ALIFE 2025 Proceedings Skill

Status: ✅ Production Ready (Mathpix extracted) Trit: +1 (PLUS - generative/creative) Pages: 337 | Papers: 80+ | Figures: 153 | Equations: 100+

Paper Index (Selected)

Page	Title	Theme
1	Chemical Computer (BZ oscillators)	Chemical Computing
5	Institution Bootstrapping Problem	Social Simulation
9	Mapping Road to Synthetic Ecosystems	Ecosystems
13	Structural Cellular Hash Chemistry	Cellular Automata
17	Evolutionary Advantage of Guilt	Evolution
25	Stable Scalable Boid Patterns	Swarm Intelligence
37	BUNCH: Hierarchical Filtering	Emergence Detection
49	Hummingbird Kernel: Chaotic LV Sampling	Optimization
57	Predictive-Coding Variational RNN	Free Energy Principle
61	Neural Cellular Automata Dynamics	NCA
69	Population of Thoughts: Open-Ended Evolution	LLM + Evolution
73	Neural Cellular Automata: Cells to Pixels	NCA
77	Petri Dish NCA	NCA
99	Language Cellular Automata	NCA + NLP
103	Lenia Parameter Space	Continuous CA
107	Evolvable Chemotons	Autopoiesis
111	Category Theory for Life	Category Theory
115	Evolving Interaction Protocols	Open-Ended Evolution
127	Swarm2Algo: Emergent → Distributed Algorithms	Swarm
135	Open-Ended Evolution in Binary CA	Emergence
139	Spark: Modular Spiking Neural Networks	Neural
151	Non-Equilibrium Memories with NCA	NCA
163	Temporal Memory in Swarm Reservoir	Reservoir Computing
173	H-Lenia: Hierarchical Lenia	Continuous CA
177	Emergent Patterns in Galactic Systems	Cosmology + ALife
195	Neural Particle Automata	Particles
207	Oscillatory Dynamics for Computation	Analog Computing
219	Functional Information Decomposition	Information Theory
227	Particle Life in Sierpinski Gasket	Fractals
231	Meta-Neural Cellular Automata	Meta-learning
251	Autotelic RL for Cellular Automata	RL + CA
255	Developmental Pattern Formation	Morphogenesis
267	Adversarial Environment for NCA	Adversarial
275	Growing Neural Cellular Automata	Developmental
283	Self-Organising Digital Circuits	Digital Morphogenesis
287	Scaffolding via Morphogenetic Gradients	Development
295	Swarm Size Estimation via Diffusion	Swarm
301	Gridarians: LLM-Driven ALife	LLM + ALife
309	UIUA: Array Language for ALife	Programming Languages

Key Equations

Boid Flocking (Separation/Alignment/Cohesion)

\sum_{j} w_s(T_i, T_j) \frac{\vec{\xi}_{i,j}(t)}{|\vec{\xi}_{i,j}(t)|} + 
\sum_{j} w_a(T_i, T_j) \frac{\vec{v}_j(t) - \vec{v}_i(t)}{N_{a,i}} + 
\sum_{j} w_c(T_i, T_j) \frac{-\vec{\xi}_{i,j}(t)}{N_{c,i}}

Lotka-Volterra Dynamics (Chaotic Sampling)

\frac{dx_i}{dt} = x_i\left(r_i + \sum_{j=1}^{4} A_{ij} x_j\right)

Free Energy Minimization

\mathcal{F} = \underbrace{\sum_{t=1}^{T}\left[\sum_{l}^{L} \frac{\mathbf{w}^l}{R_z^l} \delta(l, r, t)\right]}_{\text{complexity}} - \underbrace{\frac{1}{R_X}\left[\sum_{t=1}^{T}\|\mathbf{X}_t - \overline{\mathbf{X}}_t\|_2^2\right]}_{\text{accuracy}}

H-Lenia Hierarchical Update

\left[\left[A_i^t + \Delta t G(K * A_i^t)\right]_0^1 + \sum_{j \in N(i)} k_{ji} \cdot E_{ji}^t(\Delta_{j \rightarrow i}^t)\right]_0^1

