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

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.

Links

The information of original entity IDs is not available in the Huggingface release; To map entities back to their original hierarchies, refer to this Zenodo release.

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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