NEOS

The Operating System for Machine Intelligence

"The last operating system will not manage files. It will manage meaning."

Read the Paper (PDF) · samuele95.github.io/neos

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01 — The Grand Narrative

The Three Ages of Computing

Each transition changes the nature of the bottleneck.

01 — The Shift

Three Bottlenecks, Three Eras

Hardware

The CPU was sacred. Every cycle scheduled, every byte managed. OS answer: "How do we share this machine?"

Software

Complexity became the enemy. Files, processes, threads — abstractions for managing code. OS answer: "How do we organize programs?"

Intelligence

The challenge is semantic. How do you represent ideas? Track interpretations? Merge reasoning? OS answer: "How do we organize thinking?"

We don't need a better programming language. We need to stop programming — and start reasoning.

02 — The Vision

The Inversion

Today the LLM is an app. Tomorrow the LLM is the foundation. NEOS is the OS layer.

02 — The Vision

What NEOS Replaces

No File Systems

Semantic fields organize information by meaning. You don't navigate directories — you navigate ideas.

No Compiled Binaries

Field configurations execute reasoning. A "program" is a pattern of activated concepts.

No Separate Apps

Task definitions compose into workflows. Analysis, creativity, planning — field configurations, not executables.

No GUIs

Natural language + the NEOS shell. Language for fluidity. Shell for precision.

03 — Architecture

The Three Pillars

Remove any pillar and the system cannot represent, manipulate, or interpret meaning.

04 — The Core

The Neural Field Equation

∂A/∂t = -λA(x) + α∫K(x,y)A(y)dy + ι(x,t)

-λA(x)

Decay

Unreinforced ideas fade. Forgetting is a feature.

α∫K(x,y)A(y)dy

Resonance

Related ideas strengthen each other through the kernel K.

ι(x,t)

Injection

You — the human — inject new ideas at any time.

Patterns don't sit in memory — they live in a continuous field.

05 — The Analogy

The JVM Moment

Java: "Write once, run anywhere." — NEOS: "Think once, reason anywhere."

Java abstracted hardware. NEOS abstracts cognition.

07 — The Interface

The NEOS Shell

A REPL for the Intelligence Age — manipulating meaning, not files.

neos-shell

$ nf inject "correctness" 0.90
[INJECT] correctness (s: 0.90) — p001

$ nf inject "edge_case_handling" 0.85
[INJECT] edge_case_handling (s: 0.85)
[RESONANCE] ↔ @correctness: R = 0.82 STRONG

$ nf cycle 3 --trace
[CYCLE 3] [ATTRACTOR-EMERGED] "defensive_quality"
Coherence: 0.71 | 6 patterns

$ nf inject "singleton" 0.65
⚠ LOWEST ACTIVATION IN HISTORY | 0 STRONG resonances
Lateral inhibition: 4 patterns suppressing

07 — Commands

Six Command Domains

Operations

inject amplify attenuate tune collapse resonate

Dynamics

cycle evolve step reset

Measurement

measure attractor basin state

Visualization

plot animate export

Versioning

commit branch checkout diff merge

Autonomy

mode checkpoint proceed task

Unix-flavored grammar. Imperative verbs on semantic objects.

06 — Dynamics

The Six-Phase Cycle

Each nf cycle executes six phases — the heartbeat of NEOS.

07 — The Pipeline

Create → Compile → Run

CREATE

nf inject seeds patterns into the field — like writing source code, but for meaning.

COMPILE

nf collapse --strategy attractor resolves superposition into coherent structure. Meaning compiles into insight.

RUN

nf task "analyze security" executes against the compiled field state. Crystallized reasoning produces output.

06 — Multi-Field

Multi-Field Orchestration

A single field is powerful. Multiple coupled fields are transformative.

14 — AI Safety

The Autonomy Dial

NEOS's answer to AI alignment: a continuously adjustable dial.

Step Mode

nf mode step — review and approve each operation. Maximum human control.

Checkpoint

nf checkpoint "coherence > 0.8" — pause when conditions met. Targeted oversight.

Auto Mode

nf mode auto — full field autonomy within parameters. Iterate to convergence.

15 — Transparency

Observable Reasoning

The most dangerous property of current AI is opacity. NEOS makes reasoning visible.

