Add full RNA eval metrics and structure figures

.gitattributes

@@ -34,3 +34,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
 figures/validation_lddt_curve.png filter=lfs diff=lfs merge=lfs -text
+figures/rna_structure_plddt_collage.png filter=lfs diff=lfs merge=lfs -text

README.md

@@ -22,13 +22,28 @@ model-index:
     metrics:
     - type: lddt_complex_best
       name: lDDT complex best
-      value: 0.758663
+      value: 0.755899
     - type: lddt_complex_mean
       name: lDDT complex mean
-      value: 0.746286
+      value: 0.743375
     - type: lddt_complex_rank1
       name: lDDT complex rank1
-      value: 0.746743
+      value: 0.742393
+    - type: tm_score_complex_best
+      name: TM-score complex best
+      value: 0.927163
+    - type: tm_score_complex_rank1
+      name: TM-score complex rank1
+      value: 0.914028
+    - type: tm_score_c1prime_best
+      name: TM-score C1' best
+      value: 0.620936
+    - type: tm_score_c1prime_rank1
+      name: TM-score C1' rank1
+      value: 0.591564
+    - type: plddt_rank1
+      name: pLDDT rank1
+      value: 80.828687
 ---
 
 # Protenix-RNA
@@ -42,8 +57,12 @@ Protenix-RNA is a Protenix fine-tuned PyTorch checkpoint optimized for RNA struc
 | `checkpoints/best_ema_0.999.pt` | EMA checkpoint selected at step 12,999. |
 | `config.yaml` | Resolved fine-tuning/evaluation config. |
 | `validation_comparison.csv` | lDDT-only validation comparison against the base and previous fine-tuned checkpoints. |
+| `eval/full_eval_base_vs_best_summary.csv` | Full validation aggregate metrics for Protenix-RNA vs base Protenix. |
+| `eval/top100_base_vs_best_summary.csv` | Aggregate metrics on the top 100 targets selected by Protenix-RNA TM-score C1' best. |
+| `eval/top100_base_vs_best_comparison.csv` | Per-target top-100 comparison CSV with base, Protenix-RNA, and delta columns. |
+| `eval/selected_best_top100.csv` | The selected top-100 target rows from the Protenix-RNA full eval. |
 | `checkpoint_info.json` | Source path, checkpoint step, and artifact metadata. |
-| `figures/` | Validation comparison and lDDT progression plots. |
+| `figures/` | Validation, TM-score, pLDDT, and structure-collage plots. |
 
 The checkpoint is a `torch.load(..., weights_only=False)` dictionary with keys `model`, `optimizer`, `scheduler`, and `step`. The stored step is `12999`.
 
@@ -58,10 +77,54 @@ The checkpoint is a `torch.load(..., weights_only=False)` dictionary with keys `
 - Protein MSA and templates: disabled
 - EMA decay: 0.999
 - Selection metric: `rna_finetune_val/ema0.999_lddt/complex/best.avg`, maximize
+- Full eval settings: seed 42, bf16, `N_sample=5`, `N_step=20`, `N_cycle=4`, `max_n_token=768`
+- Full eval size after token filtering: 1,490 target rows from 195 PDB IDs
 
