Structural Compression for Phylogenetic Inference under Alignment Instability and Indel-Rich Evolution

预印本 Preprint · arXiv

2026

偏爱的

Text Distance from Nested and Hierarchical Repetitions: A Compression-Based Perspective

预印本 Preprint · arXiv

把文本距离建立在嵌套与层级重复上，而不是逐字比对。

2026

偏爱的

Measuring Language Complexity from Hierarchical Reuse of Recurring Patterns

预印本 Preprint · arXiv

语言的复杂度，可以从重复模式被层层复用的程度里读出来。

以演化为引导的模块重组：分阶段 AlphaFold 3 筛选设计双链抗体

Evolution-Guided Modular Recombination Enables Paired-Chain Antibody Design through Staged AlphaFold 3 Screening

审稿中 Under review

层级序列重组与分子动力学筛选：从头设计 GLP-1R/GCGR/GIPR 三靶点激动多肽

Efficient de novo Design of GLP-1R/GCGR/GIPR Triple-Agonist Peptides through Hierarchical Sequence Recombination and Molecular Dynamics Screening

审稿中 Under review

Ladderpath: An Efficient Algorithm for Revealing Nested Hierarchy in Sequences

Array

2025

偏爱的

Compression-Based Tokenization Improves Language Modeling of Hierarchical Genomic Structure

预印本 Preprint · 浪淘沙

换一种基于压缩的分词方式，语言模型更贴基因组本身的层级结构。

Diversity-repeatability trade-off governs hierarchical cell fate coding in multicellular development

预印本 Preprint · chinaXiv

Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations

J. Chemical Information and Modeling

Correlating Measures of Hierarchical Structures in Artificial Neural Networks with Their Performance

npj Complexity · 入选 Nature Portfolio 精选集

Evolutionary Tinkering Enriches the Hierarchical and Nested Structures in Amino Acid Sequences

Physical Review Research

2022

偏爱的

Ladderpath Approach: How Tinkering and Reuse Increase Complexity and Information

Entropy

梯径理论比较完整的一次表述，建议从这一篇读起。

2021

偏爱的

Exploring and mapping chemical space with molecular assembly trees

Science Advances

把化学空间里的分子关系画成一棵树。

Theoretical Perspective on Synthetic Man-Made Life: Learning from the Origin of Life

Quantitative Biology

2020

偏爱的

On the definition of a self-sustaining chemical reaction system and its role in heredity

Biology Direct

给“自持化学反应系统”一个清楚的定义，并讲清它与遗传的关系。

Side reactions do not completely disrupt linear self-replicating chemical reaction systems

Artificial Life

2018

偏爱的

Mathematical modeling reveals spontaneous emergence of self-replication in chemical reaction systems

J. Biological Chemistry

自我复制可以从普通的化学反应网络里自发冒出来——这条线的起点。

Is the golden ratio a universal constant for self-replication?

PLOS ONE

Complex Systems Science in the AI Era: A Pivotal Paradigm for Scientific Research

National Science Review · Forum

The “Weaken-Fill-Repair” Model for Cell Budding: Linking Cell Wall Biosynthesis with Mechanics

iScience

Opinion Cascade under Perception Bias in Social Networks

Chaos

2022

偏爱的

Resonance Algorithm: An Intuitive Algorithm to Find All Shortest Paths between Two Nodes

Complex & Intelligent Systems

把最短路径问题交给一套“共振”机制来解。

Insights into Resource Consumption, Cross-Feeding, System Collapse, Stability and Biodiversity from an Artificial Ecosystem

J. Royal Society Interface