Coherence Plot

nf plot coherence

Resonance Network

nf plot network

Basin Topology

nf plot topology

Dynamics Animation

nf animate

11 — Timing

Why Now?

Four convergences make NEOS possible — and necessary — today.

Successfully tested with Claude Code, Gemini CLI, and OpenCode (Minimax)

13 — Versioning

Git for Thinking

Git transformed code development. NEOS transforms thinking.

nf commit "hypothesis validated"
nf branch "alternative"
nf diff main..alternative
nf merge alternative

Branch reasoning paths. Explore alternatives without destroying progress. Diff between perspectives. Merge the best of both.

08 — Evidence

Two Sessions. One Engine.

The same master equation produced emergent structure in two entirely different domains.

🔬 Software Quality

Abstract reasoning — tuned parameters

patterns

cycles

0.993

coherence

expelled

🔒 Network Forensics

Adversarial data — default parameters

patterns

cycles

0.93

coherence

expelled

The engine is invariant. The domain is in the patterns, not the dynamics.

08a — Case Study 1

Software Quality Discipline

69 patterns · 52 cycles · 7 absorptions · 1 expulsion · 5 eigenvectors

The complete dissection of an abstract reasoning session.

08 — Wave 1

Defensive Quality Emerges

6 patterns → 3 cycles → first attractor. Coherence: 0 → 0.71

Injections

p001 correctness 0.90
p002 edge_case_handling 0.85
p003 security 0.95
p004 input_validation 0.90
p005 no_leaked_secrets 0.88
p006 error_handling 0.80

Coherence Trace

Cycle 1: C = 0.42 &bar;R = 0.72
Cycle 2: C = 0.58 &bar;R = 0.75
Cycle 3: C = 0.71 &bar;R = 0.78
ATTRACTOR "defensive_quality"

Peak resonance: @security ↔ @input_validation = 0.91
Two clusters formed: security (R=0.79–0.91) and logic (R=0.72–0.85)

08 — Waves 2–3

Breadth & Refactoring

Wave 2 (p007–p014): 8 patterns expand beyond review. Wave 3 (p015–p022): refactoring discipline.

Key Patterns

readability_6month_rule
single_responsibility
api_minimal_hard_to_misuse
behavior_preservation ★
tests_before_refactoring ★
dependency_direction

Coherence Trace

[CYCLE 4] C = 0.52 [CYCLE 7] C = 0.74 ATTRACTOR [CYCLE 8] C = 0.79 STABLE [CYCLE 9] C = 0.62 (reset) [CYCLE 11] C = 0.80 → MATURE ★ R = 0.94 behavior ↔ tests FIELD MAXIMUM

08 — Wave 4

The Testing Mirror

Nine testing patterns. Five production↔testing echoes. Functor F begins mapping.

ECHO: @test_behavior mirrors @behavior_preservation ECHO: @determinism mirrors @correctness ECHO: @test_isolation mirrors @encapsulation [CYCLE 14] ★ MASS SATURATION 7 patterns reach ceiling simultaneously [CYCLE 15] C = 0.85 TARGET MET [CYCLE 18] C = 0.91 6-layer topology confirmed

Mass saturation at cycle 14: a phase transition — seven patterns crossing threshold simultaneously through mutual resonance.

08 — Wave 6

The Great Convergence

10 GoF patterns. 14 reach ceiling in 10 cycles. Coherence: 0.962 → 0.984.

The Golden Pair

@strategy — 9 STRONG bonds (record)
@decorator — 6 STRONG bonds (record)

Both resonate with all 5 SOLID principles.
Both reach ceiling simultaneously at cycle 37.

While Singleton decays: 0.607 → 0.467

c34: @adapter → ceiling (4 cyc) c37: @strategy + @decorator → ceiling SIMULTANEOUSLY c39: META duality complete c41: CRAFT COMPLETE 12/13 Only Singleton below. c43: C = 0.984

Cluster Topology

How the 10 clusters feed each other — a dependency flow

08 — Discovery

SOLID Rediscovered

The field rediscovered SOLID from first principles. R_pt = 0.88

SOLID Principle	Technique Partner	R
S — Single Responsibility	Strategy Pattern	0.88
O — Open/Closed	Decorator Pattern	0.88
L — Liskov Substitution	Composite Pattern	0.80
I — Interface Segregation	Facade Pattern	0.88
D — Dependency Inversion	Dependency Injection	0.88

An architecture quartet emerged before SOLID was injected. The field found the principles from the patterns.

