Decoding the algorithmic information
compressed in natural complex systems.
compressed in natural complex systems.
KEYWORDS
Algorithmic Information Theory (AIT)
Complex Systems
Ladderpath
Information Compression
Autocatalytic Sets
Origin of Life
Self-replication
01
AIT, Compression, Ladderpath
Measuring molecules, protein sequences, genomes and neural networks on one common ruler: how much algorithmic information is compressed into a structure, how repetition and novelty stack up layer by layer, how the system evolves. Our open-source tool lppack is actively maintained.
SELECTED WORK, NOT EXHAUSTIVE
2026
2026
PICK
Text Distance from Nested and Hierarchical Repetitions: A Compression-Based Perspective
Preprint · arXiv
Text distance built on nested, hierarchical repetition rather than character-by-character alignment.
2026
PICK
Measuring Language Complexity from Hierarchical Reuse of Recurring Patterns
Preprint · arXiv
The complexity of a language can be read off from how deeply its recurring patterns are reused.
2026
Evolution-Guided Modular Recombination Enables Paired-Chain Antibody Design through Staged AlphaFold 3 Screening
Under review
2026
Efficient de novo Design of GLP-1R/GCGR/GIPR Triple-Agonist Peptides through Hierarchical Sequence Recombination and Molecular Dynamics Screening
Under review
2025
PICK
Compression-Based Tokenization Improves Language Modeling of Hierarchical Genomic Structure
Preprint · Langtaosha
With a compression-based tokenizer, a language model fits the genome’s own hierarchical structure far better.
2025
2024
Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations
J. Chemical Information and Modeling
2024
Correlating Measures of Hierarchical Structures in Artificial Neural Networks with Their Performance
npj Complexity · Nature Portfolio collection
2024
Evolutionary Tinkering Enriches the Hierarchical and Nested Structures in Amino Acid Sequences
Physical Review Research
2022
PICK
Ladderpath Approach: How Tinkering and Reuse Increase Complexity and Information
Entropy
The most complete statement of ladderpath theory so far. If you read one, read this one.
2021
PICK
Exploring and mapping chemical space with molecular assembly trees
Science Advances
Drawing the relationships between molecules in chemical space as a tree.
02
Origin of Life, Self-replication
Mathematical models of how life that can copy itself evolved out of non-life that cannot: autocatalytic sets, self-sustaining chemical reaction systems, and related questions.
SELECTED WORK, NOT EXHAUSTIVE
2023
2020
PICK
On the definition of a self-sustaining chemical reaction system and its role in heredity
Biology Direct
A clear definition of a self-sustaining chemical reaction system, and what it has to do with heredity.
2020
2018
PICK
Mathematical modeling reveals spontaneous emergence of self-replication in chemical reaction systems
J. Biological Chemistry
Self-replication can emerge spontaneously from an ordinary chemical reaction network. Where this line of work began.
03
Other Complex Systems
Problems we took on simply because they were interesting: a “weaken–fill–repair” mechanical model of cell budding, a resonance algorithm for shortest paths, collapse and biodiversity in artificial ecosystems.
SELECTED WORK, NOT EXHAUSTIVE
2026
Complex Systems Science in the AI Era: A Pivotal Paradigm for Scientific Research
National Science Review · Forum
2024
2022
PICK
Resonance Algorithm: An Intuitive Algorithm to Find All Shortest Paths between Two Nodes
Complex & Intelligent Systems
Handing the shortest-path problem over to a “resonance” mechanism.
04
Patents
2026
A method and system for assessing tissue and organ state from a cell-population connectome
Pending
2026
A class of peptides with GLP-1R agonist activity, and their preparation and use
Pending
2023
A method and apparatus for peptide generation
Granted
2022
A method, apparatus, electronic device and storage medium for recipe management
Granted