Lenia Growth Function

G_{\mu,\sigma}(x) = 2e^{-\frac{(x-\mu)^2}{2\sigma^2}} - 1

Neural Particle Automata

[\Delta x_i, \Delta S_i] = f_\theta(S_i, \tilde{S}_i, \nabla S_i, \nabla \rho_i)

Restricted Boolean Network

f_i = \left(\sum_j w_{ij} \cdot x_j\right) > 0

Reaction-Diffusion Laplacian

\nabla^2 Y_i \approx \frac{\sum_j Y_j - Y_i}{\Delta x} \propto J_{Y_{nb}}^Y - J_Y^Y

Information Synergy

I_{\text{syn}}(X \rightarrow Y) = I_{\text{tot}} - \sum_{i=1}^{n} I_{\text{ind}}(X_i)

Research Themes

1. Neural Cellular Automata (NCA)

• From Cells to Pixels (Pajouheshgar et al.)
• Petri Dish NCA (Zhang, Risi, Darlow)
• Language Cellular Automata (Najarro et al.)
• Growing NCA (Sato, Masumori, Ikegami)
• Meta-NCA with Linear Attention

2. Lenia & Continuous CA

• Visualizing Lenia Parameter Space
• H-Lenia: Hierarchical Extension
• Glider Equation for Asymptotic Lenia

3. Evolution & Open-Endedness

• Open-Ended Evolution in Binary CA
• Evolvable Chemotons
• Population of Thoughts (LLM + Evolution)
• Attack of the Clones (Diversity in GP)

4. Chemical Computing

• BZ Oscillator Reservoir Computing
• Chemical Computer Construction
• Environmentally Driven Autocatalysis

5. Swarm Intelligence

• Swarm2Algo: Emergent → Algorithms
• Pheromone-mediated Ant Movement
• Swarm Size Estimation
• Temporal Memory in Swarm Reservoir

6. LLM + ALife

• Gridarians: LLM-Driven ALife
• LLM-Driven Social Behaviors
• Strategy Extraction via LLM Annotation
• Internalized Culture in LLM Societies

7. Category Theory & Formal Methods

• Integrative Formulation via Category Theory
• Functional Information Decomposition
• UIUA Array Language for ALife

Extracted Resources

/Users/bob/ies/paper_extracts/alife2025/
├── ALIFE2025_full.md          # 925KB markdown
├── ALIFE2025_tex.zip          # 11MB LaTeX + images
├── tex_extracted/
│   └── fed660c6-.../
│       ├── *.tex              # 7283 lines LaTeX
│       └── images/            # 153 figures
└── conversion_status.json

Integration with Gay.jl

using Gay

# Assign deterministic colors to papers
function paper_color(title::String)
    seed = UInt64(0x414C494645)  # "ALIFE"
    Gay.color_at(hash(title) ⊻ seed, 1)
end

# GF(3) theme classification
THEMES = Dict(
    :nca => -1,        # MINUS: Structure-preserving
    :evolution => 0,   # ERGODIC: Process
    :emergence => +1   # PLUS: Novel patterns
)

Commands

just alife-toc              # Show table of contents
just alife-paper 42         # Get paper at page 42
just alife-equation "lenia" # Find Lenia equations
just alife-figure 15        # Get figure by number
just alife-theme "nca"      # List NCA papers

See Also

• acsets-algebraic-databases

  - Model ALife structures categorically

• gay-mcp

  - Deterministic coloring for visualization

• hatchery-papers

  - Academic paper patterns

• glass-bead-game

  - Interdisciplinary connections

Citation

@proceedings{alife2025,
  title     = {Companion Proceedings of the Artificial Life Conference 2025},
  booktitle = {ALIFE 25: Ciphers of Life},
  editor    = {Witkowski, Olaf and Adams, Alyssa M. and Sinapayen, Lana and 
               Baltieri, Manuel and Khosravy, Mahdi},
  year      = {2025},
  pages     = {337}
}

---

Extraction: Mathpix PDF ID

fed660c6-4d3d-4bb6-bb3c-f9b039187660

Source:

/Users/bob/Downloads/ALIFE2025ProceedingsCompanion (1).pdf