Add deduplicated leakage-safe FHI-aims splits

Adds deterministic train/validation/test CSV partitions, duplicate-removal audit metadata, and dataset-card configuration. The original release remains available as legacy_original.

README.md

@@ -12,6 +12,18 @@ tags:
 pretty_name: "Multi-fidelity DFT delta corrections for crystal structures"
 size_categories:
   - 10K<n<100K
+configs:
+  - config_name: legacy_deduplicated_leakage_safe_v1
+    default: true
+    data_files:
+      - split: train
+        path: repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/train.csv.gz
+      - split: validation
+        path: repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/validation.csv.gz
+      - split: test
+        path: repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/test.csv.gz
+  - config_name: legacy_original
+    data_files: data.parquet
 ---
 
 # Multi-fidelity DFT delta corrections for crystal structures
@@ -30,6 +42,13 @@ The dataset was constructed to train and evaluate machine-learning models that
 predict the correction needed to "upgrade" a cheap DFT calculation to a more
 expensive one, without running the expensive calculation.
 
+The default configuration is now `legacy_deduplicated_leakage_safe_v1`. It
+removes redundant exact copies, excludes conflicting duplicate groups, and
+uses connected components of ICSD identity and exact starting-structure hash
+to prevent leakage between train, validation, and test. The original 59,235-row
+release remains available as the `legacy_original` configuration for
+reproducibility.
+
 ### Key quantities
 
 | Symbol | Column | Description |
@@ -46,6 +65,10 @@ expensive one, without running the expensive calculation.
 |------|--------|------|-------------|
 | `data.parquet` | Parquet (snappy) | ~92 MB | Tabular delta corrections + DFT settings + features |
 | `graph_data.pt` | PyTorch `torch.save` | ~352 MB | Pre-processed graph dataset for GNN training |
+| `repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/train.csv.gz` | Compressed CSV | ~25.4 MiB | Deduplicated training partition (39,951 rows) |
+| `repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/validation.csv.gz` | Compressed CSV | ~3.3 MiB | Deduplicated validation partition (4,940 rows) |
+| `repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/test.csv.gz` | Compressed CSV | ~3.4 MiB | Deduplicated test partition (5,217 rows) |
+| `repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/audit.json` | JSON | ~3 KB | Deduplication policy, leakage checks, counts, and source hashes |
 
 ---
 
@@ -62,6 +85,22 @@ print(df["basis_size"].value_counts())
 print(df["delta_total_energy_per_atom"].describe())
 ```
 
+### Recommended leakage-safe configuration
+
+```python
+from datasets import load_dataset
+
+dataset = load_dataset(
+    "dtsdts/multifidelity-dft-deltas",
+    "legacy_deduplicated_leakage_safe_v1",
+)
+print(dataset)
+# train: 39,951; validation: 4,940; test: 5,217
+```
+
+The hosted partitions retain the `split` column used to create them. The
+historical partition label is preserved separately as `source_split`.
+
 ### Graph data (PyTorch / PyG)
 
 ```python
@@ -136,12 +175,26 @@ Columns follow the pattern `{stat}_{feature}` where `stat` ∈ {`max`, `min`, `m
 
 ## Dataset Statistics
 
-- **Total rows:** 59,235
+- **Original release:** 59,235 rows
+- **Recommended deduplicated release:** 50,108 rows
+- **Recommended split:** 39,951 train / 4,940 validation / 5,217 test
+- **Exact duplicate copies removed:** 6,200
+- **Conflicting duplicate rows excluded:** 971 rows across 360 groups
+- **Cross-partition leakage:** 0 shared ICSD numbers and 0 shared exact structure hashes
 - **Unique structures:** ~14,500
 - **Basis sizes:** `minimal`, `standard`, `tier1`, `tier2`
 - **k-point densities:** 2, 4, 8
 - **Elements covered:** H through Bi (excluding lanthanides/actinides; a small number of heavy-element structures are filtered)
-- **Train / val / test split:** 80 / 10 / 10 by unique crystal structure
+- **Split method:** deterministic connected components of ICSD number and exact starting-structure hash
+
+### Deduplication policy
+
+An exact duplicate key combines the exact starting-structure hash with the
+normalized physical FHI-aims setting. For identical copies, the row with the
+lexicographically smallest padded source-row identifier is retained. If rows
+with the same key disagree in their target values, the entire conflicting
+group is excluded rather than selecting or averaging a label. See the included
+`audit.json` for the complete reconciliation and SHA-256 hashes.
 
