Duplicate from ogutsevda/graph-pannuke

Co-authored-by: Sevda OGUT <ogutsevda@users.noreply.huggingface.co>

.gitattributes

@@ -0,0 +1,60 @@
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.avro filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.lz4 filter=lfs diff=lfs merge=lfs -text
+*.mds filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text
+# Audio files - uncompressed
+*.pcm filter=lfs diff=lfs merge=lfs -text
+*.sam filter=lfs diff=lfs merge=lfs -text
+*.raw filter=lfs diff=lfs merge=lfs -text
+# Audio files - compressed
+*.aac filter=lfs diff=lfs merge=lfs -text
+*.flac filter=lfs diff=lfs merge=lfs -text
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+# Image files - uncompressed
+*.bmp filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.tiff filter=lfs diff=lfs merge=lfs -text
+# Image files - compressed
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.webp filter=lfs diff=lfs merge=lfs -text
+# Video files - compressed
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.webm filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,120 @@
+---
+license: cc-by-nc-sa-4.0
+task_categories:
+  - graph-ml
+tags:
+  - histopathology
+  - node-classification
+  - pytorch-geometric
+pretty_name: Graph-PanNuke
+size_categories:
+  - 1K<n<10K
+---
+
+# Graph-PanNuke: A Cell-Graph Dataset for Nucleus Classification from PanNuke
+
+<p align="center">
+  <img src="animation.gif" alt="Graph-PanNuke teaser – cell-graph construction from a histopathology patch" width="600"/>
+</p>
+
+**Graph-PanNuke** is a node-level classification dataset derived from the [PanNuke](https://warwick.ac.uk/fac/sci/dcs/research/tia/data/pannuke/) pan-cancer histology dataset. We use all slides at 40× magnification. Each tissue patch is converted into a **cell-graph** where nodes represent detected cell nuclei and edges encode spatial proximity. The task is predicting the cell type of each nucleus across 5 classes. Note that node features describe cell morphology, texture, and color intensity whereas edge features are Euclidean distance in micrometers.
+
+This dataset is part of the paper [GrapHist: Graph Self-Supervised Learning for Histopathology](https://arxiv.org/pdf/2603.00143).
+
+> ⚠️ **Edge Weight Note**: While the architecture in GrapHist supports both positive and negative edge weights, by default edge features represent Euclidean distances—meaning farther nodes have larger, positive values. This can be counterintuitive for many graph neural network models. We recommend experimenting with edge weights, such as using their inverse (e.g., `1/distance`) or negative distance (e.g., `-distance`), to better capture proximity and benefit learning.
+
+## Dataset Summary
+
+| Property | Value |
+|---|---|
+| **# Patches** | 7,208 |
+| **Avg # Nodes** | 22.66 |
+| **Avg # Edges** | 57.16 |
+| **# Classes** | 5 |
+
+## Node Classes
+
+| Label ID | Class Name |
+|---|---|
+| 0 | Neoplastic |
+| 1 | Inflammatory |
+| 2 | Connective |
+| 3 | Dead |
+| 4 | Epithelial |
+
+## Data Structure
+
+```
+graph-pannuke/
+├── README.md
+├── animation.gif
+└── data/
+    ├── fold_1/
+    │   ├── Bile-duct_1_01455.pt
+    │   ├── Breast_3_00420.pt
+    │   └── ...
+    ├── fold_2/
+    │   └── ...
+    └── fold_3/
+        └── ...
+```
+
+Each `.pt` file is a PyTorch Geometric `Data` object with the following attributes:
+
+| Attribute | Shape | Description |
+|---|---|---|
+| `x` | `[num_nodes, 96]` | Node feature matrix |
+| `edge_index` | `[2, num_edges]` | Graph connectivity in COO format |
+| `edge_attr` | `[num_edges, 1]` | Edge features |
+| `labels` | `[num_nodes]` | Per-node class label |
+| `sample_id` | `str` | Unique patch identifier |
+
+---
+
+## Quick Start
+
+```python
+import torch
+
+# Load a single graph
+graph = torch.load("data/fold_1/Bile-duct_1_01455.pt", weights_only=False)
+
+print(graph)
+# Data(x=[23, 96], edge_index=[2, 61], edge_attr=[61, 1], sample_id='...', labels=[23])
+
+print(f"Nodes: {graph.x.shape[0]}, Edges: {graph.edge_index.shape[1]}")
+print(f"Node labels: {graph.labels}")
+```
+
+---
+
+## Citation
+
+If you use this dataset, please cite both our work, and the original PanNuke dataset:
+
+**GrapHist (this dataset):**
+```bibtex
+@misc{ogut2026graphist,
+    title={GrapHist: Graph Self-Supervised Learning for Histopathology}, 
+    author={Sevda Öğüt and Cédric Vincent-Cuaz and Natalia Dubljevic and Carlos Hurtado and Vaishnavi Subramanian and Pascal Frossard and Dorina Thanou},
+    year={2026},
+    eprint={2603.00143},
+    url={https://arxiv.org/abs/2603.00143}, 
+}
+```
+
+**PanNuke (source annotations):**
+```bibtex
+@article{gamper2020pannuke,
+  title={Pannuke dataset extension, insights and baselines},
+  author={Gamper, Jevgenij and Koohbanani, Navid Alemi and Benes, Ksenija and Graham, Simon and Jahanifar, Mostafa and Khurram, Syed Ali and Azam, Ayesha and Hewitt, Katherine and Rajpoot, Nasir},
+  journal={arXiv preprint arXiv:2003.10778},
+  year={2020}
+}
+```
+
+---
+
+## License
+
+This dataset is released under the [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) license.

