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  1. atlas_affinity_cache_min/16pk_A/meta.json +41 -0
  2. atlas_affinity_cache_min/1ah7_A/meta.json +41 -0
  3. atlas_affinity_cache_min/1b2s_E/meta.json +41 -0
  4. atlas_affinity_cache_min/1bkp_A/meta.json +41 -0
  5. atlas_affinity_cache_min/1btk_A/meta.json +41 -0
  6. atlas_affinity_cache_min/1bx7_A/q.npy +3 -0
  7. atlas_affinity_cache_min/1bx7_A/topk_neighbors.npy +3 -0
  8. atlas_affinity_cache_min/1bx7_A/topk_weights.npy +3 -0
  9. atlas_affinity_cache_min/1bxy_A/meta.json +41 -0
  10. atlas_affinity_cache_min/1cuo_A/q.npy +3 -0
  11. atlas_affinity_cache_min/1cuo_A/topk_neighbors.npy +3 -0
  12. atlas_affinity_cache_min/1cuo_A/topk_weights.npy +3 -0
  13. atlas_affinity_cache_min/1d2t_A/q.npy +3 -0
  14. atlas_affinity_cache_min/1d2t_A/topk_neighbors.npy +3 -0
  15. atlas_affinity_cache_min/1d2t_A/topk_weights.npy +3 -0
  16. atlas_affinity_cache_min/1doi_A/q.npy +3 -0
  17. atlas_affinity_cache_min/1doi_A/topk_neighbors.npy +3 -0
  18. atlas_affinity_cache_min/1doi_A/topk_weights.npy +3 -0
  19. atlas_affinity_cache_min/1dpt_A/meta.json +41 -0
  20. atlas_affinity_cache_min/1ear_A/q.npy +3 -0
  21. atlas_affinity_cache_min/1ear_A/topk_neighbors.npy +3 -0
  22. atlas_affinity_cache_min/1ear_A/topk_weights.npy +3 -0
  23. atlas_affinity_cache_min/1ef1_D/meta.json +41 -0
  24. atlas_affinity_cache_min/1ez3_B/meta.json +41 -0
  25. atlas_affinity_cache_min/1f20_A/q.npy +3 -0
  26. atlas_affinity_cache_min/1f20_A/topk_neighbors.npy +3 -0
  27. atlas_affinity_cache_min/1f20_A/topk_weights.npy +3 -0
  28. atlas_affinity_cache_min/1f3u_G/q.npy +3 -0
  29. atlas_affinity_cache_min/1f3u_G/topk_neighbors.npy +3 -0
  30. atlas_affinity_cache_min/1f3u_G/topk_weights.npy +3 -0
  31. atlas_affinity_cache_min/1f9p_A/meta.json +41 -0
  32. atlas_affinity_cache_min/1fm4_A/meta.json +41 -0
  33. atlas_affinity_cache_min/1fn9_A/q.npy +3 -0
  34. atlas_affinity_cache_min/1fn9_A/topk_neighbors.npy +3 -0
  35. atlas_affinity_cache_min/1fn9_A/topk_weights.npy +3 -0
  36. atlas_affinity_cache_min/1fs1_A/meta.json +41 -0
  37. atlas_affinity_cache_min/1fx4_A/meta.json +41 -0
  38. atlas_affinity_cache_min/1fxo_G/meta.json +41 -0
  39. atlas_affinity_cache_min/1g38_A/q.npy +3 -0
  40. atlas_affinity_cache_min/1g38_A/topk_neighbors.npy +3 -0
  41. atlas_affinity_cache_min/1g38_A/topk_weights.npy +3 -0
  42. atlas_affinity_cache_min/1g6g_A/q.npy +3 -0
  43. atlas_affinity_cache_min/1g6g_A/topk_neighbors.npy +3 -0
  44. atlas_affinity_cache_min/1g6g_A/topk_weights.npy +3 -0
  45. atlas_affinity_cache_min/1g7s_A/q.npy +3 -0
  46. atlas_affinity_cache_min/1g7s_A/topk_neighbors.npy +3 -0
  47. atlas_affinity_cache_min/1g7s_A/topk_weights.npy +3 -0
  48. atlas_affinity_cache_min/1gqe_A/meta.json +41 -0
  49. atlas_affinity_cache_min/1gqv_A/q.npy +3 -0
  50. atlas_affinity_cache_min/1gqv_A/topk_neighbors.npy +3 -0
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