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smamooler
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PICLe

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Token Classification

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bc2gm

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The dataset generation failed because of a cast error

Error code:   DatasetGenerationCastError
Exception:    DatasetGenerationCastError
Message:      An error occurred while generating the dataset

All the data files must have the same columns, but at some point there are 2 new columns ({'pmid', 'offsets'}) and 1 missing columns ({'id'}).

This happened while the json dataset builder was generating data using

hf://datasets/smamooler/PICLe/chemprotchem/test_sentence.json (at revision 46c05f4a01c03d19caaf49217a4eb945726a10c5)

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1871, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 623, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2293, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2241, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              pmid: string
              text: string
              type: string
              entities: list<item: string>
                child 0, item: string
              offsets: list<item: list<item: int64>>
                child 0, item: list<item: int64>
                    child 0, item: int64
              -- schema metadata --
              pandas: '{"index_columns": [], "column_indexes": [], "columns": [{"name":' + 672
              to
              {'id': Value(dtype='string', id=None), 'type': Value(dtype='string', id=None), 'text': Value(dtype='string', id=None), 'entities': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None)}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1438, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1050, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 925, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1001, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1742, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1873, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 2 new columns ({'pmid', 'offsets'}) and 1 missing columns ({'id'}).
              
              This happened while the json dataset builder was generating data using
              
              hf://datasets/smamooler/PICLe/chemprotchem/test_sentence.json (at revision 46c05f4a01c03d19caaf49217a4eb945726a10c5)
              
              Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)

Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

id string	type string	text string	entities sequence
0	gene	Physical mapping 220 kb centromeric of the human MHC and DNA sequence analysis of the 43 - kb segment including the RING1 , HKE6 , and HKE4 genes .	[ "human MHC", "RING1", "HKE6", "HKE4 genes" ]
1	gene	The synthesis of endo - adduct [ 4aS , 5S , 8R , 8aR , SS ] - 9d resulting from cycloaddition on the substituted C ( 2 ) - C ( 3 ) double bond was achieved in a chemo - and diastereoselective way from quinone 1d in the presence of ZnBr ( 2 ) .	[]
2	gene	DNA elements recognizing NF - Y and Sp1 regulate the human multidrug - resistance gene promoter .	[ "NF - Y", "Sp1", "human multidrug - resistance gene promoter" ]
3	gene	Radioimmunoassay of plasma gonadotropins ; problems of specificity	[ "plasma gonadotropins" ]
4	gene	Patients randomized into the active treatment groups A30 ( n = 49 ) and A60 ( n = 48 ) received topical treatment with 3 . 0 % diclofenac in 2 . 5 % hyaluronan gel 0 . 5 g twice daily for 30 or 60 days , respectively .	[]
5	gene	As tat itself dramatically increases HIV - 1 gene expression , it too is presumably regulated in the latent state , and may also be activated by mitogenic stimulation .	[ "tat" ]
6	gene	To clarify the difference , both the Crk II and Crk II - 23 , proteins were expressed in E . coli and examined their binding capacity in vitro .	[ "Crk II", "Crk II - 23" ]
7	gene	CONCLUSIONS : Systemic factors that increase bone mineral density appear to be involved in the pathogenesis of ossification of the posterior longitudinal ligament , and these factors may be activated after middle age .	[]
8	gene	Thus , in V . furnissii , the E . coli manX equivalent comprises two genes , which are separated in the genome by two other genes of the ptsM complex .	[ "E . coli manX equivalent", "ptsM complex" ]
9	gene	Id - 1H and Id - 2H seem to be human homologues of mouse Id - 1 and Id - 2 , respectively , and have potential to encode 154 and 135 amino acid proteins .	[ "Id - 1H", "Id - 2H", "mouse Id - 1", "Id - 2" ]
10	gene	Characterization of insertion mutations in the Saccharomyces cerevisiae MSH1 and MSH2 genes : evidence for separate mitochondrial and nuclear functions .	[ "Saccharomyces cerevisiae MSH1", "MSH2 genes" ]
11	gene	Transcription of FN promoter - chloramphenicol acetyltransferase fusion genes carrying the base substitution in one or more of these G - rich sequences both in vivo and in vitro revealed that the base substitution in any G - rich sequence results in reduction of promoter activity , although the downstream GC box ( GCd ) plays a primary role .	[ "FN promoter", "chloramphenicol acetyltransferase" ]
12	gene	Morphologically , corrugation of the internal elastic lamina of vessels was often observed in the vehicle - treated group , but was not prominent in the GLNVA - treated groups or healthy controls .	[]
13	gene	A GT - rich sequence binding the transcription factor Sp1 is crucial for high expression of the human type VII collagen gene ( COL7A1 ) in fibroblasts and keratinocytes .	[ "transcription factor Sp1", "human type VII collagen gene", "COL7A1" ]
14	gene	Each received 20 mL of one of three test solutions : levobupivacaine control , levobupivacaine and fentanyl 2 microg / mL , or levobupivacaine and fentanyl 3 microg / mL .	[]
15	gene	The XPR2 gene from Yarrowia lipolytica encodes an inducible alkaline extracellular protease .	[ "XPR2 gene", "alkaline extracellular protease" ]
16	gene	CONCLUSIONS : This study shows that the annual rate of de novo aneurysm formation is relatively high ( 0 . 89 % ) and that the cumulative risk becomes significant after 9 years .	[]
17	gene	It was found that Nopp140 binds primarily to the CK2 regulatory subunit , beta .	[ "Nopp140", "CK2 regulatory subunit , beta" ]
18	gene	Juvenile idiopathic inflammatory myopathies : the value of magnetic resonance imaging in the detection of muscle involvement .	[]
19	gene	Previous analysis of this motif in the lactose permease ( A .	[ "lactose permease" ]
20	gene	Combined chemotherapy with VM 26 and BCNU for recurrent malignant gliomas after operation and irradiation .	[]
21	gene	Like other IAPs , ch - IAP1 contains the N - terminal baculovirus IAP repeats and C - terminal RING finger motifs .	[ "IAPs", "ch - IAP1", "N - terminal baculovirus IAP repeats" ]
22	gene	Effects of long - term use of raloxifene , a selective estrogen receptor modulator , on thyroid function test profiles .	[ "estrogen receptor" ]
23	gene	The donors of 10 patients were ABO - incompatible , and for five pairs the ABO incompatibility was major .	[]