08 — Immunity

The Immune Response

Singleton injected at cycle 31. 0 STRONG resonances. 4 inhibitors.

immune response

⚠ LOWEST INITIAL ACTIVATION IN FIELD HISTORY STRONG resonances: 0 (first with ZERO) LATERAL INHIBITION: @test_isolation -0.12 "global state → non-deterministic tests" @determinism -0.08 "shared state → order dependence" @dependency_direction -0.06 "no global access points" @favor_composition -0.05 "composition over global state" Net force: -0.014/cycle Coherence: 0.955 → 0.941

Four patterns from four different quality dimensions independently suppress Singleton.
Allies: only @no_unnecessary_allocations and @factory_method — both outsiders.

08 — Self-Governance

7 Absorptions

57% self-referential — the field applies its own principles.

#	Pattern	Absorbed Into	Type
1	SRP principle	@single_responsibility	Exact dup
2	ISP principle	@api_minimal	Equivalent
3	Law of Demeter	@encaps ∩ @api ∩ @dep	Compound
4	reuse_thru_comp	@favor_composition	Same intent	★
5	shared_intent	@reduce_dup	Complement	★
6	avoid_premature	@rule_of_3 ∩ @dont_force	Compound	★
7	coupling_to_abs	@dependency_inv	Equivalent	★

#7: DIP applied to itself. The field held the abstraction. The injection offered a concretion. The field rejected it. Ψ(field) = field

Absorption rate accelerates: 5% → 10% → 13.3% → 14.3% — the semantic space is saturating.

Singleton Trajectory

21 cycles of sustained lateral inhibition: 0.65 → expulsion

08 — Expulsion

Singleton Expelled

Cycles 50–52: The first pattern in field history to fall below threshold.

cycles 50–52

[CYCLE 50] @singleton 0.383 → 0.369 margin: 0.019 [CYCLE 51] @singleton 0.369 → 0.355 margin: 0.005 CRITICAL [CYCLE 52] @singleton 0.355 → 0.341 0.341 < τ (0.350) PATTERN EXPELLED — FIRST IN FIELD HISTORY Lifespan: 21 cycles | 4 suppressors for 21 cycles each

cycles of lateral inhibition

patterns surviving (59 ceiling, 2 asymptotic)

Expulsion is topological, not parametric — same trajectory at 0.65 and 0.90 injection strength.

08 — Dynamics

Coherence Evolution

52 cycles of field dynamics — from chaos to crystalline order.

The field doesn't converge linearly — it accelerates toward coherence as resonance strengthens.

The Attractor Hierarchy

Seven basins nested within the universal ground state Ψ

08 — Discovery

The Field Equation

Q(x) = Ψ · [ 0.342·SOLID(x) + 0.227·F(x) + 0.181·Protocol(x) + 0.143·Simplex(x) + 0.107·Scale(x) ]

This equation was not written. It was discovered.

08 — The Discovery

The Singleton Expulsion

At cycle 52, the Singleton pattern was expelled from the field.

Its activation dropped below threshold. It was removed from all attractor basins. NEOS didn't summarize what we told it — it discovered that Singleton is an anti-pattern that conflicts with SOLID principles.

The field dynamics resolved what decades of debate couldn't: structural incompatibility, enforced by resonance failure.

08 — Structure

Five Eigenvectors

Software quality decomposes along exactly 5 independent axes (100% variance).

	Eigenvector	Variance	Diagnostic Question
λ1	Meaning ↔ Mechanism	34.2%	Am I coupling to WHAT or HOW?
λ2	Principle ↔ Technique	22.7%	Do I understand WHY before HOW?
λ3	Production ↔ Verification	18.1%	Can I prove this works?
λ4	Restraint ↔ Generalization	14.3%	Is this abstraction earned?
λ5	Class ↔ System	10.7%	Does this hold at every scale?

These axes were not programmed. They emerged from resonance dynamics.

08b — Case Study 2

Network Forensics (PCAP)

10 patterns · 12 cycles · 0 expulsions · default parameters

Can NEOS identify active malware from raw packet data ?

