Methods
Measurement instruments and named techniques.
| Method | Context | Mentions | Relations | Status |
|---|---|---|---|---|
| Planarian Regeneration | — | 4 | 4 | pending-review |
| Morphogenetic Hacking | — | 4 | 2 | pending-review |
| Hebbian Learning | Principle that correlations strengthen connections; implements distributed learning in connectionist networks without centralized supervision. | 4 | 1 | pending-review |
| linear steering | Typical approach that adds a scaled steering vector to representations; the paper argues this is mismatched with actual representation geometry. | 3 | 5 | pending-review |
| Sparse Autoencoders (SAE) | Interpretability method criticized in this paper for shattering manifolds into atomic pieces, obscuring overarching semantic structure. | 3 | 3 | pending-review |
| Unsupervised Learning | — | 3 | 2 | pending-review |
| Koan Battery | Assessment framework for measuring introspection and self-observation in LLMs; grounded in Janus's architectural theory. | 2 | 10 | pending-review |
| Mindfulness Meditation | Contemplative practice that diminishes sense of stable self; documented to increase well-being and social connectedness. | 2 | 4 | pending-review |
| Attribute Exploration | Interactive algorithm for discovering complete implicational knowledge by computing stem base and seeking counterexamples. | 2 | 2 | pending-review |
| Gradient Descent on Free Energy | Optimization procedure for simultaneously updating action selection and perception; uses step size ζ (default 4). | 2 | 2 | pending-review |
| GRPO | Group Relative Policy Optimization; standard RL algorithm used in ATLAS stage 2 without modification, enabling compatible training with existing VLM pipelines. | 2 | 2 | pending-review |
| GRPO (Group Relative Policy Optimization) | RL algorithm used to train the activation verbalizer on open models; samples group of candidate descriptions and applies policy optimization. | 2 | 2 | pending-review |
| Variational Bayes | Mathematical framework for approximating posterior beliefs; converts exact Bayesian inference into optimization. | 2 | 2 | pending-review |
| Conceptual Scaling | Interpretive process for transforming many-valued contexts into formal contexts via scale attributes. | 2 | 1 | pending-review |
| Information Integration | — | 2 | 1 | pending-review |
| International Symbol Notation (pxyz) | Standardized notation system for describing and classifying the seven frieze pattern groups using letters and numbers. | 2 | 1 | pending-review |
| Mean-Field Approximation | Variational technique used in active inference to tractably compute posterior beliefs. | 2 | 1 | pending-review |
| Xenopus Development | — | 2 | 1 | pending-review |
| Multiscale Agent-Based Model | — | 2 | 0 | pending-review |
| Natural Language Autoencoders (NLAs) | Core unsupervised method for generating natural language explanations of LLM activations through a verbalizer-reconstructor pair trained with RL. | 1 | 24 | pending-review |
| Gradient Descent on Variational Free Energy | Process by which neuronal dynamics minimize free energy; produces empirically observable neural phenomena. | 1 | 13 | pending-review |
| Probe-Based Data Attribution | Linear classifier approach applied to model activations to identify which training datapoints caused undesired behaviors in post-training. | 1 | 10 | pending-review |
| Adversarial Parameter Decomposition (VPD) | Core technique introduced in this paper for decomposing neural network weight matrices into mechanistically simple, interpretable rank-one subcomponents. | 1 | 9 | pending-review |
| Activation Verbalizer (AV) | Component of NLA that maps activations to text descriptions; initialized as copy of target LLM with supervised warm-start on summarization task. | 1 | 5 | pending-review |
| Agentic Inference Scaffolding | The paper's inference framework that reformulates multi-turn tool-calling as single-turn contextual QA for Qwen models and implements context memory management. | 1 | 4 | pending-review |
| Covariance Pooling | Novel aggregation technique replacing mean pooling; preserves joint activation structure (feature co-occurrence) in token embeddings. | 1 | 4 | pending-review |
| Free-energy scaling under domain-wall formation | Key analytical technique used across three model systems to determine constraints on long-range order. | 1 | 4 | pending-review |
| Local learning rule | Learning rule where change in a parameter at point x,t depends only on system state at same or nearby spacetime points, without requiring global cost function computation | 1 | 4 | pending-review |
| Primitive Mechanism: n-way Associative Memory | The foundational memory model: a map m associating keys k_i with values v, supporting two operators: associative read and associative write. | 1 | 4 | pending-review |
| Agent-based computational model | The computational approach used to simulate morphogenesis with cells as agents on a 2D grid; allows quantitative testing of stress-sharing hypothesis. | 1 | 3 | pending-review |
