Hugging Face's logo

kundajelab
/
encode-chrombpnet-DNASE-ENCSR945KSP-ENCSR211GRM

chrombpnet
encode
chromatin-accessibility
DNASE
epicardium
hg38
Model card Files
xet
 Community
chang-m-yun commited on
Commit
509cf0d
·
verified ·
1 Parent(s): 691b5d3

Add files using upload-large-folder tool

Browse files
This view is limited to 50 files because it contains too many changes.   See raw diff
Files changed (50) hide show
  1. .gitattributes +2 -0
  2. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.args.json +23 -0
  3. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.batch_loss.tsv +0 -0
  4. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.bias_formatting.stderr.txt +38 -0
  5. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.bias_formatting.stdout.txt +1 -0
  6. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet.params.json +11 -0
  7. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet_formatting.stdout.txt +1 -0
  8. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet_model_params.tsv +9 -0
  9. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet_no_bias_formatting.stderr.txt +1 -0
  10. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.epoch_loss.csv +14 -0
  11. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.stdout.txt +0 -0
  12. fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.stdout_v1.txt +0 -0
  13. fold_0/model.bias_scaled.fold_0.ENCSR945KSP.h5 +3 -0
  14. fold_0/model.bias_scaled.fold_0.ENCSR945KSP.tar +3 -0
  15. fold_0/model.chrombpnet.fold_0.ENCSR945KSP.h5 +3 -0
  16. fold_0/model.chrombpnet.fold_0.ENCSR945KSP.tar +3 -0
  17. fold_0/model.chrombpnet_nobias.fold_0.ENCSR945KSP.h5 +3 -0
  18. fold_0/model.chrombpnet_nobias.fold_0.ENCSR945KSP.tar +3 -0
  19. fold_1/model.bias_scaled.fold_1.ENCSR945KSP.h5 +3 -0
  20. fold_1/model.bias_scaled.fold_1.ENCSR945KSP.tar +3 -0
  21. fold_1/model.chrombpnet.fold_1.ENCSR945KSP.h5 +3 -0
  22. fold_1/model.chrombpnet.fold_1.ENCSR945KSP.tar +3 -0
  23. fold_1/model.chrombpnet_nobias.fold_1.ENCSR945KSP.h5 +3 -0
  24. fold_1/model.chrombpnet_nobias.fold_1.ENCSR945KSP.tar +3 -0
  25. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.args.json +23 -0
  26. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.batch_loss.tsv +0 -0
  27. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.bias_formatting.stderr.txt +38 -0
  28. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.bias_formatting.stdout.txt +1 -0
  29. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet.params.json +11 -0
  30. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_data_params.tsv +3 -0
  31. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_formatting.stderr.txt +40 -0
  32. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_formatting.stdout.txt +1 -0
  33. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_model_params.tsv +9 -0
  34. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_no_bias_formatting.stderr.txt +1 -0
  35. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_no_bias_formatting.stdout.txt +1 -0
  36. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.epoch_loss.csv +16 -0
  37. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stderr.txt +0 -0
  38. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stdout.txt +3 -0
  39. fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stdout_v1.txt +3 -0
  40. fold_2/model.bias_scaled.fold_2.ENCSR945KSP.h5 +3 -0
  41. fold_2/model.bias_scaled.fold_2.ENCSR945KSP.tar +3 -0
  42. fold_2/model.chrombpnet.fold_2.ENCSR945KSP.h5 +3 -0
  43. fold_2/model.chrombpnet.fold_2.ENCSR945KSP.tar +3 -0
  44. fold_2/model.chrombpnet_nobias.fold_2.ENCSR945KSP.h5 +3 -0
  45. fold_2/model.chrombpnet_nobias.fold_2.ENCSR945KSP.tar +3 -0
  46. fold_3/model.bias_scaled.fold_3.ENCSR945KSP.h5 +3 -0
  47. fold_3/model.bias_scaled.fold_3.ENCSR945KSP.tar +3 -0
  48. fold_3/model.chrombpnet.fold_3.ENCSR945KSP.h5 +3 -0
  49. fold_3/model.chrombpnet.fold_3.ENCSR945KSP.tar +3 -0
  50. fold_3/model.chrombpnet_nobias.fold_3.ENCSR945KSP.h5 +3 -0
.gitattributes CHANGED
@@ -33,3 +33,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
33
  *.zip filter=lfs diff=lfs merge=lfs -text
34
  *.zst filter=lfs diff=lfs merge=lfs -text
35
  *tfevents* filter=lfs diff=lfs merge=lfs -text
 