24	gene	Alternative splicing of the human serotonin transporter gene .	[ "human serotonin transporter gene" ]
25	gene	Interestingly , basal MAPK , but not Raf - 1 , activity was constitutively enhanced in Jak1 - deficient HeLa cells .	[ "MAPK", "Raf - 1", "Jak1" ]
26	gene	This case report describes the treatment of a patient with periodontosis .	[]
27	gene	The aim of this work was to organize chemical data in a client - server environment using Database Management System and Web fashion for the client interface .	[]
28	gene	Cerumen management in hearing conservation : the Dallas ( Texas ) Independent School District program .	[]
29	gene	Lactate , pyruvate and actual pH values in the venous blood of newborn calves	[]
30	gene	This article focuses on a general approach to the use of ARV agents .	[]
31	gene	Platelets and RBCs from each animal were labeled with 51Cr and 99mTc , respectively , and were rapidly injected into the right atrium while blood was sampled from the ascending aorta .	[]
32	gene	The comparisons of swimming performance before and after treatments with deltamethrin have shown a significant effect on locomotory ability of rainbow trout which at the end of strong exposure ( e . g .	[]
33	gene	Protection levels of 33 . 3 % , 36 . 6 % and 37 . 0 % were achieved in groups which had received , respectively , 1000 20 - krad cercariae , 1000 10 - krad cercariae , 2000 40 - krad cercariae and 2000 60 - krad cercariae .	[]
34	gene	In Types I and II , capillary walls became thinner and more capillary lumens were visiable .	[]
35	gene	Thus , primate vs . rodent promoter selectivity mediated by the TBP - TAFI complex is likely to be the result of cumulative subtle differences between individual subunits that lead to species - specific properties of RNA polymerase I transcription .	[ "TBP", "TAFI", "RNA polymerase I" ]
36	gene	The effects of pretreatment with the non - competitive NMDA antagonist ( + ) MK - 801 on the behavioral alterations induced by repeated restraint stress were investigated .	[]
37	gene	When gene conversion is initiated by a double - strand break ( DSB ) , any nonhomologous DNA that may be present at the ends must be removed before new DNA synthesis can be initiated .	[]
38	gene	In this reconstituted system , RNAP IIA , but not RNAP IIB , can transcribe from the DHFR promoter .	[ "RNAP IIA", "RNAP IIB", "DHFR promoter" ]
39	gene	The cDNA clones encode a polypeptide of 657 amino acids with a bHLH ( basic - helix - loop - helix ) domain , characteristic of a large family of transcription factors , and a PAS ( Per - Arnt - Sim ) domain in the amino - terminal half region .	[ "PAS", "Per", "Arnt", "Sim" ]
40	gene	FTF ( Joint Council of Civil Servants and Functionaries ) : clarification about membership in the main organizations	[]
41	gene	Lumbar spine bone mineral density ( BMD ) by dual - energy X - ray absorptiometry ( DXA ) increased by 0 . 6 % , 3 . 6 % and 8 . 1 % after 48 weeks in groups L , M and H respectively , responses in groups M and H being significantly higher than in L ( p < 0 . 05 , Mann - Whitney U - test ) .	[]
42	gene	Synergy between interferon - gamma and tumor necrosis factor - alpha in transcriptional activation is mediated by cooperation between signal transducer and activator of transcription 1 and nuclear factor kappaB .	[ "interferon - gamma", "tumor necrosis factor - alpha", "signal transducer and activator of transcription 1", "nuclear factor kappaB" ]
43	gene	1H and 15N magnetic resonance assignments , secondary structure , and tertiary fold of Escherichia coli DnaJ ( 1 - 78 ) .	[ "Escherichia coli DnaJ ( 1 - 78 )" ]
44	gene	A cDNA for human microfibril - associated glycoprotein - 2 ( MAGP - 2 ) was used to screen a human leukocyte genomic DNA library in EMBL - 3 vector .	[ "human microfibril - associated glycoprotein - 2", "MAGP - 2" ]
45	gene	Furthermore , ERK phosphorylation was substantially prolonged in LC / BRY - treated cells compared to those exposed to BRY alone , and pretreatment with the highly specific MEK inhibitors , PD98059 , U0126 , and SL327 , opposed ERK activation while protecting cells from LC / BRY - induced lethality .	[ "ERK", "MEK", "ERK" ]
46	gene	The cholesterol 7alpha - hydroxylase gene ( CYP7A ) is transcriptionally regulated by a number of factors , including hormones , bile acids , and diurnal rhythm .	[ "cholesterol 7alpha - hydroxylase gene", "CYP7A" ]
47	gene	CNS preventive treatment without cranial irradiation was effective in all the groups of ALL patients .	[]
48	gene	Additionally , the members of this family display strong sequence homologies between their larger C - terminal effector binding / oligomerization domains .	[]
