Update training results

Author: eric-czech

experiments/plantcad/README.md

@@ -119,14 +119,18 @@ python -m experiments.plantcad.scripts.exp_pc1_train \
 rm -rf local_store/evaluation/dna-conservation*; python -m experiments.plantcad.scripts.exp_pc1_eval --prefix local_store --force_run_failed true
 
 # Checkpoint upload
-find local_store | grep -E 'hf/step-[0-9]+$' | xargs -I {} echo "hf upload plantcad/_dev_marin_plantcad1_v2_train {} {} --repo-type model" | bash /dev/stdin
-
+#   HF checkpoints
+find local_store | grep -E 'hf/step-[0-9]+$' | xargs -I {} echo "hf upload plantcad/_dev_marin_plantcad1_v3_train {} {} --repo-type model" | bash /dev/stdin
+#   Levanter checkpoints
 find local_store | grep -E 'checkpoints/step-[0-9]+$' | \
 grep -E 'step-26780$|step-24102|step-21424|step-18746$' | \
-xargs -I {} echo "hf upload plantcad/_dev_marin_plantcad1_v2_train {} {} --repo-type model" | \
+xargs -I {} echo "hf upload plantcad/_dev_marin_plantcad1_v3_train {} {} --repo-type model" | \
 bash /dev/stdin
 ```
 
+### Eval results
+
+Iteration 1:
 ```bash
 > python -m experiments.plantcad.misc.agg_eval_results
 roc_auc  step                                                                                                  checkpoint_path
@@ -145,7 +149,7 @@ roc_auc  step
 0.593178 21749 hf://plantcad/_dev_marin_plantcad1_v1_train/local_store/checkpoints/plantcad-train-300m-r02-432442/hf/step-21749
 ```
 
-Second iteration:
+Iteration 2:
 
 ```
  python experiments/plantcad/misc/agg_eval_results.py
@@ -163,6 +167,24 @@ Second iteration:
 0.657452 26782 hf://plantcad/_dev_marin_plantcad1_v2_train/local_store/checkpoints/plantcad-train-600m-r12-7ea0fc/hf/step-26782
 ```
 
+Iteration 3:
+
+```
+> python -m experiments.plantcad.misc.agg_eval_results
+ roc_auc  step                                                                                                  checkpoint_path
+0.665902  2678  hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-2678
+0.672563  5356  hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-5356
+0.673937  8034  hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-8034
+0.675633 10712 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-10712
+0.678089 13390 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-13390
+0.684904 16068 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-16068
+0.680056 18746 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-18746
+0.677681 21424 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-21424
+0.679077 24102 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-24102
+0.681293 26780 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-26780
+0.680195 26782 hf://plantcad/_dev_marin_plantcad1_v3_train/local_store/checkpoints/plantcad-train-600m-r16-a1bc43/hf/step-26782
+```
+
 ## EDA
 
 Stats on kuleshov-group/Angiosperm_16_genomes:

experiments/plantcad/evaluation.py

@@ -52,7 +52,7 @@
 class DnaEvalBaseConfig:
     """Base configuration for DNA evaluation with fields needed for training callbacks"""
 
-    dataset_path: str = "plantcad/evolutionary-constraint-example"
+    dataset_path: str = "plantcad/evolutionary-constraint"
     """Dataset repository path"""
 
     dataset_config: str | None = "10k"
@@ -730,7 +730,7 @@ def run_conservation_eval(config: DnaEvalConfig) -> dict[str, float]:
 #     checkpoint_path="/path/to/hf/checkpoint",
 #     device="cuda",  # or "cpu" for CPU inference
 #     num_workers=None,  # defaults to number of GPUs
-#     dataset_path="plantcad/evolutionary-constraint-example",
+#     dataset_path="plantcad/evolutionary-constraint",
 #     dataset_config="10k",
 #     max_samples=1000
 # )