 
 
33
  *.zip filter=lfs diff=lfs merge=lfs -text
34
  *.zst filter=lfs diff=lfs merge=lfs -text
35
  *tfevents* filter=lfs diff=lfs merge=lfs -text
36
+ fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stdout.txt filter=lfs diff=lfs merge=lfs -text
37
+ fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.args.json ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
3
+ "bigwig": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//preprocessing/bigWigs/ENCSR945KSP.bigWig",
4
+ "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias//filtered.peaks.bed",
5
+ "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias//filtered.nonpeaks.bed",
6
+ "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias//chrombpnet",
7
+ "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json",
8
+ "trackables": [
9
+ "logcount_predictions_loss",
10
+ "loss",
11
+ "logits_profile_predictions_loss",
12
+ "val_logcount_predictions_loss",
13
+ "val_loss",
14
+ "val_logits_profile_predictions_loss"
15
+ ],
16
+ "epochs": 50,
17
+ "early_stop": 5,
18
+ "batch_size": 64,
19
+ "learning_rate": 0.001,
20
+ "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias//chrombpnet_model_params.tsv",
21
+ "seed": 1234,
22
+ "architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
23
+ }
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.batch_loss.tsv ADDED
The diff for this file is too large to render. See raw diff
 
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.bias_formatting.stderr.txt ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
2
+ INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
3
+ 2023-08-18 17:15:56.575397: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-08-18 17:15:58.931397: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
5
+ 2023-08-18 17:15:58.935222: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
6
+ 2023-08-18 17:16:00.059175: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:c0:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
8
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
9
+ 2023-08-18 17:16:00.059263: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
+ 2023-08-18 17:16:00.080619: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
11
+ 2023-08-18 17:16:00.080671: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
12
+ 2023-08-18 17:16:00.091393: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
13
+ 2023-08-18 17:16:00.096384: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
14
+ 2023-08-18 17:16:00.114254: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
15
+ 2023-08-18 17:16:00.118955: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
16
+ 2023-08-18 17:16:00.119976: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
17
+ 2023-08-18 17:16:00.153369: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
18
+ 2023-08-18 17:16:00.153846: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
19
+ To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
20
+ 2023-08-18 17:16:00.155391: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-08-18 17:16:00.179045: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
22
+ pciBusID: 0000:c0:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
23
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
24
+ 2023-08-18 17:16:00.179093: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
+ 2023-08-18 17:16:00.179125: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
26
+ 2023-08-18 17:16:00.179147: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
27
+ 2023-08-18 17:16:00.179168: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
28
+ 2023-08-18 17:16:00.179187: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
29
+ 2023-08-18 17:16:00.179206: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
30
+ 2023-08-18 17:16:00.179225: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
31
+ 2023-08-18 17:16:00.179244: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
32
+ 2023-08-18 17:16:00.219774: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
33
+ 2023-08-18 17:16:00.222188: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
34
+ 2023-08-18 17:16:02.938099: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
+ 2023-08-18 17:16:02.938230: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
36
+ 2023-08-18 17:16:02.938244: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
37
+ 2023-08-18 17:16:02.945029: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 75650 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-80GB, pci bus id: 0000:c0:00.0, compute capability: 8.0)
38
+ 2023-08-18 17:16:04.340323: W tensorflow/python/util/util.cc:348] Sets are not currently considered sequences, but this may change in the future, so consider avoiding using them.
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.bias_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/new_model_formats/bias_model_scaled
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet.params.json ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "counts_loss_weight": "9.5",
3
+ "filters": "512",
4
+ "n_dil_layers": "8",
5
+ "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/bias_model_scaled.h5",
6
+ "inputlen": "2114",
7
+ "outputlen": "1000",
8
+ "max_jitter": "500",
9
+ "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json",
10
+ "negative_sampling_ratio": "0.1"
11
+ }
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/new_model_formats/chrombpnet
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet_model_params.tsv ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ counts_loss_weight 9.5
2
+ filters 512
3
+ n_dil_layers 8
4
+ bias_model_path /scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/bias_model_scaled.h5
5
+ inputlen 2114
6
+ outputlen 1000
7
+ max_jitter 500
8
+ chr_fold_path /scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json
9
+ negative_sampling_ratio 0.1
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.chrombpnet_no_bias_formatting.stderr.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias/new_model_formats/chrombpnet_wo_bias
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.epoch_loss.csv ADDED
@@ -0,0 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ epoch,logcount_predictions_loss,logits_profile_predictions_loss,loss,val_logcount_predictions_loss,val_logits_profile_predictions_loss,val_loss
2
+ 0,0.7604690194129944,381.10858154296875,388.33306884765625,0.1926606446504593,375.6330261230469,377.46337890625
3
+ 1,0.22481995820999146,372.70098876953125,374.83636474609375,0.1625724583864212,372.4829406738281,374.0273132324219
4
+ 2,0.20141029357910156,370.2423400878906,372.156005859375,0.15302243828773499,371.2597961425781,372.71331787109375
5
+ 3,0.18548238277435303,369.3049621582031,371.06695556640625,0.1500202864408493,369.9160461425781,371.341064453125
6
+ 4,0.17869889736175537,368.083984375,369.7814025878906,0.14099164307117462,370.22393798828125,371.5632629394531
7
+ 5,0.1700761467218399,367.4091491699219,369.0253601074219,0.14301647245883942,371.82989501953125,373.1884460449219
8
+ 6,0.16361083090305328,366.791015625,368.3454895019531,0.1359490156173706,371.9958190917969,373.28741455078125
9
+ 7,0.15039576590061188,363.1390380859375,364.5679931640625,0.13744834065437317,369.6300964355469,370.9361877441406
10
+ 8,0.14544357359409332,361.6427917480469,363.0243225097656,0.13561660051345825,370.5085754394531,371.7966613769531
11
+ 9,0.1422058343887329,360.7020263671875,362.0531005859375,0.13617482781410217,369.8953857421875,371.1888732910156
12
+ 10,0.1410018652677536,358.6872863769531,360.027099609375,0.13161905109882355,370.9993591308594,372.2495422363281
13
+ 11,0.13611237704753876,356.4003601074219,357.6938171386719,0.13074778020381927,370.67254638671875,371.9145812988281
14
+ 12,0.13335390388965607,355.14862060546875,356.41552734375,0.12996405363082886,373.1700439453125,374.40460205078125
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.stdout.txt ADDED
The diff for this file is too large to render. See raw diff
 
fold_0/logs.models.fold_0.ENCSR945KSP/logfile.modelling.fold_0.ENCSR945KSP.stdout_v1.txt ADDED
The diff for this file is too large to render. See raw diff
 