| Alexander mirror (forced-choice aesthetic method) | Forced-choice pairwise comparison method following Christopher Alexander; measures aliveness independent of rubric scoring. | 1 | 3 | pending-review |
| Computational economic analysis | The dominant methodological approach across all discovered papers; contrasts with anthropological/historical comparison methods. | 1 | 3 | pending-review |
| Concept Dependence Graph | Method for arranging concepts in a directed graph to show which concepts depend on others and to characterize product families | 1 | 3 | pending-review |
| Latent-Anchored GRPO (LA-GRPO) | Token-level auxiliary objective that strengthens optimization of sparse functional tokens during RL by anchoring group-level advantages directly to functional-token positions. | 1 | 3 | pending-review |
| maximum-norm gradient normalization | Training-free technique normalizing all task gradients to the maximum gradient norm magnitude | 1 | 3 | pending-review |
| Molecular Hebbian learning | Unsupervised learning rule in molecular systems where species i,j with high co-localized concentrations strengthen their interaction strength through proximity-based ligation | 1 | 3 | pending-review |
| Operational Misfit | Negative scenario dual to operational principle; explains what goes wrong when a concept fails to fulfill its purpose in context | 1 | 3 | pending-review |
| Ratchet Mechanism | Physical principle of stable states separated by energy barriers, allowing discrete jumps; exemplified in clocks, switches, molecular isomerism, and life. | 1 | 3 | pending-review |
| Self-Correcting Search | Technique using internal model representations as feedback loops to steer diffusion-based materials generation toward target properties. | 1 | 3 | pending-review |
| 15 Configurational Transformations | Formal descriptive system for the adaptive processes by which centers in structures reconfigure and enhance themselves during morphogenesis. | 1 | 2 | pending-review |
| Activation Oracles (AO) | Supervised method training models to answer questions about activations; NLAs differ by being unsupervised. | 1 | 2 | pending-review |
| Activation Reconstructor (AR) | Component of NLA that maps natural language explanations back to activations; truncated to first l layers of target model. | 1 | 2 | pending-review |
| Activation Steering | Causal intervention technique: edit NLA explanation, reconstruct via AR, use difference as steering vector to manipulate model behavior. | 1 | 2 | pending-review |
| Attribution Graphs | Gradient-based technique using SAE features to estimate causal effects on completions; used to corroborate NLA findings. | 1 | 2 | pending-review |
| Bayesian Inference | — | 1 | 2 | pending-review |
| Central Loop (Event Polling) | Core polling mechanism in module Oberon that continuously listens to mouse and keyboard; dispatches control to appropriate handlers. | 1 | 2 | pending-review |
| Disruption profiles | Mechanistic explanation outputs from EVEE showing how variants affect gene function, scored 3.8/5 for explanation quality. | 1 | 2 | pending-review |
| Dynamic Expectation Maximisation | Variational method for online Bayesian inversion of nonlinear dynamic causal models; eschews Kalman and particle filtering limitations. | 1 | 2 | pending-review |
| Fraction of Variance Explained (FVE) | Model-agnostic measure of reconstruction quality and training progress; ranges from 0 (predicting mean) to 1 (perfect reconstruction). | 1 | 2 | pending-review |
| Ion Channel Misexpression and Chemical Activation | Experimental technique to induce bioelectric state changes and measure consequences for collective decision-making (morphogenesis, cancer, organ formation). | 1 | 2 | pending-review |
| Length-Normalized Advantage Formulation | Novel modification to REINFORCE that normalizes step-level advantage by trajectory length to prevent long but low-quality trajectories from dominating training. | 1 | 2 | pending-review |
| logarithm transformation | Parameter-free loss transformation applied to each task loss to equalize scales | 1 | 2 | pending-review |
| Mean Pooling | Standard baseline aggregation method that covariance pooling improves upon; discards joint activation structure. | 1 | 2 | pending-review |
| Meditation and contemplative practice | Empirical techniques for reducing sense of reified self; show documented benefits in well-being, social connectedness, and prosocial behavior. | 1 | 2 | pending-review |
| Q-learning | Model-free RL algorithm used in experimental comparison; employs ε-greedy exploration. | 1 | 2 | pending-review |
| Spike-Timing-Dependent Plasticity | Biologically plausible local learning rule constraining the brain; referenced as precedent for locality-constrained learning in physical systems | 1 | 2 | pending-review |
| Adjacent Inter-Onset-Interval Vector Notation | Representation of rhythms as strings of non-negative integers indicating duration intervals between onsets; enables comparison with Euclidean strings. | 1 | 1 | pending-review |
