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

bp

<100k 1M-10M >10M

Sequencing Coverage (×) Fold coverage

×

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

Expected Citations (5 years) For impact validation

AI/ML Analysis Result

0%

Overfitting detected → Will be converted to Entropy

Workflow Sequence

1

Input Data → AI/ML Process

At

Overfitting → Entropy Conversion

Ab

Fractal Geometry Analysis

Ex

400 Regions → Harmonic

T

Permutation → Gamma → Valence

V

Final Cn → 50% Gate Rule

AI/ML Data Analysis

Analyzing input data to detect ML overfitting patterns

CL5D 5-Agent Processing

Sequential mathematical processing through all agents

At

Entropy

Pending

Ab

Fractal

Pending

Ex

Harmonic

Pending

T

Valence

Pending

V

Conjugate

Pending

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%

At

Entropy

Ab

Fractal

Ex

Harmonic

T

Valence

V

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

Phase II: Evolutionary Components

Evolution

Range: <0.000123 - 0.0001

Decay

Range: <0.0001 - 0.00002

Conjugate

Equilibrium Balance

Benchmark

0.00002

Target Score

Conjugate Balance Recommendations

Mathematical Path to Conjugate Balance

1

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

2

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

3

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

4

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.18181092

CL5D Genome Assembly Assessment © 2026-01-09 by Mrinmoy Chakraborty is licensed under CC BY 4.0