From 60b18c281b7c4bada96d66203f74fe153c4334ed Mon Sep 17 00:00:00 2001
From: Raktim Mitra <raktim@localhost>
Date: Thu, 26 Feb 2026 10:41:52 -0800
Subject: [PATCH] mc: yaml changes

---
 models/rfd3/configs/experiment/rfd3na.yaml          | 13 +++++++------
 .../rfd3/configs/experiment/rfd3na_fine_tune.yaml   | 11 ++++++-----
 .../rfd3/configs/experiment/rfd3na_no_distill.yaml  |  7 ++++---
 3 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/models/rfd3/configs/experiment/rfd3na.yaml b/models/rfd3/configs/experiment/rfd3na.yaml
index e1194be..8739992 100644
--- a/models/rfd3/configs/experiment/rfd3na.yaml
+++ b/models/rfd3/configs/experiment/rfd3na.yaml
@@ -2,17 +2,18 @@
 # Training configuration for RFD3
 
 defaults:
-  - /debug/default
+  #- /debug/default
   - override /model: rfd3_base
-  #- override /logger: wandb
+  - override /logger: wandb
   - override /datasets: design_base_rfd3na
   - _self_
 
 name: rfd3na_scratch_clean_test
 tags: [print-model]
 
+#ckpt: null
 #ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na-fine-tune/2026-02-17_15-21_JOB_3608285/ckpt/epoch-0590.ckpt
-#ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na_scratch/2026-02-17_17-56_JOB_3620867/ckpt/epoch-0030.ckpt
+ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na_scratch_clean_test/2026-02-19_01-58_JOB_3986244/ckpt/epoch-0180.ckpt
 
 
 model:
@@ -58,7 +59,7 @@ datasets:
   max_atoms_in_crop: 2560  # ~10x crop size.
   global_transform_args:
     meta_conditioning_probabilities:
-      p_is_nucleic_ss_example: 1.0
+      p_is_nucleic_ss_example: 0.25
       p_nucleic_ss_show_partial_feats: 0.7
       p_canonical_bp_filter: 0.2
       #calculate_NA_SS: 0.3
@@ -79,11 +80,11 @@ datasets:
   train:
     # These are the ratios used in the preprint but we set all pdb sampling by default since not everyone might download the distillation data.
     pdb:
-      probability: 0.5
+      probability: 0.6
     rna_monomer_distillation:
       probability: 0.3
     monomer_distillation:
-      probability: 0.2
+      probability: 0.1
 
   val:
     pseudoknot:
diff --git a/models/rfd3/configs/experiment/rfd3na_fine_tune.yaml b/models/rfd3/configs/experiment/rfd3na_fine_tune.yaml
index e731063..3210c5c 100644
--- a/models/rfd3/configs/experiment/rfd3na_fine_tune.yaml
+++ b/models/rfd3/configs/experiment/rfd3na_fine_tune.yaml
@@ -8,9 +8,10 @@ defaults:
   - override /datasets: design_base_rfd3na
   - _self_
 
-name: rfd3na-fine-tune
+name: rfd3na-fine-tune-ss0.5
 tags: [print-model]
-ckpt_path: /projects/ml/aa_design/models/rfd3_latest_foundry.ckpt
+#ckpt_path: /projects/ml/aa_design/models/rfd3_latest_foundry.ckpt
+ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na-fine-tune-ss0.5/2026-02-23_23-57_JOB_4717793/ckpt/epoch-0820.ckpt
 
 model:
   net:
@@ -55,7 +56,7 @@ datasets:
   max_atoms_in_crop: 2560  # ~10x crop size.
   global_transform_args:
     meta_conditioning_probabilities:
-      p_is_nucleic_ss_example: 0.25
+      p_is_nucleic_ss_example: 0.5
       p_nucleic_ss_show_partial_feats: 0.7
       p_canonical_bp_filter: 0.2
       #calculate_NA_SS: 0.3
@@ -76,11 +77,11 @@ datasets:
   train:
     # These are the ratios used in the preprint but we set all pdb sampling by default since not everyone might download the distillation data.
     pdb:
-      probability: 0.5
+      probability: 0.6
     rna_monomer_distillation:
       probability: 0.3
     monomer_distillation:
-      probability: 0.2
+      probability: 0.1
 
   val:
     pseudoknot:
diff --git a/models/rfd3/configs/experiment/rfd3na_no_distill.yaml b/models/rfd3/configs/experiment/rfd3na_no_distill.yaml
index e3642cc..abb302b 100644
--- a/models/rfd3/configs/experiment/rfd3na_no_distill.yaml
+++ b/models/rfd3/configs/experiment/rfd3na_no_distill.yaml
@@ -10,7 +10,8 @@ defaults:
 
 name: rfd3na_no_distill
 tags: [print-model]
-ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na_no_distill/2026-02-17_15-21_JOB_3608348/ckpt/epoch-0020.ckpt
+#ckpt_path: null
+ckpt_path: /net/scratch/raktim/training/logs/train/rfd3na_no_distill/2026-02-19_02-16_JOB_3988845/ckpt/epoch-0170.ckpt
 
 model:
   net:
@@ -76,9 +77,9 @@ datasets:
   train:
     # These are the ratios used in the preprint but we set all pdb sampling by default since not everyone might download the distillation data.
     pdb:
-      probability: 0.6
+      probability: 0.7
     rna_monomer_distillation:
-      probability: 0.4
+      probability: 0.3
     monomer_distillation:
       probability: 0.0