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- atlas_affinity_cache_min/1ab1_A/meta.json +41 -0
- atlas_affinity_cache_min/1ab1_A/q.npy +3 -0
- atlas_affinity_cache_min/1ab1_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1ab1_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1b2s_F/q.npy +3 -0
- atlas_affinity_cache_min/1b2s_F/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1b2s_F/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1by2_A/q.npy +3 -0
- atlas_affinity_cache_min/1by2_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1by2_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1c96_A/q.npy +3 -0
- atlas_affinity_cache_min/1c96_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1c96_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1chd_A/meta.json +41 -0
- atlas_affinity_cache_min/1chd_A/q.npy +3 -0
- atlas_affinity_cache_min/1chd_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1chd_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1d3y_B/q.npy +3 -0
- atlas_affinity_cache_min/1d3y_B/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1d3y_B/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dj0_B/q.npy +3 -0
- atlas_affinity_cache_min/1dj0_B/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dj0_B/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dk8_A/meta.json +41 -0
- atlas_affinity_cache_min/1dk8_A/q.npy +3 -0
- atlas_affinity_cache_min/1dk8_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dk8_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dwk_A/q.npy +3 -0
- atlas_affinity_cache_min/1dwk_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dwk_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dzf_A/meta.json +41 -0
- atlas_affinity_cache_min/1dzf_A/q.npy +3 -0
- atlas_affinity_cache_min/1dzf_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dzf_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1fk5_A/meta.json +41 -0
- atlas_affinity_cache_min/1fk5_A/q.npy +3 -0
- atlas_affinity_cache_min/1fk5_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1fk5_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1gwe_A/q.npy +3 -0
- atlas_affinity_cache_min/1gwe_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1gwe_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1hbn_E/meta.json +41 -0
- atlas_affinity_cache_min/1hbn_E/q.npy +3 -0
- atlas_affinity_cache_min/1hbn_E/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1hbn_E/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1hc9_B/q.npy +3 -0
- atlas_affinity_cache_min/1hc9_B/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1hc9_B/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1huf_A/meta.json +41 -0
- atlas_affinity_cache_min/1huf_A/q.npy +3 -0
atlas_affinity_cache_min/1ab1_A/meta.json
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{
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"entry": "1ab1_A",
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"n_frames": 3003,
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"n_ca": 46,
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"n_replicates": 3,
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"rep_names": [
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"R1",
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"R2",
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"R3"
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],
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"traj_lengths": [
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1001,
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1001,
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1001
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],
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"xtc_files": [
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"1ab1_A_R1.xtc",
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"1ab1_A_R2.xtc",
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"1ab1_A_R3.xtc"
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],
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"pca_dim": 50,
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"tica_dim": 3,
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"tica_evals": [
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0.8528020977973938,
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],
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"lag": 10,
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"sigma_k": 30,
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"top_k": 64,
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"contact_cutoff_A": 12.0,
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"min_seq_sep": 3,
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"max_pairs": 20000,
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"n_ca_pairs_used": 390,
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| 35 |
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"feature": "CA_pairwise_distances",
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| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
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| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
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| 38 |
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"dtype_q": "float32",
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"dtype_topk_neighbors": "uint16",
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"dtype_topk_weights": "float16"
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}
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atlas_affinity_cache_min/1ab1_A/q.npy
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atlas_affinity_cache_min/1ab1_A/topk_neighbors.npy
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atlas_affinity_cache_min/1ab1_A/topk_weights.npy
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atlas_affinity_cache_min/1b2s_F/q.npy
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atlas_affinity_cache_min/1b2s_F/topk_neighbors.npy
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atlas_affinity_cache_min/1b2s_F/topk_weights.npy
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atlas_affinity_cache_min/1by2_A/q.npy
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atlas_affinity_cache_min/1by2_A/topk_neighbors.npy
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atlas_affinity_cache_min/1by2_A/topk_weights.npy
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atlas_affinity_cache_min/1c96_A/q.npy
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atlas_affinity_cache_min/1c96_A/topk_neighbors.npy
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atlas_affinity_cache_min/1c96_A/topk_weights.npy
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atlas_affinity_cache_min/1chd_A/meta.json
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{
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"entry": "1chd_A",
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| 3 |
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"n_frames": 3003,
|
| 4 |
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"n_ca": 203,
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| 5 |
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"n_replicates": 3,
|
| 6 |
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"rep_names": [
|
| 7 |
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"R1",
|
| 8 |
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"R2",
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| 9 |
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"R3"
|
| 10 |
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],
