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push trained model weights for 0_baseline_LSTM and 2_multitask_dense … #178

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Dec 20, 2022
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push trained model weights for 0_baseline_LSTM and 2_multitask_dense … #178

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80c0839
push trained model weights for 0_baseline_LSTM and 2_multitask_dense …
Nov 30, 2022
0dbac60
uncomment models in p2a_model_ids target
Nov 30, 2022
28fc7ae
comment out 1 and 1a models
jsadler2 Dec 13, 2022
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4 changes: 2 additions & 2 deletions 2a_model.R
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Expand Up @@ -189,8 +189,8 @@ p2a_targets_list <- list(
list(model_id = "0_baseline_LSTM",
snakefile_dir = "0_baseline_LSTM",
config_path = stringr::str_remove(p2a_config_baseline_LSTM_yml, "2a_model/src/models/")),
# the 1_ models use the same model and therefore the same Snakefile
# as the 0_baseline_LSTM run
#the 1_ models use the same model and therefore the same Snakefile
#as the 0_baseline_LSTM run
list(model_id = "1_metab_multitask",
snakefile_dir = "0_baseline_LSTM",
config_path = stringr::str_remove(p2a_config_metab_multitask_yml, "2a_model/src/models/")),
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model_checkpoint_path: "."
all_model_checkpoint_paths: "."
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model_checkpoint_path: "."
all_model_checkpoint_paths: "."
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model_checkpoint_path: "."
all_model_checkpoint_paths: "."
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model_checkpoint_path: "."
all_model_checkpoint_paths: "."
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model_checkpoint_path: "."
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model_checkpoint_path: "."
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model_checkpoint_path: "."
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model_checkpoint_path: "."
all_model_checkpoint_paths: "."
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model_checkpoint_path: "."
all_model_checkpoint_paths: "."
2 changes: 1 addition & 1 deletion 2a_model/out/models/add_weights.sh
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files=(checkpoint .data-00000-of-00001 .index .snakemake_timestamp)

models=(0_baseline_LSTM 1_metab_multitask 1a_multitask_do_gpp_er)
models=(0_baseline_LSTM 2_multitask_dense)

for f in ${files[@]}; do
for d in ${models[@]}; do
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8 changes: 4 additions & 4 deletions 2a_model/src/models/0_baseline_LSTM/config.yml
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exp_name: "0_baseline_LSTM"
exp_name: 0_baseline_LSTM
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I specify that these should be quoted in the function that builds the config files so I was surprised to see that the quoted formatting gets lost when built on Tallgrass. I've played with this a bit before and I think if we updated the version of the {yaml} R package and added it to the container these config files would keep the quoted format as before. I've added a note in #158.

It's good to know that the models still run even though these new config files don't have quotes around exp_name and y_vars.

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I think python will automatically read these as strings since they aren't numbers

y_vars:
- "do_min"
- "do_mean"
- "do_max"
- do_min
- do_mean
- do_max
lambdas:
- 1
- 1
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18 changes: 9 additions & 9 deletions 2a_model/src/models/1_metab_multitask/1a_multitask_do_gpp_er.yml
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@@ -1,13 +1,13 @@
exp_name: "1a_multitask_do_gpp_er"
exp_name: 1a_multitask_do_gpp_er
y_vars:
- "do_min"
- "do_mean"
- "do_max"
- "GPP"
- "ER"
- "K600"
- "depth"
- "temp.water"
- do_min
- do_mean
- do_max
- GPP
- ER
- K600
- depth
- temp.water
lambdas:
- 1
- 1
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18 changes: 9 additions & 9 deletions 2a_model/src/models/1_metab_multitask/config.yml
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exp_name: "1_metab_multitask"
exp_name: 1_metab_multitask
y_vars:
- "do_min"
- "do_mean"
- "do_max"
- "GPP"
- "ER"
- "K600"
- "depth"
- "temp.water"
- do_min
- do_mean
- do_max
- GPP
- ER
- K600
- depth
- temp.water
lambdas:
- 1
- 1
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18 changes: 9 additions & 9 deletions 2a_model/src/models/2_multitask_dense/config.yml
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@@ -1,13 +1,13 @@
exp_name: "2_multitask_dense"
exp_name: 2_multitask_dense
y_vars:
- "do_min"
- "do_mean"
- "do_max"
- "GPP"
- "ER"
- "K600"
- "depth"
- "temp.water"
- do_min
- do_mean
- do_max
- GPP
- ER
- K600
- depth
- temp.water
lambdas:
- 1
- 1
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54 changes: 37 additions & 17 deletions 2a_model/src/models/config_base.yml
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@@ -1,6 +1,6 @@
out_dir: "../../../out/models"
out_dir: ../../../out/models
seed: False
num_replicates: 1
num_replicates: 10
trn_offset: 1.0
tst_val_offset: 1.0
epochs: 100
Expand All @@ -10,27 +10,47 @@ recurrent_dropout: 0.2
finetune_learning_rate: 0.01
early_stopping: False
validation_sites:
- "01472104"
- "01473500"
- "01481500"
- '01472104'
- '01473500'
- 01481500
test_sites:
- "01475530"
- "01475548"
- '01475530'
- 01475548
train_start_date: '1980-01-01'
train_end_date: '2014-10-01'
val_start_date: '2014-10-01'
val_end_date: '2015-10-01'
test_start_date: '2015-10-01'
test_end_date: '2022-10-01'
x_vars:
- "pr"
- "SLOPE"
- "tmmx"
- "tmmn"
- "srad"
- "CAT_BASIN_SLOPE"
- "CAT_ELEV_MEAN"
- "CAT_IMPV11"
- "CAT_CNPY11_BUFF100"
- "CAT_TWI"
- tmmn
- tmmx
- pr
- srad
- SLOPE
- TOTDASQKM
- CAT_BASIN_SLOPE
- TOT_BASIN_SLOPE
- CAT_ELEV_MEAN
- CAT_RDX
- CAT_BFI
- CAT_EWT
- CAT_TWI
- CAT_PPT7100_ANN
- TOT_PPT7100_ANN
- CAT_RUN7100
- CAT_CNPY11_BUFF100
- CAT_IMPV11
- TOT_IMPV11
- CAT_NLCD11_wetland
- TOT_NLCD11_wetland
- CAT_SANDAVE
- CAT_PERMAVE
- TOT_PERMAVE
- CAT_RFACT
- CAT_WTDEP
- TOT_WTDEP
- CAT_NPDES_MAJ
- CAT_NDAMS2010
- CAT_NORM_STORAGE2010

2 changes: 1 addition & 1 deletion _targets.R
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Expand Up @@ -110,7 +110,7 @@ base_config_options <- list(
out_dir = "../../../out/models",
# random seed for training; If FALSE, no seed. Otherwise, specify the seed:
seed = FALSE,
num_replicates = 1,
num_replicates = 10,
trn_offset = 1,
tst_val_offset = 1,
epochs = 100,
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