update scripte

ylab-hi · Dec 2, 2024 · f5313fd · f5313fd
1 parent 94b70d2
commit f5313fd
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Showing 3 changed files with 24 additions and 23 deletions.
diff --git a/configs/experiment/hyena.yaml b/configs/experiment/hyena.yaml
@@ -16,7 +16,7 @@ callbacks:
   early_stopping:
     patience: 15
 
-tags: ["vcap_004_300000"]
+tags: ["vcap_002_300000_both"]
 
 seed: 12345
 
@@ -25,10 +25,10 @@ trainer:
   max_epochs: 60
 
 data:
-  train_data_path: ${paths.root_dir}/data/600_000_both_samples/train.parquet
-  val_data_path: ${paths.root_dir}/data/600_000_both_samples/val.parquet
-  test_data_path: ${paths.root_dir}/data/600_000_both_samples/test.parquet
-  batch_size: 8
+  train_data_path: ${paths.root_dir}/data/300_000_both_samples/train.parquet
+  val_data_path: ${paths.root_dir}/data/300_000_both_samples/val.parquet
+  test_data_path: ${paths.root_dir}/data/300_000_both_samples/test.parquet
+  batch_size: 12
   num_workers: 63
   pin_memory: False
   max_val_samples: 3000

diff --git a/scripts/chop.sh b/scripts/chop.sh
@@ -1,22 +1,20 @@
 #!/bin/bash
 set -euo pipefail # Combines the set commands into one line
 
-predict_folder="vcap_caduceus"
+# predict_folder="vcap_caduceus"
 
-cargo run --bin predict -r -- \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_0/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_1/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_2/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_3/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_4/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_5/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_6/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_7/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_8/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_9/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_10/predicts/0/ \
-	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_hyena/RNA004.fastq_11/predicts/0/ \
-	--fq data/dorado_without_trim_fqs/RNA004.fastq -t 10 -o vcap_004_hyena_all
+cargo run --bin deepchopper-chop -r -- \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_0/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_1/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_2/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_3/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_4/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_5/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_6/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_7/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_8/predicts/0/ \
+	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap002_hyena_both_model_hyena/VCaP.fastq_9/predicts/0/ \
+	--fq data/dorado_without_trim_fqs/VCaP.fastq -t 10 -o vcap002_hyena_both_model
 
 cargo run --bin predict -r -- \
 	--pdt /projects/b1171/ylk4626/project/DeepChopper/logs/eval/runs/vcap_004_cnn_model_cnn/RNA004.fastq_0/predicts/0/ \

diff --git a/scripts/predict.sh b/scripts/predict.sh
@@ -2,7 +2,10 @@
 set -euo pipefail # Combines the set commands into one line
 
 # Paths to checkpoint files
-hyena_ckpt_path="/projects/b1171/ylk4626/project/DeepChopper/logs/train/runs/2024-04-08_23-19-20/checkpoints/epoch_005_f1_0.9933.ckpt"
+# hyena_ckpt_path="/projects/b1171/ylk4626/project/DeepChopper/logs/train/runs/2024-04-08_23-19-20/checkpoints/epoch_005_f1_0.9933.ckpt"
+
+# train with both rna 002 data
+hyena_ckpt_path="/projects/b1171/ylk4626/project/DeepChopper/logs/train/runs/2024-11-14_14-14-01/checkpoints/epoch_010_f1_0.9930.ckpt"
 
 # rna 004 only
 # hyena_ckpt_path="/projects/b1171/ylk4626/project/DeepChopper/logs/train/runs/2024-07-02_15-20-53/checkpoints/epoch_008_f1_0.9946.ckpt"
@@ -11,8 +14,8 @@ cnn_ckpt_path="/projects/b1171/ylk4626/project/DeepChopper/logs/train/runs/2024-
 caduceus_ckpt_path="/projects/b1171/ylk4626/project/DeepChopper/logs/train/runs/2024-05-25_19-42-45/checkpoints/epoch_002_f1_0.9982.ckpt"
 
 # Default model selection
-sample_name="MCF7_hyena_model"
-data_folder="data/dorado_without_trim_fqs/MCF7.fastq_chunks"
+sample_name="vcap002_hyena_both_model"
+data_folder="data/dorado_without_trim_fqs/VCaP.fastq_chunks"
 
 num_workers=60
 batch_size=64