-## Validation
+## Full RNA Evaluation
 
-Higher is better for all metrics shown here.
+Higher is better for lDDT, TM-score, and pLDDT. Lower is better for loss.
+
+| Metric | Base Protenix | Protenix-RNA | Delta |
+|---|---:|---:|---:|
+| lDDT complex best | 0.5565 | 0.7559 | +0.1994 |
+| lDDT complex mean | 0.5428 | 0.7434 | +0.2005 |
+| lDDT complex rank1 | 0.5423 | 0.7424 | +0.2001 |
+| TM-score complex best | 0.8413 | 0.9272 | +0.0859 |
+| TM-score complex rank1 | 0.8198 | 0.9140 | +0.0942 |
+| TM-score C1' best | 0.4611 | 0.6209 | +0.1599 |
+| TM-score C1' rank1 | 0.4235 | 0.5916 | +0.1681 |
+| pLDDT rank1 | 69.06 | 80.83 | +11.77 |
+| Loss | 1244.81 | 834.44 | -410.36 |
+
+These values come from a full comparison run against `protenix_base_default_v1.0.0` using the same RNA validation setup and saved predictions for both checkpoints.
+
+![Full RNA validation TM-score and lDDT comparison](figures/full_eval_tm_lddt_comparison.png)
+
+![Full RNA validation pLDDT comparison](figures/plddt_comparison.png)
+
+## Top-100 Structure Comparison
+
+The top-100 set is selected from the full Protenix-RNA eval by `tm_score_c1prime_best`, then matched against base-model predictions from the same validation set. This subset is useful for inspecting best-case RNA behavior; it is not an unbiased dataset average.
+
+| Top-100 metric | Base Protenix | Protenix-RNA | Delta |
+|---|---:|---:|---:|
+| TM-score C1' best | 0.8082 | 0.9904 | +0.1822 |
+| TM-score C1' rank1 | 0.7768 | 0.9602 | +0.1833 |
+| TM-score complex best | 0.9332 | 0.9848 | +0.0516 |
+| TM-score complex rank1 | 0.9297 | 0.9806 | +0.0509 |
+| lDDT complex best | 0.7749 | 0.9211 | +0.1463 |
+| lDDT complex rank1 | 0.7717 | 0.9176 | +0.1459 |
+| pLDDT rank1 | 86.88 | 91.85 | +4.96 |
+
+![Top-100 RNA target metric comparison](figures/top100_tm_lddt_comparison.png)
+
+The following collage shows rank-1 predicted structures from representative top-100 targets, colored by atom pLDDT stored in the mmCIF B-factor field.
+
+![RNA structure pLDDT collage](figures/rna_structure_plddt_collage.png)
+
+## Checkpoint Selection Trace
+
+This checkpoint was originally selected from the EMA validation loop by lDDT-complex best at step 12,999.
 
 | Metric | Base Protenix | Prior FT s9499 | Protenix-RNA s12999 | Gain vs base | Gain vs s9499 |
 |---|---:|---:|---:|---:|---:|
@@ -69,10 +132,6 @@ Higher is better for all metrics shown here.
 | lDDT mean | 0.5420 | 0.7261 | 0.7463 | +0.2043 | +0.0202 |
 | lDDT rank1 | 0.5417 | 0.7254 | 0.7467 | +0.2050 | +0.0214 |
 
-Validation settings: RNA validation split, seed 42, bf16, `N_sample=5`, `N_step=20`, `N_cycle=4`, `max_n_token=768`, RNA MSA enabled. The step 12,999 values come from the EMA validation loop that produced the uploaded checkpoint.
-
-![RNA validation lDDT comparison](figures/lddt_comparison.png)
-
 ![RNA validation lDDT during fine-tuning](figures/validation_lddt_curve.png)
 
 ## Usage

eval/full_eval_base_vs_best_summary.csv

@@ -0,0 +1,9 @@
+metric,best_finetuned,base,delta
+lddt_complex_best,0.7558994238735527,0.5564552312917126,0.1994441925818401
+lddt_complex_rank1,0.7423933597622059,0.5422795812188778,0.20011377854332812
+tm_score_complex_best,0.9271632821489406,0.84125209276274,0.08591118938620057
+tm_score_complex_rank1,0.9140280159590866,0.8198382741501254,0.09418974180896111
+tm_score_c1prime_best,0.6209358050806005,0.46106288228949566,0.15987292279110488
+tm_score_c1prime_rank1,0.5915635808247883,0.42347763139115235,0.16808594943363597
+plddt_rank1,80.82868698335463,69.05649377581894,11.772193207535693
+loss,834.4439859464765,1244.8086456340006,-410.3646596875242

eval/selected_best_top100.csv

@@ -0,0 +1,101 @@
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eval/top100_base_vs_best_summary.csv

@@ -0,0 +1,8 @@
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