs} = c^{αr,βs} (inverse metric equals genotypic covariance matrix).
- The Lande equation transforms to covariant gradient ascent: dx̄^i/dt = G^{ij}(x̄) ∂ℱ(x̄)/∂x̄^j, where G^{ij} = C^{ij} (inverse phenotype metric equals phenotypic covariance).
- Evolution implements specific learning algorithms determined by functional relation g(κ) between metric and noise covariance, with three regimes identified: quantum (α=1), efficient learning (α=1/2), and equilibration (α=0).
摘要: We develop a generally covariant description of evolutionary dynamics that operates consistently in both genotype and phenotype spaces. We show that the maximum entropy principle yields a fundamental identification between the inverse metric tensor and the covariance matrix, revealing the Lande equation as a covariant gradient ascent equation. This demonstrates that evolution can be modeled as a learning process on the fitness landscape, with the specific learning algorithm determined by the functional relation between the metric tensor and the noise covariance arising from microscopic dynamics. While the metric (or the inverse genotypic covariance matrix) has been extensively characterized empirically, the noise covariance and its associated observable (the covariance of evolutionary changes) have never been directly measured. This poses the experimental challenge of determining the functional form relating metric to noise covariance.