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73 lines
3.6 KiB
Text
73 lines
3.6 KiB
Text
/- Copyright (c) 2026 Sovereign Research Stack. All rights reserved.
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Released under Apache 2.0 license as described in the file LICENSE.
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Authors: Research Stack Team
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GenomicCompression.lean — Orchestrator for Genomic Compression Modules
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This module serves as the orchestrator for the Genomic Compression framework,
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importing and re-exporting all core sub-modules for genomic sequence compression
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using the unified field Φ(x) approach.
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Sub-modules:
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- Types: Basic genomic types (Nucleotide, DNASequence, AminoAcid, etc.)
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- Components: NormalizedComponents and GenomicWeights structures
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- Field: phiGenomic and related field computation functions
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- Compression: Compression operations (compressWindow, compressDNAWindows, etc.)
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- Theorems: Formal theorems about boundedness and monotonicity
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- NonDriftProof: Formal proof that transformation is mathematically derivable
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Key insights from literature:
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- 2504.03733: AI for Epigenetic Sequence Analysis → Methylation pattern compression
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- 2503.16659: Protein Representation Learning → Structural compression in latent space
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- 2504.12610: Gene Regulatory Network Inference → Network topology compression
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Per AGENTS.md §1.4: Q16_16 fixed-point for hardware extraction.
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Per AGENTS.md §2: PascalCase types, camelCase functions.
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Per AGENTS.md §4: Every def has eval witness or theorem.
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TODO(lean-port): Extract formal lemmas from 2504.03733 epigenetic analysis
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TODO(lean-port): Connect to ProteinRepresentation.lean (from 2503.16659)
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TODO(lean-port): Prove compression bounds vs standard codecs (gzip, bzip2)
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-/
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import Mathlib.Data.Nat.Basic
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import Mathlib.Data.Real.Basic
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import Mathlib.Tactic
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import Semantics.FixedPoint
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import Semantics.Functions.MathQuery
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import Semantics.GenomicCompression.Types
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import Semantics.GenomicCompression.Components
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import Semantics.GenomicCompression.Field
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import Semantics.GenomicCompression.Compression
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import Semantics.GenomicCompression.Theorems
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import Semantics.GenomicCompression.NonDriftProof
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namespace Semantics.GenomicCompression
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-- Re-export all core types and structures
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open Types
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open Components
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open Field
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open Compression
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open Theorems
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open NonDriftProof
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open Semantics.Q16_16
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-- ═══════════════════════════════════════════════════════════════════════════
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-- Orchestrator Notes
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-- ═══════════════════════════════════════════════════════════════════════════
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-- Core genomic compression functionality has been extracted to sub-modules:
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-- - Types: Basic genomic types (Nucleotide, DNASequence, AminoAcid, etc.)
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-- - Components: NormalizedComponents and GenomicWeights structures
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-- - Field: phiGenomic and related field computation functions
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-- - Compression: Compression operations (compressWindow, compressDNAWindows, etc.)
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-- - Theorems: Formal theorems about boundedness and monotonicity
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-- - NonDriftProof: Formal proof that transformation is mathematically derivable
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--
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-- Swarm, Triumvirate, and Topology sections remain in this file for now.
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-- These should be moved to separate modules or removed as they are unrelated
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-- to the core genomics compression purpose.
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-- ═══════════════════════════════════════════════════════════════════════════
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end Semantics.GenomicCompression
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