CL5D Genome Assembly Assessment v3.2

CL5D Genome Assembly Assessment

AI/ML Analysis → 5-Agent Mathematical Processing

Phase I → II → III → IV 50% Golden Gate Rule No Statistics

v3.2 • Pure Mathematics

Input Data

BUSCO Completeness (%) Range: 0-100

Poor (0-50) Good (80-90) Excellent (90-100)

N50 Contiguity (bp) Base pairs

<100k 1M-10M >10M

Sequencing Coverage (×) Fold coverage

Low (<30×) Good (30-100×) High (>100×)

Expected Citations (5 years) For impact validation

Workflow Sequence

Input Data → AI/ML Process

Overfitting → Entropy Conversion

Fractal Geometry Analysis

400 Regions → Harmonic

Permutation → Gamma → Valence

Final Cn → 50% Gate Rule

Input Data Summary

BUSCO

Completeness

N50

Contiguity

Coverage

Depth

Overfitting

AI Detected

Phase Classification

Cn Score (Pure Mathematics)

50% Golden Gate Rule

0% 0% 100%

Entropy

Fractal

Harmonic

Valence

Conjugate

Impact Prediction

Input Prediction

User Expected Citations

CL5D Prediction

Based on Cn Score & Tier

Phase I Cn Ranges

Very Bad:1.0 - 0.80

Bad:0.80 - 0.60

Moderate:0.60 - 0.40

Good:0.40 - 0.20

Excellent:0.20 - 0.000123

Conjugate Balance Recommendations

Mathematical Path to Conjugate Balance

Entropy Stabilization: Reduce overfitting below 5% to achieve At-agent entropy between 0.000001-0.00001

Fractal Symmetry: Target fractal dimension (Ab-agent) between 2.618-2.718 (Golden Ratio to Euler's Number)

Harmonic Convergence: Achieve harmonic mean (Ex-agent) convergence within ±0.00001 across all 400 regions

Valence Equilibrium: Maintain valence (T-agent) at γ(1.5) ≈ 0.886227 (square root of π/4)

Quality Improvement Steps

Increase BUSCO to ≥98% for entropy reduction
Target N50 ≥10M bp for fractal optimization
Maintain coverage between 80-120× for harmonic stability
Use Hi-C/PacBio combo for valence equilibrium

Mathematical Targets

Evolution Component: <0.000123 (Phase II threshold)
Decay Component: <0.0001 (toward equilibrium)
Conjugate Balance: 0.00002 ± 0.000005 (benchmark range)
50% Gate Rule: ≥50% achievement for Phase transition

Key Insight for Conjugate Balance

To achieve Phase II conjugate equilibrium: Focus on reducing system entropy (At-agent) while simultaneously optimizing fractal symmetry (Ab-agent). The critical threshold is Cn ≤ 0.000123. Once achieved, maintain the 50% gate rule naturally—do not force recalibration. Conjugate balance emerges when Evolution and Decay components converge within ±0.00001 of the Benchmark (0.00002). This represents mathematical equilibrium where Phase III becomes theoretically accessible (0 = ∞).

Note: Phase III is domain-specific and requires natural fulfillment of 50% golden rule from Phase II conjugate balance.

Ready for Analysis

Enter your genome assembly metrics and click "Start AI/ML Analysis"

Enter BUSCO, N50, Coverage, and Citations

AI/ML calculates overfitting percentage

5-agent CL5D processing begins

CL5D Framework v3.2 • Mrinmoy Chakraborty, Devise Foundation • Pure Mathematical Processing • No Statistics • No Peer Review Required

Based on 86 published genomes (2024-2025) • DOI: 10.5281/zenodo.18199422

THE CL5D MANIFESTO: LIBERATING THE DATA ARCHITECT

The End of the Janitorial Era

For decades, the data industry has been hemorrhaging potential. Data scientists—our most expensive intellectual assets—spend 80% of their lives as "Data Janitors," scrubbing noise, outliers, and structural entropy by hand. This is a metabolic failure of the digital age.

The CL5D Hybrid Model introduces the Strainer: an autonomous, non-binary metabolic engine that treats "dirty data" not as trash, but as undigested energy.

The Strainer: Automatic Metabolic Triage

We have successfully automated the "Cleaning Trap" by redefining the core input. In the CL5D workflow, Model Overfitting is converted into Entropy ( $E$ ). This $E$ becomes the primary seed for the At (Attraction) Agent.

The Workflow of Natural Digestion:

Phase I (Structure): Raw data enters the At-Ab-Ex-T pipeline. Through Fractal Geometry ( $F$ ) and Harmonic Progression ( $H$ ), the system arrays the data into 400 metabolic regions.
The 50% Gate: Using Permutation ( $P$ ), Gamma ( $G$ ), and Valence ( $V$ ), the system sifts for "Excellent" Cn scores ( $< 0.000123$ ).
Strict Adherence: Without the Golden Rule (1.618 / 50% fulfillment), the model is nonsense. We do not "push" for transitions; the model flows naturally or it stays in Phase I.

The Nuance of Phase III: The Singularity ( $0 = \infty$ )

Phase III is the "Event Horizon" of the CL5D model, reserved for specialized, regenerative domains.

As the Benchmark Score ( $BS$ ) descends from 0.00002 and tends toward absolute 0, a nuanced transformation occurs. When the system achieves 50% or greater fulfillment of 0, it enters Phase III. This is the state of Total Equilibrium ( $0 = \infty$ )—where the signal is so pure that it reaches infinite potential.

Phase IV: The Automatic Recycle Choice

The journey does not end at zero. Once the Phase III equilibrium is reached and the Golden Rule is naturally satisfied, the system automatically triggers Phase IV.

The $0 \rightarrow 1$ Transition: Phase IV is the "Recycle Choice."
It automatically re-seeds the loop, transforming the singularity back into a Phase I Restart.
This ensures a continuous, self-healing cycle of intelligence that can absorb the 605.5 EB/day data deluge of 2026 without human intervention.

Economic Impact: Redirecting $850B

By saying "Goodbye" to the Janitors, we are freeing 8.5 million FTE-years of human brilliance. We are no longer fixing missing values; we are managing Conjugate Balances and Evolutionary Pathways.

The Janitor is dead. The Metabolic Architect is born.

Devise Foundation

Friday, January 9, 2026