data/fold_1/Adrenal_gland_1_01171.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:08d95bb89ea947c4e5e457d47e22bb705ee826e4fe98e4c1f8ce56e0a1bdad20
+size 16320

data/fold_1/Adrenal_gland_1_01172.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6a1e089feb3064035ec5c8d08974ab2d0d58f3cfac5f9af30660c828bef98687
+size 10880

data/fold_1/Adrenal_gland_1_01173.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7e83e47614ddd47b69ebdca64c13979102545e7fca544b810d61f23b3c8937f1
+size 12032

data/fold_1/Adrenal_gland_1_01174.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f20990a3cbb6bc0312c6b94a681bba80263847d3c48f2632b3f9b104677f168d
+size 12096

data/fold_1/Adrenal_gland_1_01175.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ea2ae4d5bf9e9a25ad2457da6cb9c9336c4c7bcc3779355c0990cee333ef5630
+size 13120

data/fold_1/Adrenal_gland_1_01176.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:39e7fd242d0671bfb3790011aec96643d50f3c5399baef6ae97d61f0dc9d7333
+size 13952

data/fold_1/Adrenal_gland_1_01177.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:49103ef5cb4127f5cd817eaa193474cf38ca4048dd49cfea5a04f707e8f107cc
+size 10816

data/fold_1/Adrenal_gland_1_01178.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:dbd1b847e28abe3e231083759c2e57b9a64dbfcdec546908d084ccbcf43687cc
+size 9024

data/fold_1/Adrenal_gland_1_01179.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0226845bd31c922cb0d878ebd3b085e18a1be339f1933e9e7f501d8bfe5a03d9
+size 14400

data/fold_1/Adrenal_gland_1_01180.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5a8b44b58724cf2632b8b63422ecf339262175a2d77f7f3d146e782f1b46ff17
+size 12160

data/fold_1/Adrenal_gland_1_01181.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5239039ac0375cb9d5b3b0b82ec8458d46a6e187d2c09aa5ea7d84884fa65cb8
+size 12608

data/fold_1/Adrenal_gland_1_01182.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ccc00d1b3369a84df80d8ef3c52aca4f81240289474d24b14a42413e7b760ae7
+size 12608

data/fold_1/Adrenal_gland_1_01183.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0ceee8a3d89681cc350b9cb7307af54a4a5e1d6b765be50ae366715c9e7b36ad
+size 10368

data/fold_1/Adrenal_gland_1_01184.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eeaed8e2e934b68d161aa78ec6da4ed56deccc1085caff0e6e24492ed869bd17
+size 11712

data/fold_1/Adrenal_gland_1_01185.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3d6058c880102cca44f3ad88374ce2d89ff4b3beb74b39e395801bd59c52388b
+size 9856

data/fold_1/Adrenal_gland_1_01186.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a5ca0f65ea7b7eaa547355a97637b2069507ff4febb4d71354f320b2a184350c
+size 5888

data/fold_1/Adrenal_gland_1_01187.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:33099cb608fa3ac6358aef3c73663cde7542fa9a2bd7cba173566494f9d09f3a
+size 12608

data/fold_1/Adrenal_gland_1_01188.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b902d6a8418db4c85303bf66a50edec1e531edb5320259fd981a257894c6da85
+size 8512

data/fold_1/Adrenal_gland_1_01190.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:555f9d1473226da1d7abc5132774353b5fad97448bc9d25d2f408b13b2551351
+size 4864

data/fold_1/Adrenal_gland_1_01191.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8129f1b1e7c79a99b298f916574c0e89f39d08ae9d33732d4bafe23ea1ba1c17
+size 4864

data/fold_1/Adrenal_gland_1_01192.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:21f09353f6143b8b296a2789bf7e2aef733edb78bce64a8dbfd203038faf99e1
+size 4864