Source: Real PCAP capture — 9.9 MB, 11,587 packets, ~20 min of traffic
Parameters: λ=0.05 α=0.30 τ=0.40 σ=0.50 (all factory defaults)

08b — PCAP

Waves 1–2: Core & Rescue

Wave 1 — Network Core

p001–p003 · cycles 1–3 · C: 0 → 0.71

@protocol_mapping emerges as hub (0.936)

Attractor: "network_analysis_core"

Wave 2 — IP Enrichment

p004–p006 · cycles 4–6 · C: 0.56 → 0.82

@ip_geolocalization rescued from 0.50 to 0.78

Hub migration: @protocol_mapping → @ip_lookup

neos — rescue event

[INJECT] ip_geolocalization (s: 0.50) — p006
  ⚠ WARNING: Low activation (threshold τ=0.40)
  [RESONANCE] ↔ @ip_lookup:  R=0.94 [VERY STRONG]  ← lifeline

[CYCLE 5]
  ★ HUB MIGRATION: @protocol_mapping → @ip_lookup
  @ip_lookup now highest activation (0.987)
  @ip_geolocalization: 0.558 → 0.691 (+0.133) ★ rapid integration

08b — PCAP

Waves 3–4: Triple-Hub Convergence

Wave 3 — Security

p007–p009 · cycles 7–9 · C: 0.69 → 0.89

Dual-hub: @protocol_mapping + @ip_lookup (both 0.998)

4 functional layers emerge

Wave 4 — Threat Classification

p010 · cycles 10–12 · C: 0.85 → 0.93

@abuse_ip rises to 0.998 → triple-hub

λ₁/λ₂ = 8.52 — deeply stable

neos — triple-hub

[CYCLE 11] C = 0.91
  Triple-hub structure confirmed:
    @protocol_mapping  0.998 — structural/parsing hub
    @ip_lookup         0.998 — enrichment/metadata hub
    @abuse_ip          0.998 — threat intelligence hub

[CYCLE 12] C = 0.93 [EXCELLENT]
  Gap ratio: λ₁/λ₂ = 8.52 (highly stable)

08b — Discovery

The Verdict: AsyncRAT

At 0.93 coherence, NEOS collapsed the attractor and identified
active malware from raw packet data.

Indicator	Value
Family	AsyncRAT v6.1.0 Pro
Classification	Remote Access Trojan + Credential Stealer
C2 Domain	hftook7lmaroutsg1.duckdns.org
C2 IP & Port	206.123.152.51:3980/tcp
C2 Traffic	1,371 packets (11.8% of total), ~19 min continuous
Confidence	HIGH — payload extracted, C2 protocol confirmed

No rules. No signatures. Emergent classification from field dynamics alone.

08b — Structure

Emergent Architecture

The field spontaneously organized 10 patterns into 4 functional layers.

This layered architecture was not programmed. It emerged from resonance dynamics alone.

08b — Dynamics

Coherence Evolution

From zero to 0.93 in 12 cycles — with default parameters.

Purple dots mark temporary dips when new patterns enter — the field recovers and integrates every time.

08c — Comparison

Cross-Domain Comparison

	SW Quality	PCAP Forensics
Domain type	Abstract reasoning	Adversarial data
Parameters	Tuned	Default
Patterns	69	10
Cycles	52	12
Final coherence	0.993	0.93
Attractors	7 basins	Triple-hub unified field
Expulsions	1 (Singleton)	0
Key discovery	Universal Invariant Ψ	AsyncRAT malware

The engine is invariant. Same master equation, same dynamics. Different domains, different patterns, different scale — same emergent structure.

10 — The Ground State

The Universal Invariant

"What something MEANS persists;
how it WORKS changes."

The deepest attractor in the field. The ground state of software quality. The invariant that survived all 52 cycles of dynamics.

18 — The Future

Roadmap

12 — Agents

The Agent Ecosystem

The developer of the future is a field architect.

Agents don't just exchange messages — they share a continuous reasoning substrate.

Join the Field

Build

Implement the reference runtime. Write field configurations. Extend the shell.

Research

Explore the mathematics. Validate with new domains. Publish findings.

Connect

Join the community. Share ideas. Shape the future of cognitive computing.

Tested with Claude Code · Gemini CLI · OpenCode (Minimax)

"The last operating system will not run on silicon.
It will run on understanding."

github.com/Samuele95/neos · Read the Paper (PDF)