49	gene	Aspartame is a synthetic sweetener commonly used in soft drinks and many foods .	[]
50	gene	The rat anococcygeus muscle was used in postsynaptic studies .	[]
51	gene	The purpose of this presentation is to review the current state of knowledge regarding 5 , 8 , 11 , 14 - eicosatetraynoic acid ( ETYA , Ro 3 - 1428 ) and its effects on lipid metabolism .	[]
52	gene	A Meis1 cDNA clone that encoded a novel member of the homeobox gene family was identified .	[ "Meis1 cDNA", "homeobox gene family" ]
53	gene	The S . typhimurium aspartyl / asparaginyl beta - hydroxylase homologue ( designated lpxO ) was cloned into pBluescriptSK and expressed in Escherichia coli K - 12 , which does not contain lpxO .	[ "S . typhimurium aspartyl / asparaginyl beta - hydroxylase homologue", "lpxO", "lpxO" ]
54	gene	The levels of soluble L - selectin and ICAM - 1 in the serum were determined by the ELISA method .	[ "L - selectin", "ICAM - 1" ]
55	gene	The highest TTX content is 10 . 0 microg / g in N . livescens .	[ "TTX" ]
56	gene	On the other hand hypokalemia , induced by diuretics , may also be accompanied by a significant depletion of total body K , bringing about more general consequences .	[]
57	gene	Glutathione reductase activities in liver , kidney , lung , and brain were not affected by diet .	[ "Glutathione reductase" ]
58	gene	Here , we describe the nucleotide ( nt ) sequence and genomic organization of ipiB and ipiO .	[ "ipiB", "ipiO" ]
59	gene	Vancomycin and tetracycline eliminated toxin in stools and delayed death .	[]
60	gene	Soluble fibrin monomer complexes in thromboembolism	[ "fibrin" ]
61	gene	Comparison to the murine homologues of these molecules reveals a high degree of conservation between the products of one of these genes , Fc gamma RIIb , and the murine beta gene in primary sequence , splicing pattern , and tissue distribution .	[ "Fc gamma RIIb", "murine beta gene" ]
62	gene	Acidosis provoked by 30 % CO2 irreversibly increased the BDRT , however the TRT were not changed .	[]
63	gene	Others as for example C - 11 labeled short chain fatty acids are on the horizon .	[]
64	gene	The average progression was 11 . 6 ( SD 9 . 0 ) .	[]
65	gene	80 bp ) surrounding the site of transcription initiation .	[]
66	gene	Ultrastructure and toxin formation of Cor . diphtheriae PW - 8 cultured in the presence of penicillin	[]
67	gene	EMT was localized to chromosome 5q31 - 32 , a region that contains the genes for several growth factors and receptors as well as early activation genes , particularly those involved in the hematopoietic system .	[ "EMT" ]
68	gene	Tbx6 maps to chromosome 7 and does not appear to be linked to any known mutation .	[ "Tbx6" ]
69	gene	Kaposi ' s eruptive disease .	[]
70	gene	It is not tested yet , whether the extent of glaucoma damage should be better quantified using reference plane 1 or 2 .	[]
71	gene	Importin beta mediates nuclear translocation of Smad 3 .	[ "Importin beta", "Smad 3" ]
72	gene	The encoded protein contains an amino terminal PDZ domain , followed by a predicted coiled - coil region , a PEST domain , and a carboxy - terminal SAM domain .	[ "PDZ" ]
73	gene	Using lasers , PRK involves reshaping the cornea so that its refractive power is increased .	[]
74	gene	However , sphincter length decreased with age from 24 . 3 to 14 . 8 mm . , maximal urethral pressure from 88 . 7 to 55 cm . water and maximal urethral pressure during voluntary contraction from 221 . 4 to 166 . 3 cm . water .	[]
75	gene	Several studies have demonstrated that the corticotropin - releasing factor test ( CRF ) is useful for the aetiological diagnosis of Cushing ' s syndrome : in Cushing ' s disease , as opposed to ectopic ACTH secretion syndrome , the hypothalamus - pituitary - adrenal ( HPA ) axis can still be stimulated by CRF .	[ "corticotropin - releasing factor", "CRF", "ACTH", "CRF" ]
76	gene	Transcription initiation from this region was also detected in vivo , when the cloned rRNA gene cluster was present on a multi - copy plasmid .	[]
77	gene	The results of the transient - transfection assay showed that the Sp1 binding element located in the core region ( positions - - 64 to + 1 ) of the alpha2 - integrin promoter plays an essential role in the alpha2 - integrin promoter activity and its downregulation by Erb - B2 .	[ "Sp1 binding element", "alpha2 - integrin promoter", "alpha2 - integrin promoter", "Erb", "B2" ]
78	gene	Principal component analysis using psychosocial factors in women showed two psychosocial structures , i . e . the second principal ( high SOC , high lifestyle , and low stress ) and the 4th principal components ( high supernatural HLC , and high PHLC ) .	[]