data/fold_1/Adrenal_gland_1_01193.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1b86561b593691a3a5f9bd3181cc1ae40a3af218903384e124e8db4ae19b19a5
+size 9024

data/fold_1/Adrenal_gland_1_01194.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f062658a572888c6596f425576f06db3cc85ce2a2e9c13bacb62a8f54bda91c6
+size 5824

data/fold_1/Adrenal_gland_1_01195.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:67fc4de26500753197a00c56e2ee1ffe0ea4016f115cb6b576cfa0db01227213
+size 6720

data/fold_1/Adrenal_gland_1_01196.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ed9efa5447f805c60a34578f1e7927c307b225ea5738794570354f64712569fb
+size 7552

data/fold_1/Adrenal_gland_1_01197.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2ef36d19419b45666c6b7157b4dd0b3e66fee243f3784dc2dea127c330ce3753
+size 7552

data/fold_1/Adrenal_gland_1_01198.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:24d8eeee88363fe6c70b937a9efbfc86e41c5aac999c8ee4925fdf1d38872ef1
+size 9088

data/fold_1/Adrenal_gland_1_01199.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8ff07bb561226316abf5f921d4c2005872825fac14f69fe3290a548d45f24932
+size 8576

data/fold_1/Adrenal_gland_1_01200.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0fa11a6a29d8876f88c864032a2623704f7588997df02d12b8778b8c16d38dd3
+size 6272

data/fold_1/Adrenal_gland_1_01201.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:531ebea563dd1e86d7ec134eaa3ff5b6dfd0e8ad2cc4830a08cdee313b052627
+size 6720

data/fold_1/Adrenal_gland_1_01202.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fbc6febab1b491786d838b4b5c130ecc0464ff00e0be736c3ebde02062fc878a
+size 9472

data/fold_1/Adrenal_gland_1_01203.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9316174fe323dad4fbf988d96b644b34046dc81e30a9dae64c89dd47f0c9a45b
+size 7168

data/fold_1/Adrenal_gland_1_01204.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9aa78538ad341ba99b68feb6440d0479e3ce6b8c96296917de717b99fde76699
+size 5440

data/fold_1/Adrenal_gland_1_01205.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b83feda902ab39f747880ab5a6aafe876686f7d82926df8d20c24d1148a56f0f
+size 4032

data/fold_1/Adrenal_gland_1_01206.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:00fc439b58840428e8fd5fb670d297c7497b34bf43c3bc62a8294eadf3e67da5
+size 7552

data/fold_1/Adrenal_gland_1_01207.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:204363565d2a03e3e95c75aca23f1487dcee044d29949521ea003acb89da7932
+size 7552

data/fold_1/Adrenal_gland_1_01208.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a208b7ae1901740953459c92ff2a02f6ab222a3b18d2efcea65a9d453dc72b35
+size 7104

data/fold_1/Adrenal_gland_1_01209.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8530fc114f6fb98570cbb05c43fcc51555ff8ab35aa419c0335917795ec7e38d
+size 6336

data/fold_1/Adrenal_gland_1_01210.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7a2c331fbfec405842ddb52eb5c96e7ee98cecd9fcfaeeabde21c3dbfda1349a
+size 6720

data/fold_1/Adrenal_gland_1_01212.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f3abd24c6d52ef446d9fd18a5b5c8a2849edbd98b1d83eca3d5a2cf362453445
+size 5888

data/fold_1/Adrenal_gland_1_01213.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:28453ade6f9ec02c748a284f55d19ae8ec25c035951b50cddb690c475b7146a2
+size 5376

data/fold_1/Adrenal_gland_1_01214.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:20770eaf562eb4a346293171a5e7bf25ef6e872e2c0cc1a19b25b3232593ee7f
+size 5440

data/fold_1/Adrenal_gland_1_01215.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b9bd9477722bdfd92bf42bccc8d7e2b55e5a55be52ee51d46e3f8a222f72cc9c
+size 5888

data/fold_1/Adrenal_gland_1_01216.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:53ca6e7a1c6996437f1a8b53bb1ac3798ff885c736b1c4c3859c8047efce5c78
+size 5824

data/fold_1/Adrenal_gland_1_01217.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:20a83ed9caf6c07f5c699f5ebc33513f26d62e52158ad29b40ccb97ff6480dc1
+size 5888

data/fold_1/Adrenal_gland_1_01218.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:68913ecb888d1bba4d7a2a04abfd9e461a807c6584438b6c9384be0d421a81f5
+size 8128

data/fold_1/Adrenal_gland_1_01264.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3152b5104b0cdf0c9598ff0c23beb6c226df6c61d54e1af3ed0b9b594ace8a18
+size 11712