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| 11 |
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"traj_lengths": [
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| 12 |
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1001,
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1001,
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| 14 |
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1001
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],
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"xtc_files": [
|
| 17 |
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"1chd_A_R1.xtc",
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| 18 |
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"1chd_A_R2.xtc",
|
| 19 |
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"1chd_A_R3.xtc"
|
| 20 |
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],
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| 21 |
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"pca_dim": 50,
|
| 22 |
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"tica_dim": 3,
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| 23 |
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"tica_evals": [
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"lag": 10,
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| 29 |
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"sigma_k": 30,
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| 30 |
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"top_k": 64,
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| 31 |
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"contact_cutoff_A": 12.0,
|
| 32 |
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"min_seq_sep": 3,
|
| 33 |
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"max_pairs": 20000,
|
| 34 |
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"n_ca_pairs_used": 2829,
|
| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
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"dtype_q": "float32",
|
| 39 |
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"dtype_topk_neighbors": "uint16",
|
| 40 |
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"dtype_topk_weights": "float16"
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| 41 |
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}
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atlas_affinity_cache_min/1chd_A/q.npy
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atlas_affinity_cache_min/1chd_A/topk_neighbors.npy
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atlas_affinity_cache_min/1chd_A/topk_weights.npy
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atlas_affinity_cache_min/1d3y_B/q.npy
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atlas_affinity_cache_min/1d3y_B/topk_neighbors.npy
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atlas_affinity_cache_min/1d3y_B/topk_weights.npy
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atlas_affinity_cache_min/1dj0_B/q.npy
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atlas_affinity_cache_min/1dj0_B/topk_neighbors.npy
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atlas_affinity_cache_min/1dj0_B/topk_weights.npy
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atlas_affinity_cache_min/1dk8_A/meta.json
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|
|
|
|
|
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|
|
|
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|
|
|
|
|
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|
|
|
|
|
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|
| 1 |
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{
|
| 2 |
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|
| 3 |
+
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|
| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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"R1",
|
| 8 |
+
"R2",
|
| 9 |
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"R3"
|
| 10 |
+
],
|
| 11 |
+
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|
| 12 |
+
1001,
|
| 13 |
+
1001,
|
| 14 |
+
1001
|
| 15 |
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],
|
| 16 |
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|
| 17 |
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"1dk8_A_R1.xtc",
|
| 18 |
+
"1dk8_A_R2.xtc",
|
| 19 |
+
"1dk8_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
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|
| 22 |
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| 23 |
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| 26 |
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| 28 |
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|
| 29 |
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"sigma_k": 30,
|
| 30 |
+
"top_k": 64,
|
| 31 |
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"contact_cutoff_A": 12.0,
|
| 32 |
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"min_seq_sep": 3,
|
| 33 |
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"max_pairs": 20000,
|
| 34 |
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"n_ca_pairs_used": 1435,
|
| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
+
"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
+
"dtype_q": "float32",
|
| 39 |
+
"dtype_topk_neighbors": "uint16",
|
| 40 |
+
"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1dk8_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 3 |
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size 36164
|
atlas_affinity_cache_min/1dk8_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1dk8_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1dwk_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 36164
|
atlas_affinity_cache_min/1dwk_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1dwk_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 384512
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atlas_affinity_cache_min/1dzf_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1dzf_A",
|
| 3 |
+
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|
| 4 |
+
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|
| 5 |
+
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|
| 6 |
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|
| 7 |
+
"R1",
|
| 8 |
+
"R2",
|
| 9 |
+
"R3"
|
| 10 |
+
],
|
| 11 |
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"traj_lengths": [
|
| 12 |
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1001,
|
| 13 |
+
1001,
|
| 14 |
+
1001
|
| 15 |
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],
|
| 16 |
+
"xtc_files": [
|
| 17 |
+
"1dzf_A_R1.xtc",
|
| 18 |
+
"1dzf_A_R2.xtc",
|
| 19 |
+
"1dzf_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
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"tica_evals": [
|
| 24 |
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|
| 25 |
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|
| 26 |
+
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|
| 27 |
+
],
|
| 28 |
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"lag": 10,
|
| 29 |
+
"sigma_k": 30,
|
| 30 |
+
"top_k": 64,
|
| 31 |
+
"contact_cutoff_A": 12.0,
|
| 32 |
+
"min_seq_sep": 3,
|
| 33 |
+
"max_pairs": 20000,
|
| 34 |
+
"n_ca_pairs_used": 2215,
|
| 35 |
+
"feature": "CA_pairwise_distances",
|
| 36 |
+
"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
+
"dtype_q": "float32",
|
| 39 |
+
"dtype_topk_neighbors": "uint16",
|
| 40 |
+
"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1dzf_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
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version https://git-lfs.github.com/spec/v1
