dbonet paumateo commited on
Commit
da05564
·
0 Parent(s):

Publish current dataset release

Browse files

Co-authored-by: paumateo <paumateo@users.noreply.huggingface.co>

Files changed (7) hide show
  1. .gitattributes +60 -0
  2. NOTICE.md +17 -0
  3. README.md +70 -0
  4. data/test.parquet +3 -0
  5. data/train.parquet +3 -0
  6. data/val.parquet +3 -0
  7. metadata.json +29 -0
.gitattributes ADDED
@@ -0,0 +1,60 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ *.7z filter=lfs diff=lfs merge=lfs -text
2
+ *.arrow filter=lfs diff=lfs merge=lfs -text
3
+ *.avro filter=lfs diff=lfs merge=lfs -text
4
+ *.bin filter=lfs diff=lfs merge=lfs -text
5
+ *.bz2 filter=lfs diff=lfs merge=lfs -text
6
+ *.ckpt filter=lfs diff=lfs merge=lfs -text
7
+ *.ftz filter=lfs diff=lfs merge=lfs -text
8
+ *.gz filter=lfs diff=lfs merge=lfs -text
9
+ *.h5 filter=lfs diff=lfs merge=lfs -text
10
+ *.joblib filter=lfs diff=lfs merge=lfs -text
11
+ *.lfs.* filter=lfs diff=lfs merge=lfs -text
12
+ *.lz4 filter=lfs diff=lfs merge=lfs -text
13
+ *.mds filter=lfs diff=lfs merge=lfs -text
14
+ *.mlmodel filter=lfs diff=lfs merge=lfs -text
15
+ *.model filter=lfs diff=lfs merge=lfs -text
16
+ *.msgpack filter=lfs diff=lfs merge=lfs -text
17
+ *.npy filter=lfs diff=lfs merge=lfs -text
18
+ *.npz filter=lfs diff=lfs merge=lfs -text
19
+ *.onnx filter=lfs diff=lfs merge=lfs -text
20
+ *.ot filter=lfs diff=lfs merge=lfs -text
21
+ *.parquet filter=lfs diff=lfs merge=lfs -text
22
+ *.pb filter=lfs diff=lfs merge=lfs -text
23
+ *.pickle filter=lfs diff=lfs merge=lfs -text
24
+ *.pkl filter=lfs diff=lfs merge=lfs -text
25
+ *.pt filter=lfs diff=lfs merge=lfs -text
26
+ *.pth filter=lfs diff=lfs merge=lfs -text
27
+ *.rar filter=lfs diff=lfs merge=lfs -text
28
+ *.safetensors filter=lfs diff=lfs merge=lfs -text
29
+ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
30
+ *.tar.* filter=lfs diff=lfs merge=lfs -text
31
+ *.tar filter=lfs diff=lfs merge=lfs -text
32
+ *.tflite filter=lfs diff=lfs merge=lfs -text
33
+ *.tgz filter=lfs diff=lfs merge=lfs -text
34
+ *.wasm filter=lfs diff=lfs merge=lfs -text
35
+ *.xz filter=lfs diff=lfs merge=lfs -text
36
+ *.zip filter=lfs diff=lfs merge=lfs -text
37
+ *.zst filter=lfs diff=lfs merge=lfs -text
38
+ *tfevents* filter=lfs diff=lfs merge=lfs -text
39
+ # Audio files - uncompressed
40
+ *.pcm filter=lfs diff=lfs merge=lfs -text
41
+ *.sam filter=lfs diff=lfs merge=lfs -text
42
+ *.raw filter=lfs diff=lfs merge=lfs -text
43
+ # Audio files - compressed
44
+ *.aac filter=lfs diff=lfs merge=lfs -text
45
+ *.flac filter=lfs diff=lfs merge=lfs -text
46
+ *.mp3 filter=lfs diff=lfs merge=lfs -text
47
+ *.ogg filter=lfs diff=lfs merge=lfs -text
48
+ *.wav filter=lfs diff=lfs merge=lfs -text
49
+ # Image files - uncompressed
50
+ *.bmp filter=lfs diff=lfs merge=lfs -text
51
+ *.gif filter=lfs diff=lfs merge=lfs -text
52
+ *.png filter=lfs diff=lfs merge=lfs -text
53
+ *.tiff filter=lfs diff=lfs merge=lfs -text
54
+ # Image files - compressed
55
+ *.jpg filter=lfs diff=lfs merge=lfs -text
56
+ *.jpeg filter=lfs diff=lfs merge=lfs -text
57
+ *.webp filter=lfs diff=lfs merge=lfs -text
58
+ # Video files - compressed
59
+ *.mp4 filter=lfs diff=lfs merge=lfs -text
60
+ *.webm filter=lfs diff=lfs merge=lfs -text
NOTICE.md ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Source and license notices: HIV
2
+
3
+ ## NCI AIDS Antiviral Screen
4
+
5
+ Source: https://wiki.nci.nih.gov/display/NCIDTPdata/AIDS+Antiviral+Screen+Data
6
+
7
+ Attribution: National Cancer Institute Developmental Therapeutics Program, AIDS Antiviral Screen (May 2004 release). MoleculeNet: Wu et al., DOI 10.1039/C7SC02664A.
8
+
9
+ Source terms: https://www.cancer.gov/policies/copyright-reuse
10
+
11
+ Credit the National Cancer Institute as the source. The DTP/NCI PubChem source record provides the NCI reuse terms.
12
+
13
+ ## Modifications
14
+
15
+ Experimentally measured abilities of small molecules to inhibit HIV replication. Binary classification task. Features: Morgan fingerprints (radius=2). Split: scaffold-based 70/15/15 (DeepChem ScaffoldSplitter).
16
+
17
+ TabBioMed preprocessing and stored benchmark partitions are described in metadata.json and https://github.com/AI-sandbox/TabBioMed. No original author endorsement is implied.
README.md ADDED
@@ -0,0 +1,70 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ pretty_name: HIV
3
+ task_categories:
4
+ - tabular-classification
5
+ tags:
6
+ - tabular
7
+ - biomedical
8
+ - benchmark
9
+ - TabBioMed
10
+ - drug-discovery
11
+ - binary
12
+ size_categories:
13
+ - 10K<n<100K
14
+ configs:
15
+ - config_name: default
16
+ data_files:
17
+ - split: train
18
+ path: data/train.parquet
19
+ - split: validation
20
+ path: data/val.parquet
21
+ - split: test
22
+ path: data/test.parquet
23
+ ---
24
+
25
+ # HIV
26
+
27
+ Part of **TabBioMed** (*TabBioMed: A Large-Scale Benchmark for Biomedical Tabular Learning*), a benchmark of 94 curated biomedical
28
+ tabular datasets. Code, preprocessing and documentation: https://github.com/AI-sandbox/TabBioMed.
29
+
30
+ Experimentally measured abilities of small molecules to inhibit HIV replication. Binary classification task. Features: Morgan fingerprints (radius=2). Split: scaffold-based 70/15/15 (DeepChem ScaffoldSplitter).
31
+
32
+ | Domain | Task | Samples | Features | Classes |
33
+ |---|---|---|---|---|
34
+ | Drug Discovery | binary | 41,120 | 1,024 | 2 |
35
+
36
+ **Splits.** Fixed train/val/test split (28783/6169/6168 rows).
37
+
38
+ ## Files
39
+
40
+ - `data/**.parquet`: one row per sample. `row_idx` is the row index in the original
41
+ TabBioMed array; `f_<i>[_<name>]` are the features (in order); `target` (or `target_<j>`
42
+ for multi-target tasks) is the label. Categorical feature indices (0-based, among the
43
+ features): `[]`. Missing values are stored as nulls.
44
+ - `metadata.json`: TabBioMed task metadata (task type, categorical indices, source, description).
45
+
46
+
47
+ ```python
48
+ from datasets import load_dataset
49
+ ds = load_dataset("TabBioMed/HIV")
50
+ ```
51
+
52
+ A Croissant (1.1) description with Responsible-AI fields is distributed with the
53
+ TabBioMed release.
54
+
55
+ ## Source and license
56
+
57
+ - [NCI AIDS Antiviral Screen](https://wiki.nci.nih.gov/display/NCIDTPdata/AIDS+Antiviral+Screen+Data). National Cancer Institute Developmental Therapeutics Program, AIDS Antiviral Screen (May 2004 release). MoleculeNet: Wu et al., DOI 10.1039/C7SC02664A. [Source terms](https://www.cancer.gov/policies/copyright-reuse). Credit the National Cancer Institute as the source. The DTP/NCI PubChem source record provides the NCI reuse terms.
58
+
59
+ See `NOTICE.md` for attribution and modifications.
60
+
61
+ ## Citation
62
+
63
+ ```bibtex
64
+ @inproceedings{tabbiomed2026,
65
+ title = {TabBioMed: A Large-Scale Benchmark for Biomedical Tabular Learning},
66
+ author = {Mateo Bernad{\'o}, Pau and Polapragada, Saivenkata Nagavyjayanthi and Bonet, David and Arbiol Rakuljic, Pol and Mogas Pladevall, Laia and Comajoan Cara, Mar{\c{c}}al and Gonzalez Ferrer, Jesus and Abante, Jordi and Mas Montserrat, Daniel and Haussler, David and Ioannidis, Alexander G.},
67
+ booktitle = {Advances in Neural Information Processing Systems (NeurIPS), Evaluations and Datasets Track},
68
+ year = {2026}
69
+ }
70
+ ```
data/test.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e291516735d4eb75316b6ec668ca61ac6afe3329353c8ddc47c44923593cfe68
3
+ size 952467
data/train.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:928a8d6abd06ec783414673ece443aa0bbe369440acdc7db8123949ee904801d
3
+ size 1988473
data/val.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:1503367499eb25ae90fda08c0afcfc60ed47c4c1ccd8831a75aa521f5bbe2136
3
+ size 944661
metadata.json ADDED
@@ -0,0 +1,29 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "READY": true,
3
+ "name": "HIV",
4
+ "task": "binary",
5
+ "num_classes": 2,
6
+ "cat_idx": [],
7
+ "num_samples": 41120,
8
+ "num_features": 1024,
9
+ "imbalance_ratio": 27.4962,
10
+ "description": "Experimentally measured abilities of small molecules to inhibit HIV replication. Binary classification task. Features: Morgan fingerprints (radius=2). Split: scaffold-based 70/15/15 (DeepChem ScaffoldSplitter).",
11
+ "source": "MoleculeNet (https://moleculenet.org) — loaded via DeepChem.",
12
+ "label": "Drug Discovery",
13
+ "sub_labels": [
14
+ "Biophysics",
15
+ "Fingerprint"
16
+ ],
17
+ "license": null,
18
+ "license_url": null,
19
+ "source_licenses": [
20
+ {
21
+ "id": "hiv",
22
+ "title": "NCI AIDS Antiviral Screen",
23
+ "url": "https://wiki.nci.nih.gov/display/NCIDTPdata/AIDS+Antiviral+Screen+Data",
24
+ "license": null,
25
+ "license_url": null,
26
+ "terms_url": "https://www.cancer.gov/policies/copyright-reuse"
27
+ }
28
+ ]
29
+ }