@aleph-ai/tinyaleph 1.2.1 → 1.4.0

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Files changed (50) hide show
  1. package/README.md +609 -13
  2. package/backends/bioinformatics/binding.js +503 -0
  3. package/backends/bioinformatics/dna-computing.js +664 -0
  4. package/backends/bioinformatics/encoding.js +339 -0
  5. package/backends/bioinformatics/folding.js +454 -0
  6. package/backends/bioinformatics/genetic-code.js +269 -0
  7. package/backends/bioinformatics/index.js +522 -0
  8. package/backends/bioinformatics/transcription.js +221 -0
  9. package/backends/bioinformatics/translation.js +264 -0
  10. package/backends/cryptographic/index.js +455 -2
  11. package/backends/index.js +25 -1
  12. package/core/beacon.js +735 -0
  13. package/core/compound.js +532 -0
  14. package/core/crt-homology.js +1004 -0
  15. package/core/enochian-vocabulary.js +910 -0
  16. package/core/enochian.js +744 -0
  17. package/core/errors.js +587 -0
  18. package/core/hilbert.js +1105 -2
  19. package/core/index.js +192 -13
  20. package/core/inference.js +605 -0
  21. package/core/lambda.js +284 -33
  22. package/core/logger.js +350 -0
  23. package/core/prime.js +136 -1
  24. package/core/quaternion-semantics.js +623 -0
  25. package/core/reduction.js +391 -1
  26. package/core/resonance.js +245 -616
  27. package/core/rformer-crt.js +892 -0
  28. package/core/symbols/archetypes.js +478 -0
  29. package/core/symbols/base.js +302 -0
  30. package/core/symbols/elements.js +487 -0
  31. package/core/symbols/hieroglyphs.js +303 -0
  32. package/core/symbols/iching.js +471 -0
  33. package/core/symbols/index.js +77 -0
  34. package/core/symbols/tarot.js +211 -0
  35. package/core/symbols.js +22 -0
  36. package/core/topology.js +655 -0
  37. package/docs/README.md +54 -0
  38. package/docs/design/BIOINFORMATICS_BACKEND_DESIGN.md +493 -0
  39. package/docs/guide/06-symbolic-ai.md +370 -0
  40. package/docs/guide/README.md +2 -1
  41. package/docs/reference/05-symbolic-ai.md +570 -0
  42. package/docs/reference/06-bioinformatics.md +546 -0
  43. package/docs/reference/07-topology.md +257 -0
  44. package/docs/reference/08-observer.md +421 -0
  45. package/docs/reference/09-crt-homology.md +369 -0
  46. package/docs/reference/README.md +32 -2
  47. package/docs/theory/11-prgraph-memory.md +559 -0
  48. package/docs/theory/12-resonant-attention.md +661 -0
  49. package/modular.js +264 -4
  50. package/package.json +1 -1
package/core/index.js CHANGED
@@ -4,6 +4,26 @@
4
4
 
5
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  const { Hypercomplex } = require('./hypercomplex');
6
6
 
