Datasets:

Hierarchy-Transformers
/

DOID

child stringlengths 4 125	parent stringlengths 4 125	label int64 0 1
froelich syndrome	hypothalamic disease	1
froelich syndrome	androgenic alopecia	0
froelich syndrome	pleomorphic lipoma	0
froelich syndrome	intracranial structure hemangioma	0
froelich syndrome	pontocerebellar hypoplasia type 1	0
froelich syndrome	jansen's metaphyseal chondrodysplasia	0
froelich syndrome	autosomal recessive intellectual developmental disorder 5	0
froelich syndrome	vertebral artery insufficiency	0
froelich syndrome	erythrokeratodermia variabilis et progressiva 6	0
froelich syndrome	thyroid gland medullary carcinoma	0
froelich syndrome	cerebrotendinous xanthomatosis	0
testicular pure germ cell tumor	testicular germ cell cancer	1
testicular pure germ cell tumor	testicular malignant germ cell cancer	0
testicular pure germ cell tumor	childhood testicular germ cell tumor	0
testicular pure germ cell tumor	testicular germ cell tumor non-seminomatous	0
testicular pure germ cell tumor	autosomal dominant intellectual developmental disorder 46	0
testicular pure germ cell tumor	noonan syndrome 7	0
testicular pure germ cell tumor	hemosiderosis	0
testicular pure germ cell tumor	selective igg deficiency disease	0
testicular pure germ cell tumor	clear cell sarcoma	0
testicular pure germ cell tumor	familial hypobetalipoproteinemia 1	0
testicular pure germ cell tumor	rafiq syndrome	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	immunodeficiency-centromeric instability-facial anomalies syndrome	1
immunodeficiency-centromeric instability-facial anomalies syndrome 4	immunodeficiency-centromeric instability-facial anomalies syndrome 1	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	immunodeficiency-centromeric instability-facial anomalies syndrome 2	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	immunodeficiency-centromeric instability-facial anomalies syndrome 3	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	ewing sarcoma	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	bronchiectasis	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	fallopian tube benign neoplasm	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	spermatogenic failure 60	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	seminal vesicle chronic gonorrhea	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	intracranial structure hemangioma	0
immunodeficiency-centromeric instability-facial anomalies syndrome 4	choroid plexus carcinoma	0
epithelioid trophoblastic tumor	cervical cancer	1
epithelioid trophoblastic tumor	cervical carcinosarcoma	0
epithelioid trophoblastic tumor	cervical alveolar soft part sarcoma	0
epithelioid trophoblastic tumor	cervix melanoma	0
epithelioid trophoblastic tumor	cervix endometrial stromal tumor	0
epithelioid trophoblastic tumor	cervix carcinoma	0
epithelioid trophoblastic tumor	cervical adenosquamous carcinoma	0
epithelioid trophoblastic tumor	muscular dystrophy	0
epithelioid trophoblastic tumor	periapical granuloma	0
epithelioid trophoblastic tumor	combined oxidative phosphorylation deficiency 46	0
epithelioid trophoblastic tumor	syndromic x-linked intellectual disorder lujan-fryns-type	0
wissler-fanconi syndrome	syndrome	1
wissler-fanconi syndrome	doors syndrome	0
wissler-fanconi syndrome	ladd syndrome	0
wissler-fanconi syndrome	ollier disease	0
wissler-fanconi syndrome	trichorhinophalangeal syndrome type iii	0
wissler-fanconi syndrome	beckwith-wiedemann syndrome	0
wissler-fanconi syndrome	trichodontoosseous syndrome	0
wissler-fanconi syndrome	kinsship syndrome	0
wissler-fanconi syndrome	proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome	0
wissler-fanconi syndrome	shwachman-diamond syndrome	0
wissler-fanconi syndrome	van der woude syndrome	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism	1
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 11 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 21 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 1 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 13 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 12 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 4 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 24 without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 16 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 20 with or without anosmia	0
hypogonadotropic hypogonadism 10 with or without anosmia	hypogonadotropic hypogonadism 6 with or without anosmia	0
mononeuritis	mononeuropathy	1
mononeuritis	peroneal neuropathy	0
mononeuritis	femoral neuropathy	0
mononeuritis	tibial neuropathy	0
mononeuritis	radial neuropathy	0
mononeuritis	ulnar neuropathy	0
mononeuritis	ovarian mesodermal adenosarcoma	0
mononeuritis	pneumonic plague	0
mononeuritis	partial arterial retinal occlusion	0
mononeuritis	prostate adenocarcinoma	0
mononeuritis	bacterial esophagitis	0
periodontosis	tooth disease	1
periodontosis	teeth hard tissue disease	0
periodontosis	dental abscess	0
periodontosis	anodontia	0
periodontosis	primary failure of tooth eruption	0
periodontosis	dentinogenesis imperfecta	0
periodontosis	tooth agenesis	0
periodontosis	dental fluorosis	0
periodontosis	solitary median maxillary central incisor	0
periodontosis	dental pulp disease	0
periodontosis	combined oxidative phosphorylation deficiency 8	0
familial mediterranean fever	autoimmune disease	1
familial mediterranean fever	mikulicz disease	0
familial mediterranean fever	autoimmune disease of urogenital tract	0
familial mediterranean fever	lupus erythematosus	0
familial mediterranean fever	antisynthetase syndrome	0
familial mediterranean fever	autoimmune disease of exocrine system	0
familial mediterranean fever	autoimmune disease of cardiovascular system	0
familial mediterranean fever	granulomatosis with polyangiitis	0
familial mediterranean fever	vitiligo	0
familial mediterranean fever	cinca syndrome	0
familial mediterranean fever	autoimmune disease of eyes, ear, nose and throat	0
urocanase deficiency	histidine metabolism disease	1