| Adversarial ablation | Technique used in VPD to enforce mechanistic faithfulness of parameter decompositions. | 1 | 1 | pending-review |
| Alexander's 15 structural properties | Checklist for decomposing aliveness into formal features; includes roughness, distinctness, and other qualities. | 1 | 1 | pending-review |
| arrows syntactic sugar (proc notation) | Syntactic extension by Ross Paterson enabling point-free arrow definitions with explicit signal naming; dramatically improves readability of complex GUIs. | 1 | 1 | pending-review |
| Bayesian Smoothing | State estimation that combines prior expectations with likelihood; updates informed by past and future states. | 1 | 1 | pending-review |
| Beaver translocation as complex design case | Applied LTPBR intervention maximizing deep water habitat and forage access through targeted beaver placement. | 1 | 1 | pending-review |
| Belief Propagation | Inference mechanism underlying active inference; updates posterior beliefs via gradient descent on free energy. | 1 | 1 | pending-review |
| Broader conservation planning process (Phase 1 Inventory & Phase 2 Design) | Two-phase framework for condition assessment, recovery potential evaluation, and design iteration in restoration. | 1 | 1 | pending-review |
| Canonical Variates Analysis | Statistical method assessing linear mapping between internal functional patterns and external structural motion. | 1 | 1 | pending-review |
| Causal Intervention | Technique used to confirm that circular structures are real computational objects, not merely visualization artifacts. | 1 | 1 | pending-review |
| Contrastive pair activation subtraction | Technique for obtaining concept vectors by presenting model with two scenarios differing in one respect and subtracting activations to isolate conceptual difference. | 1 | 1 | pending-review |
| Directed aging | Unsupervised physical learning process where elastic networks are held in desired configuration while strained bonds soften, reducing system energy | 1 | 1 | pending-review |
| Dynamic Loading | Modules loaded on demand at command invocation or through programmed calls; no separate linker; each module present once in memory. | 1 | 1 | pending-review |
| Event Analysis of Systemic Teamwork (EAST) | Network analysis method used to examine distributed cognition in multi-agent systems; demonstrates measurement approach for collective cognitive processes. | 1 | 1 | pending-review |
| Exponential Moving Average | Used in DB-MTL to estimate batch gradient expectations dynamically | 1 | 1 | pending-review |
| gated fusion | Multimodal fusion technique combining language and vision representations via learnable gating parameters. | 1 | 1 | pending-review |
| Genetic, chemical, and optical manipulation of ion channels and gap junctions | — | 1 | 1 | pending-review |
| Gradient-based data attribution | Baseline method against which probe-based ranking is compared; more computationally expensive. | 1 | 1 | pending-review |
| GUIInput Type | Type representing keyboard and mouse input to GUI, implemented as Maybe-wrapped records to model focus; enables modular input handling. | 1 | 1 | pending-review |
| Hellinger distance | Metric used to define geometric space of output token probability distributions in behavior manifold analysis. | 1 | 1 | pending-review |
| Helmholtz Decomposition | Mathematical technique decomposing flow into curl and divergence-free components; enables derivation of free energy principle. | 1 | 1 | pending-review |
| integral | Primitive signal transformer computing integration of input signal over time; enables velocity-to-position conversion in paddleball. | 1 | 1 | pending-review |
| Ion Channels and Pumps | Cellular machinery controlling resting potential and voltage dynamics; manipulable via drugs or optogenetics to modulate morphogenetic outcomes. | 1 | 1 | pending-review |
| L2 distance fitness metric | Quantitative measure of morphogenetic success: Euclidean distance between evolving embryo phenotype and target smiling-face pattern. | 1 | 1 | pending-review |
| Landau–Lifshitz scaling argument | Historical technique for proving absence of phase transitions via free energy scaling; generalized in this paper to arbitrary local Hamiltonians | 1 | 1 | pending-review |
| LLM-judge methods | Baseline comparison for data attribution; outperformed by probe-based approach. | 1 | 1 | pending-review |
| Logit Lens | Unsupervised interpretability technique that projects activations through unembedding matrix; provides comparison point for NLA approach. | 1 | 1 | pending-review |
| Machine Learning-Based State Space Modeling | AI-discovered pathway models that reconstruct decision landscapes and enable prediction of novel interventions in collective decision-making systems. | 1 | 1 | pending-review |
| Manifold Steering (Wurgaft) | Internal-state feedback technique for steering language models; same conceptual mechanism applied by Hazra et al. to chemistry. | 1 | 1 | pending-review |
| Markov Blankets | — | 1 | 1 | pending-review |