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+ // CRT-Homology Module (Chinese Remainder Theorem + Birkhoff Attention + Homology Loss)
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+ const {
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+ extendedGCD,
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+ modInverse,
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+ areCoprime,
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+ softmax,
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+ ResidueEncoder,
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+ CRTReconstructor,
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+ BirkhoffProjector,
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+ HomologyLoss,
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+ CRTModularLayer,
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+ CRTFusedAttention,
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+ CoprimeSelector,
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+ createCRTLayer,
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+ createFusedAttention,
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+ DEFAULT_PRIMES_SMALL,
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+ DEFAULT_PRIMES_MEDIUM,
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+ DEFAULT_PRIMES_SEMANTIC
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+ } = require('./crt-homology');
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+
7
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  // Formal Type System (mtspbc.pdf implementation)
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  const {
9
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  NounType, AdjType, SentenceType,
@@ -30,6 +50,11 @@ const {
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  Translator, TypeDirectedTranslator,
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  LambdaEvaluator, Semantics, ConceptInterpreter
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  } = require('./lambda');
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+
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+ // Enochian Packet Layer (Section 7.4)
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+ const enochian = require('./enochian');
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+ const enochianVocabulary = require('./enochian-vocabulary');
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+
33
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  const {
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  FANO_LINES,
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  octonionMultiplyIndex,
@@ -53,20 +78,70 @@ const {
53
78
  ResonanceOperators,
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  EntropyDrivenEvolution,
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  encodeMemory,
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- symbolicCompute
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- } = require('./hilbert');
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-
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- // Prime Resonance Network components
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- const {
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- PHI, PHI_CONJ, DELTA_S,
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+ symbolicCompute,
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  QuaternionPrime,
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  PrimeResonanceIdentity,
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  PhaseLockedRing,
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  HolographicField,
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  EntangledNode,
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- ResonantFragment
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+ ResonantFragment,
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+ DELTA_S
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+ } = require('./hilbert');
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+
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+ // Golden Ratio Resonance (from symprime symbolic AI)
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+ const {
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+ ResonanceCalculator,
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+ resonanceSignature,
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+ findFibonacciSequences,
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+ PHI,
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+ PHI_THRESHOLD,
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+ PHI_BONUS,
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+ calculateResonance,
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+ findGoldenPairs,
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+ findMostResonant
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  } = require('./resonance');
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103
 
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+ // Symbol Database (200+ emoji symbols from symprime)
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+ const {
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+ SymbolDatabase,
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+ SymbolCategory,
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+ PrimeGenerator,
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+ symbolDatabase,
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+ getSymbol,
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+ getSymbolByPrime,
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+ search: searchSymbols,
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+ encode: encodeSymbols,
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+ decode: decodeSymbols
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+ } = require('./symbols');
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+
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+ // Semantic Inference Engine (from symprime)
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+ const {
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+ SemanticInference,
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+ EntityExtractor,
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+ InferenceMethod,
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+ semanticInference,
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+ entityExtractor,
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+ inferSymbol,
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+ inferSymbols,
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+ extractEntities,
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+ extractAndInfer,
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+ inferWithResonance,
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+ inferMostResonant
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+ } = require('./inference');
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+
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+ // Compound Builder (multi-symbol concepts from symprime)
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+ const {
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+ CompoundBuilder,
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+ CompoundSymbol,
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+ SymbolSequence,
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+ compoundBuilder,
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+ createCompound,
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+ getCompound,
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+ createSequence,
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+ getSequence,
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+ findCompoundsContaining
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+ } = require('./compound');
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+
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  // ResoFormer ML primitives
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  const {
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  Quaternion,
@@ -94,6 +169,14 @@ const {
94
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  ResoFormer
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  } = require('./rformer-layers');
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171
 
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+ // CRT-enhanced ResoFormer layers
173
+ const {
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+ CRTResonantAttention,
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+ HomologyRegularizedBlock,
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+ CRTResoFormer,
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+ createCRTResoFormer
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+ } = require('./rformer-crt');
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+
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  // Prime Entanglement Graph
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  const {
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  EntanglementEdge,
@@ -154,11 +237,6 @@ module.exports = {
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  EntropyDrivenEvolution,
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  encodeMemory,
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  symbolicCompute,
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-
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- // Prime Resonance Network
159
- PHI,
160
- PHI_CONJ,
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- DELTA_S,
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  QuaternionPrime,
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  PrimeResonanceIdentity,
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  PhaseLockedRing,
@@ -166,6 +244,55 @@ module.exports = {
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  EntangledNode,
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  ResonantFragment,
168
246
 