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Dataset Card for DOID

This dataset is a collection of Mixed-hop Prediction datasets created from DOID's subsumption hierarchy (TBox) for evaluating hierarchy embedding models.

Mixed-hop Prediction: This task aims to evaluate the model’s capability in determining the existence of subsumption relationships between arbitrary entity pairs, where the entities are not necessarily seen during training. The transfer setting of this task involves training models on asserted training edges of one hierarchy testing on arbitrary entity pairs of another.

See our published paper for more detail.

Dataset Structure

Each subset in this dataset follows the naming convention TaskType-NegativeType-SampleStructure:

TaskType: Either MultiHop or MixedHop, indicating the type of hierarchy evaluation task.

In this dataset, only MixedHop is available.

NegativeType: Either RandomNegatives or HardNegatives, specifying the strategy used for negative sampling.
SampleStructure: Either Triplets or Pairs, indicating the format of the samples.
- In Triplets, each sample is structured as (child, parent, negative).
- In Pairs, each sample is a labelled pair (child, parent, label), where label=1 denotes a positive subsumption and label=0 denotes a negative subsumption.

For example, to load a subset for the Mixed-hop Prediction task with random negatives and samples presented as triplets, we can use the following command:

from datasets import load_dataset
dataset = load_dataset("Hierarchy-Transformers/DOID", "MixedHop-RandomNegatives-Triplets")

Dataset Usage

For evaluation, the Pairs sample structure should be adopted, as it allows for the computation of Precision, Recall, and F1 scores.
For training, the choice between Pairs, Triplets, or more complex sample structures depends on the model's design and specific requirements.

Citation

The relevant paper has been accepted at NeurIPS 2024 (to appear).

@article{he2024language,
  title={Language models as hierarchy encoders},
  author={He, Yuan and Yuan, Zhangdie and Chen, Jiaoyan and Horrocks, Ian},
  journal={arXiv preprint arXiv:2401.11374},
  year={2024}
}

Contact

Yuan He (yuan.he(at)cs.ox.ac.uk)

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Dataset Card for DOID

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Dataset Structure

Dataset Usage

Citation

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