fold_0/model.bias_scaled.fold_0.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d045686e06223aff3aa42bfb5567be779f0ba1cf3db21e00318806c5b8f08c1e
3
+ size 2688440
fold_0/model.bias_scaled.fold_0.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:936bf8533aa221d5c612a31774a5da6c34857c8f78292ee8280657bb4e6cf4eb
3
+ size 1198080
fold_0/model.chrombpnet.fold_0.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:230f528041b4b1011b522de465dc49c6c732fb78b0b8966aec324c7bde9d9adb
3
+ size 26447928
fold_0/model.chrombpnet.fold_0.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ef79d72bec2c337f7e2e9990782bef38f02b6d8edda035f6f166820c019c6389
3
+ size 27607040
fold_0/model.chrombpnet_nobias.fold_0.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ecf4768c401823f75fb4c80caff2174705c573085a72125ee29b6923d07c9879
3
+ size 25583536
fold_0/model.chrombpnet_nobias.fold_0.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b08d3fc744f5fb5fe69fbcb98d4bb87e2be9d83199841e582f84dc8c4e2e535c
3
+ size 26081280
fold_1/model.bias_scaled.fold_1.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:752e9f46f9c9d5174c943a2b5a3725698affed73bafac5500b0589d6091fc8c3
3
+ size 2688440
fold_1/model.bias_scaled.fold_1.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3580bfb7f76fe9aad26f952b8088424d8a5a85ed6dc16371176186dd50adadef
3
+ size 1198080
fold_1/model.chrombpnet.fold_1.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8484480ba0b9f99f5a47b7d2486bc4a9522351469f231556a7ed3595e27215bb
3
+ size 26447928
fold_1/model.chrombpnet.fold_1.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:178fb55d2f87fc320521994dda72a64907db23f5f13a150105f6faa9ec900b0e
3
+ size 27607040
fold_1/model.chrombpnet_nobias.fold_1.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:93949de6b1dd0f7caadd2e442f29a6f4bac6f33efad4cfd38958ba320ddcf56b
3
+ size 25583536
fold_1/model.chrombpnet_nobias.fold_1.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9373cddadb2df33817661d062bfafa988ca2eb79ce204cd122c9b759180e9af2
3
+ size 26081280
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.args.json ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
3
+ "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//preprocessing/bigWigs/ENCSR945KSP.bigWig",
4
+ "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2//filtered.peaks.bed",
5
+ "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2//filtered.nonpeaks.bed",
6
+ "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2//chrombpnet",
7
+ "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
8
+ "trackables": [
9
+ "logcount_predictions_loss",
10
+ "loss",
11
+ "logits_profile_predictions_loss",
12
+ "val_logcount_predictions_loss",
13
+ "val_loss",
14
+ "val_logits_profile_predictions_loss"
15
+ ],
16
+ "epochs": 50,
17
+ "early_stop": 5,
18
+ "batch_size": 64,
19
+ "learning_rate": 0.001,
20
+ "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2//chrombpnet_model_params.tsv",
21
+ "seed": 1234,
22
+ "architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
23
+ }
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.batch_loss.tsv ADDED
The diff for this file is too large to render. See raw diff
 