247
+ // Constants
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+ DELTA_S,
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+
250
+ // Golden Ratio Resonance (symprime symbolic AI)
251
+ PHI,
252
+ PHI_THRESHOLD,
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+ PHI_BONUS,
254
+ ResonanceCalculator,
255
+ resonanceSignature,
256
+ findFibonacciSequences,
257
+ calculateResonance,
258
+ findGoldenPairs,
259
+ findMostResonant,
260
+
261
+ // Symbol Database (symprime symbolic AI)
262
+ SymbolDatabase,
263
+ SymbolCategory,
264
+ PrimeGenerator,
265
+ symbolDatabase,
266
+ getSymbol,
267
+ getSymbolByPrime,
268
+ searchSymbols,
269
+ encodeSymbols,
270
+ decodeSymbols,
271
+
272
+ // Semantic Inference (symprime symbolic AI)
273
+ SemanticInference,
274
+ EntityExtractor,
275
+ InferenceMethod,
276
+ semanticInference,
277
+ entityExtractor,
278
+ inferSymbol,
279
+ inferSymbols,
280
+ extractEntities,
281
+ extractAndInfer,
282
+ inferWithResonance,
283
+ inferMostResonant,
284
+
285
+ // Compound Builder (symprime symbolic AI)
286
+ CompoundBuilder,
287
+ CompoundSymbol,
288
+ SymbolSequence,
289
+ compoundBuilder,
290
+ createCompound,
291
+ getCompound,
292
+ createSequence,
293
+ getSequence,
294
+ findCompoundsContaining,
295
+
169
296
  // ResoFormer ML Primitives
170
297
  Quaternion,
171
298
  SparsePrimeState,
@@ -257,5 +384,57 @@ module.exports = {
257
384
  TypeDirectedTranslator,
258
385
  LambdaEvaluator,
259
386
  Semantics,
260
- ConceptInterpreter
387
+ ConceptInterpreter,
388
+
389
+ // Enochian Packet Layer (Section 7.4 - twist-based validation)
390
+ enochian,
391
+ enochianVocabulary,
392
+ ENOCHIAN_PRIMES: enochian.ENOCHIAN_PRIMES,
393
+ ENOCHIAN_MODES: enochian.MODES,
394
+ twistAngle: enochian.twistAngle,
395
+ totalTwist: enochian.totalTwist,
396
+ isTwistClosed: enochian.isTwistClosed,
397
+ findClosedSequences: enochian.findClosedSequences,
398
+ EnochianSymbol: enochian.EnochianSymbol,
399
+ EnochianPacket: enochian.EnochianPacket,
400
+ EnochianEncoder: enochian.EnochianEncoder,
401
+ EnochianDecoder: enochian.EnochianDecoder,
402
+ EnochianPacketBuilder: enochian.EnochianPacketBuilder,
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+ EnhancedEnochianEncoder: enochian.EnhancedEnochianEncoder,
404
+ EnhancedEnochianDecoder: enochian.EnhancedEnochianDecoder,
405
+ // Enochian Vocabulary
406
+ ENOCHIAN_ALPHABET: enochianVocabulary.ENOCHIAN_ALPHABET,
407
+ PRIME_BASIS: enochianVocabulary.PRIME_BASIS,
408
+ CORE_VOCABULARY: enochianVocabulary.CORE_VOCABULARY,
409
+ THE_NINETEEN_CALLS: enochianVocabulary.THE_NINETEEN_CALLS,
410
+ EnochianWord: enochianVocabulary.EnochianWord,
411
+ EnochianCall: enochianVocabulary.EnochianCall,
412
+ EnochianEngine: enochianVocabulary.EnochianEngine,
413
+ SedenionElement: enochianVocabulary.SedenionElement,
414
+ TwistOperator: enochianVocabulary.TwistOperator,
415
+ validateTwistClosure: enochianVocabulary.validateTwistClosure,
416
+
417
+ // CRT-Homology Module (Coprime Modular Algebra + Birkhoff Polytope + Homology Loss)
418
+ extendedGCD,
419
+ modInverse,
420
+ areCoprime,
421
+ softmax,
422
+ ResidueEncoder,
423
+ CRTReconstructor,
424
+ BirkhoffProjector,
425
+ HomologyLoss,
426
+ CRTModularLayer,
427
+ CRTFusedAttention,
428
+ CoprimeSelector,
429
+ createCRTLayer,
430
+ createFusedAttention,
431
+ DEFAULT_PRIMES_SMALL,
432
+ DEFAULT_PRIMES_MEDIUM,
433
+ DEFAULT_PRIMES_SEMANTIC,
434
+
435
+ // CRT-enhanced ResoFormer (Birkhoff attention + Homology regularization)
436
+ CRTResonantAttention,
437
+ HomologyRegularizedBlock,
438
+ CRTResoFormer,
439
+ createCRTResoFormer
261
440
  };