 ---
 

repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/audit.json

@@ -0,0 +1,78 @@
+{
+  "deduplication": {
+    "conflicting_duplicate_policy": "exclude the entire group; do not choose or average disagreeing targets",
+    "conflicting_groups_removed": 360,
+    "conflicting_rows_removed": 971,
+    "exact_duplicate_copies_removed": 6200,
+    "exact_duplicate_policy": "keep the lexicographically smallest padded source_row_id",
+    "input_groups_by_status": {
+      "conflicting": 360,
+      "exact": 6104,
+      "unique": 44004
+    },
+    "input_rows_by_status": {
+      "conflicting": 971,
+      "exact": 12304,
+      "unique": 44004
+    },
+    "key": "duplicate_group_id = structure_hash + normalized physical settings",
+    "output_duplicate_group_ids_are_unique": true
+  },
+  "output": {
+    "columns": 178,
+    "csv_bytes": 130334090,
+    "csv_path": "gitlab_upload/legacy_fhi_aims_model_ready_deduplicated_leakage_safe_split_v1_2026-09-07.csv",
+    "csv_sha256": "0f782883d4c46f6e955e5840b17575b8db62f11b0c2c81c880ee6c8a8c480d53",
+    "gzip_bytes": 32837745,
+    "gzip_path": "gitlab_upload/legacy_fhi_aims_model_ready_deduplicated_leakage_safe_split_v1_2026-09-07.csv.gz",
+    "gzip_sha256": "6e2496d3b022c111b452ee1ddc923f1d23c57735c59f4f2b61dca36cc071d2ac",
+    "rows": 50108
+  },
+  "reconciliation": {
+    "actual_output_rows": 50108,
+    "expected_output_rows": 50108,
+    "input_minus_removed_equals_output": true,
+    "split_rows_sum_to_output": true
+  },
+  "source": {
+    "columns": 177,
+    "existing_structure_hashes_in_multiple_splits": 184,
+    "path": "gitlab_upload/legacy_fhi_aims_model_ready_2026-09-07.csv",
+    "rows": 57279,
+    "sha256": "bb8019e2de15b461ac0b017b114fcc9b01480ab8f98b0d248f8cff450147440c"
+  },
+  "split": {
+    "ICSD_counts": {
+      "test": 366,
+      "train": 2775,
+      "val": 338
+    },
+    "ICSD_numbers_in_multiple_splits": 0,
+    "algorithm": "union ICSD and structure-hash identities, then sha256(salt + ':' + canonical component ID); first 64 bits mapped to [0,1)",
+    "column": "split",
+    "component_counts": {
+      "test": 356,
+      "train": 2690,
+      "val": 333
+    },
+    "group_key": "connected component of ICSD_number and structure_hash",
+    "original_column_preserved_as": "source_split",
+    "row_counts": {
+      "test": 5217,
+      "train": 39951,
+      "val": 4940
+    },
+    "salt": "legacy_fhi_aims_icsd_structure_component_split_v1",
+    "structure_hash_counts": {
+      "test": 3740,
+      "train": 28607,
+      "val": 3552
+    },
+    "structure_hashes_in_multiple_splits": 0,
+    "thresholds": {
+      "test": "[0.90,1.00)",
+      "train": "[0.00,0.80)",
+      "val": "[0.80,0.90)"
+    }
+  }
+}

repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/test.csv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a4b746c741b994dd7070f35be58f255a6c248f1a382c7ab5b1d55d40363b5eb1
+size 3577311

repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/train.csv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e003e9da7a92fe8165846c249f34fb46a87a73775659b1608ece76a70f5af006
+size 26593876

repaired/legacy_fhi_aims_deduplicated_leakage_safe_v1/validation.csv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:97ebd44921b0f9d6f91b953b75d1a9542b92c3d860caa0468fc61cb69f60e243
+size 3472741