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.bias_formatting.stderr.txt ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
2
+ INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
3
+ 2023-08-18 17:15:56.489366: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-08-18 17:15:58.885440: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
5
+ 2023-08-18 17:15:58.889234: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
6
+ 2023-08-18 17:15:59.506652: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:4b:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
8
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
9
+ 2023-08-18 17:15:59.506781: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
+ 2023-08-18 17:15:59.530052: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
11
+ 2023-08-18 17:15:59.530174: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
12
+ 2023-08-18 17:15:59.540147: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
13
+ 2023-08-18 17:15:59.544924: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
14
+ 2023-08-18 17:15:59.562017: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
15
+ 2023-08-18 17:15:59.566457: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
16
+ 2023-08-18 17:15:59.567398: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
17
+ 2023-08-18 17:15:59.582214: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
18
+ 2023-08-18 17:15:59.582612: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
19
+ To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
20
+ 2023-08-18 17:15:59.583805: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-08-18 17:15:59.605875: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
22
+ pciBusID: 0000:4b:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
23
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
24
+ 2023-08-18 17:15:59.605907: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
+ 2023-08-18 17:15:59.605930: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
26
+ 2023-08-18 17:15:59.605945: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
27
+ 2023-08-18 17:15:59.605958: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
28
+ 2023-08-18 17:15:59.605971: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
29
+ 2023-08-18 17:15:59.605983: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
30
+ 2023-08-18 17:15:59.605995: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
31
+ 2023-08-18 17:15:59.606008: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
32
+ 2023-08-18 17:15:59.654073: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
33
+ 2023-08-18 17:15:59.655385: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
34
+ 2023-08-18 17:16:02.772340: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
+ 2023-08-18 17:16:02.772486: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
36
+ 2023-08-18 17:16:02.772501: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
37
+ 2023-08-18 17:16:02.779469: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 75650 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-80GB, pci bus id: 0000:4b:00.0, compute capability: 8.0)
38
+ 2023-08-18 17:16:04.123236: W tensorflow/python/util/util.cc:348] Sets are not currently considered sequences, but this may change in the future, so consider avoiding using them.
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.bias_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/new_model_formats/bias_model_scaled
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet.params.json ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "counts_loss_weight": "9.5",
3
+ "filters": "512",
4
+ "n_dil_layers": "8",
5
+ "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/bias_model_scaled.h5",
6
+ "inputlen": "2114",
7
+ "outputlen": "1000",
8
+ "max_jitter": "500",
9
+ "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
10
+ "negative_sampling_ratio": "0.1"
11
+ }
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_data_params.tsv ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ counts_sum_min_thresh 12.0
2
+ counts_sum_max_thresh 1388.78
3
+ trainings_pts_post_thresh 177218
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_formatting.stderr.txt ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
2
+ INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
3
+ 2023-08-18 17:09:26.833345: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-08-18 17:09:30.352300: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
5
+ 2023-08-18 17:09:30.358373: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
6
+ 2023-08-18 17:09:30.383197: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
8
+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
9
+ 2023-08-18 17:09:30.383305: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
+ 2023-08-18 17:09:30.414841: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
11
+ 2023-08-18 17:09:30.414992: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
12
+ 2023-08-18 17:09:30.431734: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
13
+ 2023-08-18 17:09:30.440104: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
14
+ 2023-08-18 17:09:30.466478: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
15
+ 2023-08-18 17:09:30.473323: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
16
