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  1. atlas_affinity_cache_min/1aol_A/q.npy +3 -0
  2. atlas_affinity_cache_min/1aol_A/topk_neighbors.npy +3 -0
  3. atlas_affinity_cache_min/1aol_A/topk_weights.npy +3 -0
  4. atlas_affinity_cache_min/1b25_D/meta.json +41 -0
  5. atlas_affinity_cache_min/1b2s_E/q.npy +3 -0
  6. atlas_affinity_cache_min/1b2s_E/topk_neighbors.npy +3 -0
  7. atlas_affinity_cache_min/1b2s_E/topk_weights.npy +3 -0
  8. atlas_affinity_cache_min/1b2s_F/meta.json +41 -0
  9. atlas_affinity_cache_min/1bgf_A/q.npy +3 -0
  10. atlas_affinity_cache_min/1bgf_A/topk_neighbors.npy +3 -0
  11. atlas_affinity_cache_min/1bgf_A/topk_weights.npy +3 -0
  12. atlas_affinity_cache_min/1bxy_A/q.npy +3 -0
  13. atlas_affinity_cache_min/1bxy_A/topk_neighbors.npy +3 -0
  14. atlas_affinity_cache_min/1bxy_A/topk_weights.npy +3 -0
  15. atlas_affinity_cache_min/1by2_A/meta.json +41 -0
  16. atlas_affinity_cache_min/1dci_C/q.npy +3 -0
  17. atlas_affinity_cache_min/1dci_C/topk_neighbors.npy +3 -0
  18. atlas_affinity_cache_min/1dci_C/topk_weights.npy +3 -0
  19. atlas_affinity_cache_min/1dfu_P/q.npy +3 -0
  20. atlas_affinity_cache_min/1dfu_P/topk_neighbors.npy +3 -0
  21. atlas_affinity_cache_min/1dfu_P/topk_weights.npy +3 -0
  22. atlas_affinity_cache_min/1dlj_A/q.npy +3 -0
  23. atlas_affinity_cache_min/1dlj_A/topk_neighbors.npy +3 -0
  24. atlas_affinity_cache_min/1dlj_A/topk_weights.npy +3 -0
  25. atlas_affinity_cache_min/1dpt_A/q.npy +3 -0
  26. atlas_affinity_cache_min/1dpt_A/topk_neighbors.npy +3 -0
  27. atlas_affinity_cache_min/1dpt_A/topk_weights.npy +3 -0
  28. atlas_affinity_cache_min/1dtd_B/q.npy +3 -0
  29. atlas_affinity_cache_min/1dtd_B/topk_neighbors.npy +3 -0
  30. atlas_affinity_cache_min/1dtd_B/topk_weights.npy +3 -0
  31. atlas_affinity_cache_min/1egw_B/meta.json +41 -0
  32. atlas_affinity_cache_min/1ez3_B/q.npy +3 -0
  33. atlas_affinity_cache_min/1ez3_B/topk_neighbors.npy +3 -0
  34. atlas_affinity_cache_min/1ez3_B/topk_weights.npy +3 -0
  35. atlas_affinity_cache_min/1fd3_A/meta.json +41 -0
  36. atlas_affinity_cache_min/1fm4_A/q.npy +3 -0
  37. atlas_affinity_cache_min/1fm4_A/topk_neighbors.npy +3 -0
  38. atlas_affinity_cache_min/1fm4_A/topk_weights.npy +3 -0
  39. atlas_affinity_cache_min/1g2r_A/q.npy +3 -0
  40. atlas_affinity_cache_min/1g2r_A/topk_neighbors.npy +3 -0
  41. atlas_affinity_cache_min/1g2r_A/topk_weights.npy +3 -0
  42. atlas_affinity_cache_min/1gnt_A/q.npy +3 -0
  43. atlas_affinity_cache_min/1gnt_A/topk_neighbors.npy +3 -0
  44. atlas_affinity_cache_min/1gnt_A/topk_weights.npy +3 -0
  45. atlas_affinity_cache_min/1gwe_A/meta.json +41 -0
  46. atlas_affinity_cache_min/1h16_A/q.npy +3 -0
  47. atlas_affinity_cache_min/1h16_A/topk_neighbors.npy +3 -0
  48. atlas_affinity_cache_min/1h16_A/topk_weights.npy +3 -0
  49. atlas_affinity_cache_min/1hc9_B/meta.json +41 -0
  50. atlas_affinity_cache_min/1hp1_A/q.npy +3 -0
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