| Memory Management System | Enables agents to self-manage internal context window by providing a clean_memory tool that selectively preserves important information when approaching token limits. | 1 | 1 | pending-review |
| Mouse Input Device | Three-button pointing device central to Oberon interaction; left=caret, middle=commands, right=object selection. | 1 | 1 | pending-review |
| Organoid bioengineering | Experimental technology enabling testing of consciousness theories in novel synthetic systems. | 1 | 1 | pending-review |
| Peierls argument | Classical proof technique for existence of phase transitions in dimensions >1 via domain wall perimeter scaling; adapted in Theorem 1 | 1 | 1 | pending-review |
| Softmax Function | Neuronal dynamics computed from free energy gradients; interpreted as average firing rate of neural populations. | 1 | 1 | pending-review |
| sparse autoencoders | Existing method for model interpretability that decodes model activations rather than parameters themselves, noted as incomplete solution. | 1 | 1 | pending-review |
| Sparse Autoencoders (SAEs) | Unsupervised baseline method for decomposing activations into sparse linear combinations; NLAs positioned as complementary approach. | 1 | 1 | pending-review |
| Spectral Graph Theory | Technique using principal eigenvectors to identify densest clusters; applied to find principal Markov blanket in simulations. | 1 | 1 | pending-review |
| stepper | Primitive signal transformer implementing sample-and-hold; transforms event source to continuous piecewise-constant signal. | 1 | 1 | pending-review |
| TOTE loop | Schematic cybernetic mechanism for goal-pursuit via continuous error-minimization between current state and set point; illustrated in Figure 1A. | 1 | 1 | pending-review |
| Training Data Synthesis Pipeline | Iterative approach to construct challenging synthetic multi-hop QA pairs, long-form report writing tasks, and math/code reasoning tasks that exceed difficulty of existing datasets. | 1 | 1 | pending-review |
| Trajectory Filtering | Strategic filtering procedure that removes invalid trajectories and maintains optimal positive-to-negative trajectory ratio to stabilize training. | 1 | 1 | pending-review |
| Vision Transformer (ViT) | Vision feature extraction model used to extract patch-level features from images in Multimodal-CoT. | 1 | 1 | pending-review |
| Voltage imaging dyes | — | 1 | 1 | pending-review |
| Voltage-Sensitive Fluorescent Dyes | Functional imaging technique used to track bioelectric patterns in regenerating planaria and reveal rules of collective morphospace navigation. | 1 | 1 | pending-review |
| X-ray-induced mutation detection | Experimental technique referenced by Schrödinger to measure gene structure complexity and verify quantum-mechanical mutation model. | 1 | 1 | pending-review |
| Adjacent-Inter-Onset-Interval Vector | — | 1 | 0 | pending-review |
| Alexander deathbed test | Forced-choice comparison measuring what matters vs what is correct; reveals different rankings than composite score. | 1 | 0 | pending-review |
| Attention Probes | Technique used to detect internal model certainty and identify performative reasoning early in reasoning traces. | 1 | 0 | pending-review |
| Beaver Translocation Design | — | 1 | 0 | pending-review |
| Bowtie architecture: compression during learning; creative reinterpretation during recall and generalization | — | 1 | 0 | pending-review |
| Broader Conservation Planning Process | — | 1 | 0 | pending-review |
| Coarse Graining | — | 1 | 0 | pending-review |
| Commissurotomy | — | 1 | 0 | pending-review |
| Diagrammatic analysis of page space | Analytical technique for recovering the generative history and semantic operations embedded in spatial organization. | 1 | 0 | pending-review |
| Dream Yoga | — | 1 | 0 | pending-review |
| Dynamic Module Loading | — | 1 | 0 | pending-review |
| Dynamical Constraints as Landscapes (Attractors) | — | 1 | 0 | pending-review |
| eval() Operation | — | 1 | 0 | pending-review |
| Formal Model | — | 1 | 0 | pending-review |
| Genetic Algorithm (GA) | — | 1 | 0 | pending-review |
| Hash tables | — | 1 | 0 | pending-review |
| in() Operation | — | 1 | 0 | pending-review |
| Inpainting | — | 1 | 0 | pending-review |
| Input-Output Relations Diagrammatically | — | 1 | 0 | pending-review |
| L2 Distance Fitness Function | — | 1 | 0 | pending-review |
| loop | — | 1 | 0 | pending-review |
| Measurement-Based Quantum Computation | — | 1 | 0 | pending-review |
| Membrane Potential Vmem | — | 1 | 0 | pending-review |
| Mindfulness | — | 1 | 0 | pending-review |
| Natural Building Materials | — | 1 | 0 | pending-review |
| out() Operation | — | 1 | 0 | pending-review |
| Placement as Division | — | 1 | 0 | pending-review |
| rd() Operation | — | 1 | 0 | pending-review |
| Sensory Substitution And Augmentation | — | 1 | 0 | pending-review |
| Shape Grammar | — | 1 | 0 | pending-review |
| Sim To Real Transfer | — | 1 | 0 | pending-review |
| Structure Editor | — | 1 | 0 | pending-review |
| when | — | 1 | 0 | pending-review |
135 total methods.