+ 2023-08-18 17:09:30.474835: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
17
+ 2023-08-18 17:09:30.477147: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
18
+ 2023-08-18 17:09:30.477556: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
19
+ To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
20
+ 2023-08-18 17:09:30.478563: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-08-18 17:09:30.478858: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
22
+ pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
23
+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
24
+ 2023-08-18 17:09:30.478896: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
+ 2023-08-18 17:09:30.478933: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
26
+ 2023-08-18 17:09:30.478957: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
27
+ 2023-08-18 17:09:30.478981: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
28
+ 2023-08-18 17:09:30.479004: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
29
+ 2023-08-18 17:09:30.479027: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
30
+ 2023-08-18 17:09:30.479050: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
31
+ 2023-08-18 17:09:30.479073: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
32
+ 2023-08-18 17:09:30.479470: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
33
+ 2023-08-18 17:09:30.481053: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
34
+ 2023-08-18 17:09:32.621172: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
+ 2023-08-18 17:09:32.621244: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
36
+ 2023-08-18 17:09:32.621264: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
37
+ 2023-08-18 17:09:32.628955: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 14957 MB memory) -> physical GPU (device: 0, name: Tesla P100-PCIE-16GB, pci bus id: 0000:03:00.0, compute capability: 6.0)
38
+ 2023-08-18 17:09:35.405579: W tensorflow/python/util/util.cc:348] Sets are not currently considered sequences, but this may change in the future, so consider avoiding using them.
39
+ /opt/conda/lib/python3.7/site-packages/tensorflow/python/keras/layers/core.py:1059: UserWarning: is not loaded, but a Lambda layer uses it. It may cause errors.
40
+ , UserWarning)
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/new_model_formats/chrombpnet
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_model_params.tsv ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ counts_loss_weight 9.5
2
+ filters 512
3
+ n_dil_layers 8
4
+ bias_model_path /scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/bias_model_scaled.h5
5
+ inputlen 2114
6
+ outputlen 1000
7
+ max_jitter 500
8
+ chr_fold_path /scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json
9
+ negative_sampling_ratio 0.1
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_no_bias_formatting.stderr.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/new_model_formats/chrombpnet_wo_bias
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.chrombpnet_no_bias_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR945KSP//chrombpnet_model_encsr146kfx_bias_fold_2/new_model_formats/chrombpnet_wo_bias
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.epoch_loss.csv ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ epoch,logcount_predictions_loss,logits_profile_predictions_loss,loss,val_logcount_predictions_loss,val_logits_profile_predictions_loss,val_loss
2
+ 0,1.6590232849121094,384.2583923339844,400.01861572265625,0.24510273337364197,400.251708984375,402.58001708984375
3
+ 1,0.24447672069072723,371.68292236328125,374.00592041015625,0.20821325480937958,395.8525695800781,397.8305358886719
4
+ 2,0.21256159245967865,368.85430908203125,370.8735046386719,0.17531822621822357,395.2852783203125,396.9509582519531
5
+ 3,0.1943541020154953,367.5766906738281,369.4234924316406,0.17199589312076569,395.84075927734375,397.47467041015625
6
+ 4,0.18355649709701538,366.444091796875,368.1883850097656,0.20500589907169342,395.8382263183594,397.7857360839844
7
+ 5,0.17100365459918976,365.63104248046875,367.255859375,0.17370560765266418,396.3869323730469,398.0371398925781
8
+ 6,0.15529976785182953,362.7561950683594,364.2320251464844,0.15892954170703888,392.4450988769531,393.95477294921875
9
+ 7,0.15163348615169525,361.1380920410156,362.5787048339844,0.15481148660182953,393.99285888671875,395.4635925292969
10
+ 8,0.14557330310344696,360.1066589355469,361.4894714355469,0.1507824957370758,392.70306396484375,394.1355285644531
11
+ 9,0.14246024191379547,359.2108459472656,360.56427001953125,0.1447809934616089,391.648681640625,393.0244140625
12
+ 10,0.13848228752613068,358.482421875,359.7977600097656,0.14332954585552216,393.0680236816406,394.42938232421875
13
+ 11,0.1368163824081421,356.8476867675781,358.1479797363281,0.14545680582523346,394.1112365722656,395.4930419921875
14
+ 12,0.1361248791217804,356.0652160644531,357.3592529296875,0.15752337872982025,393.3839416503906,394.8802490234375
15
+ 13,0.1271435171365738,353.39727783203125,354.6053466796875,0.14203965663909912,395.5292053222656,396.87847900390625
16
+ 14,0.12532037496566772,352.3334655761719,353.5244445800781,0.14606274664402008,395.2288513183594,396.6164855957031
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stderr.txt ADDED
The diff for this file is too large to render. See raw diff
 