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| 3 |
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size 36164
|
atlas_affinity_cache_min/1dzf_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1dzf_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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size 384512
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atlas_affinity_cache_min/1fk5_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
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|
| 1 |
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{
|
| 2 |
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"entry": "1fk5_A",
|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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| 7 |
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"R1",
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| 8 |
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"R2",
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| 9 |
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"R3"
|
| 10 |
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],
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| 11 |
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| 12 |
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1001,
|
| 13 |
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1001,
|
| 14 |
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1001
|
| 15 |
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],
|
| 16 |
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"xtc_files": [
|
| 17 |
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"1fk5_A_R1.xtc",
|
| 18 |
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"1fk5_A_R2.xtc",
|
| 19 |
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"1fk5_A_R3.xtc"
|
| 20 |
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],
|
| 21 |
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|
| 22 |
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|
| 23 |
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| 24 |
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|
| 25 |
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| 28 |
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|
| 29 |
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|
| 30 |
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"top_k": 64,
|
| 31 |
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"contact_cutoff_A": 12.0,
|
| 32 |
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"min_seq_sep": 3,
|
| 33 |
+
"max_pairs": 20000,
|
| 34 |
+
"n_ca_pairs_used": 981,
|
| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
+
"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
+
"dtype_q": "float32",
|
| 39 |
+
"dtype_topk_neighbors": "uint16",
|
| 40 |
+
"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1fk5_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 36164
|
atlas_affinity_cache_min/1fk5_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1fk5_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
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|
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|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1gwe_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
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|
|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 36164
|
atlas_affinity_cache_min/1gwe_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1gwe_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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version https://git-lfs.github.com/spec/v1
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size 384512
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atlas_affinity_cache_min/1hbn_E/meta.json
ADDED
|
@@ -0,0 +1,41 @@
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1hbn_E",
|
| 3 |
+
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|
| 4 |
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|
| 5 |
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|
| 6 |
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"rep_names": [
|
| 7 |
+
"R1",
|
| 8 |
+
"R2",
|
| 9 |
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"R3"
|
| 10 |
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],
|
| 11 |
+
"traj_lengths": [
|
| 12 |
+
1001,
|
| 13 |
+
1001,
|
| 14 |
+
1001
|
| 15 |
+
],
|
| 16 |
+
"xtc_files": [
|
| 17 |
+
"1hbn_E_R1.xtc",
|
| 18 |
+
"1hbn_E_R2.xtc",
|
| 19 |
+
"1hbn_E_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
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|
| 24 |
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|
| 25 |
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|
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| 27 |
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],
|
| 28 |
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"lag": 10,
|
| 29 |
+
"sigma_k": 30,
|
| 30 |
+
"top_k": 64,
|
| 31 |
+
"contact_cutoff_A": 12.0,
|
| 32 |
+
"min_seq_sep": 3,
|
| 33 |
+
"max_pairs": 20000,
|
| 34 |
+
"n_ca_pairs_used": 6324,
|
| 35 |
+
"feature": "CA_pairwise_distances",
|
| 36 |
+
"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
+
"dtype_q": "float32",
|
| 39 |
+
"dtype_topk_neighbors": "uint16",
|
| 40 |
+
"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1hbn_E/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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| 3 |
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size 36164
|
atlas_affinity_cache_min/1hbn_E/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1hbn_E/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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size 384512
|
atlas_affinity_cache_min/1hc9_B/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
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|
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|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:982f0de784c48b676da03cbf59d6ce3b0912f82cba819b4088001a3115a7c3a5
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1hc9_B/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:1734aab8dd37a6878bda3be92754515f94c49d08c454b11ef3f89b1b70d9a6ff
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1hc9_B/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:25e22c23101adad0ae8f333319e7d70bee8ca2d14b79b6caa167405dfb7f0279
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1huf_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1huf_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 140,
|
| 5 |
+
"n_replicates": 3,
|
| 6 |
+
"rep_names": [
|
| 7 |
+
"R1",
|
| 8 |
+
"R2",
|
| 9 |
+
"R3"
|
| 10 |
+
],
|
| 11 |
+
"traj_lengths": [
|
| 12 |
+
1001,
|
| 13 |
+
1001,
|
| 14 |
+
1001
|
| 15 |
+
],
|
| 16 |
+
"xtc_files": [
|
| 17 |
+
"1huf_A_R1.xtc",
|
| 18 |
+
"1huf_A_R2.xtc",
|
| 19 |
+
"1huf_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.8830632567405701,
|
| 25 |
+
0.8447571396827698,
|
| 26 |
+
0.7588571310043335
|
| 27 |
+
],
|
| 28 |
+
"lag": 10,
|
| 29 |
+
"sigma_k": 30,
|
| 30 |
+
"top_k": 64,
|
| 31 |
+
"contact_cutoff_A": 12.0,
|
| 32 |
+
"min_seq_sep": 3,
|
| 33 |
+
"max_pairs": 20000,
|
| 34 |
+
"n_ca_pairs_used": 1512,
|
| 35 |
+
"feature": "CA_pairwise_distances",
|
| 36 |
+
"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
+
"dtype_q": "float32",
|
| 39 |
+
"dtype_topk_neighbors": "uint16",
|
| 40 |
+
"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1huf_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:1d034210cb72dd97ec783a8b52c341bb611f6ad9e122aa026786f90c6cca09b0
|
| 3 |
+
size 36164
|