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stdout.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6c8ac52bbe3996a18b75c2486a949f228f266686a836f4b9e4aa6aa803b19a78
3
+ size 11722733
fold_2/logs.models.fold_2.ENCSR945KSP/logfile.modelling.fold_2.ENCSR945KSP.stdout_v1.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:38d20dd332d1acbb4a020236bb226d288b2c30b61787f605c820eb7e3e20718c
3
+ size 11721060
fold_2/model.bias_scaled.fold_2.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:61912dcac80f47c6d3ace91f9f145aadb8412a732bd60854225b960278faed2f
3
+ size 2688440
fold_2/model.bias_scaled.fold_2.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d9ab4aabd6fd4ccb7f4cdf3eeeae00dd92ffe124f9e7e5384a72bec4af5beb66
3
+ size 1198080
fold_2/model.chrombpnet.fold_2.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b3ef9c53e23dd1341121055a47fe19155da09778eb99c7b05449f5aa96e8a14c
3
+ size 26447928
fold_2/model.chrombpnet.fold_2.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:52553132b51172cd98ca9720e58da37ae8e4c27d6f809c74bc1062179af851e6
3
+ size 27607040
fold_2/model.chrombpnet_nobias.fold_2.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4afd93b04256ccafc3e042da1360dcf6561170d5c1c84e8ac4bb2d6ffb38dd20
3
+ size 25583536
fold_2/model.chrombpnet_nobias.fold_2.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:29ade6c320e39b8936ba6d6cdf69c92ec6651b2a82e1fbaff2e716085a64481b
3
+ size 26081280
fold_3/model.bias_scaled.fold_3.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:75987e0d66e8bc2c5368b78369d2759fabf03aea10b4f7f904cad03ad682063d
3
+ size 2688440
fold_3/model.bias_scaled.fold_3.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:14bbd30ad06c2e89250e3302262d599cf1b8a175f5e29514820a77c0808e1171
3
+ size 1198080
fold_3/model.chrombpnet.fold_3.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2308b5039b6633fc983dac2f2f7b182d38d73e2435a9bd03a9c7ae403a4667e8
3
+ size 26447928
fold_3/model.chrombpnet.fold_3.ENCSR945KSP.tar ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:1d102c97a2900540bf1296f7e8e07e9e005e94329052b249b7bba0f8438fff41
3
+ size 27607040
fold_3/model.chrombpnet_nobias.fold_3.ENCSR945KSP.h5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f003ec6bca7e303256e3b14ff6d778c032c32fb2f3125b7e1ef9da901ff66afe
3
+ size 25583536