79	gene	Expression of FNCAT increased on serum treatment indicating that the region of the FN gene between positions + 69 and - 510 bp mediated serum responsiveness .	[ "FNCAT", "FN gene" ]
80	gene	Interaction of the v - rel protein with an NF - kappa B DNA binding site .	[ "v - rel protein", "NF - kappa B DNA binding site" ]
81	gene	This increase is not the result of alterations in the deposition of inhaled particles of capsaicin brought about by volume restriction .	[]
82	gene	Providing appropriate care to both sexes .	[]
83	gene	To test this hypothesis , we developed a system of transient transfection of rat adipocytes with constructs containing glyceraldehyde - 3 - phosphate dehydrogenase ( GAPDH ) and fatty acid synthetase ( FAS ) promoters fused to gene reporter CAT .	[ "glyceraldehyde - 3 - phosphate dehydrogenase", "GAPDH", "fatty acid synthetase", "FAS", "gene reporter CAT" ]
84	gene	In the green unicellular alga Chlamydomonas eugametos , cellular division is readily synchronized by light / dark cycles .	[]
85	gene	SHBG concentrations in women were also significantly higher at T - 2 and T - 3 when compared to T - 1 values .	[ "SHBG" ]
86	gene	Simvastatin decreased levels of total cholesterol by 20 . 8 % , LDL cholesterol by 29 . 7 % , triglycerides by 13 . 6 % , apolipoprotein B by 22 . 4 % , alpha - tocopherol by 16 . 2 % , beta - carotene by 19 . 5 % , and ubiquinol - 10 by 22 . 0 % ( P < . 001 for all ) and increased levels of HDL cholesterol by 7 . 0 % ( P < . 001 ) and serum insulin by 13 . 2 % ( P = . 005 ) .	[ "LDL cholesterol", "apolipoprotein B", "HDL cholesterol", "serum insulin" ]
87	gene	The more severe the CRF , the more likely that total HDL and HDL2 cholesterol will be low .	[ "HDL", "HDL2 cholesterol" ]
88	gene	They are growth - inhibited by TGF - beta1 .	[ "TGF - beta1" ]
89	gene	To investigate the in vivo role of this chimeric bZIP protein in oncogenic transformation , its expression was directed to the lymphoid compartments of transgenic mice .	[ "chimeric bZIP protein" ]
90	gene	This is consistent with the need for a nuclear retinoid receptor function in RA - induced ERK2 activation .	[ "retinoid receptor", "ERK2" ]
91	gene	In the virus - infected cells , translation of the M1 protein was reduced to 10 to 20 % of that of the wild - type virus ; however , the translation of neither the nucleoprotein nor NS1 was significantly interfered with , indicating the important role of NS1 in translational stimulation of the M1 protein .	[ "M1 protein", "NS1", "NS1", "M1 protein" ]
92	gene	Some cells were excited , others inhibited by , and only some were directionally sensitive to the optomotor stimulus .	[]
93	gene	LT - beta transcription is maximal in the thymic medulla and in splenic white pulp .	[ "LT - beta" ]
94	gene	A novel Cdc42Hs mutant induces cellular transformation .	[ "Cdc42Hs mutant" ]
95	gene	Interactions were also detected between full - length HSF1 and the small subunit ( gamma ) of TFIIA .	[ "HSF1", "TFIIA" ]
96	gene	We report that Nim1 possesses intrinsic serine - kinase , threonine - kinase and tyrosine - kinase activities .	[ "Nim1", "serine - kinase", "threonine - kinase", "tyrosine - kinase" ]
97	gene	A short conserved motif is required for repressor domain function in the myeloid - specific transcription factor CCAAT / enhancer - binding protein epsilon .	[ "CCAAT / enhancer - binding protein epsilon" ]
98	gene	Androgen ablation - - 50 years later .	[]
99	gene	In conclusion , ORCA3 regulates jasmonate - responsive expression of the Str gene via direct interaction with the JERE .	[ "ORCA3", "Str gene" ]

End of preview.

This repository contains the data used in the PICLe paper. Is consists of the original and corrupted samples for the following datasets:

BC2GM
BC5CHEM
BC5DISEASE
CHEMPROTCHEM
CHEMPROTGENE

The corruption schemes include:

Random ID Label: We replace ground-truth entity labels with random in-distribution entities. For each input sentence, every entity in the ground-truth annotation is replaced by an indistribution (ID) entity randomly sampled from all labels in training samples of the dataset.
Swapped ID Labels: We swap entity labels in the ground-truth demonstrations with the entity labels of a randomly chosen sample in the training split. Contrary to Random ID Label where the number of entities is preserved, the number of entities in each annotation changes compared to the original ground-truth.
Random OOD Label: We replace entity labels in the ground-truth demonstrations with a random out-of-distribution (OOD) English word.
Random OOD Label from Text: We replace ground-truth entity labels with words randomly selected from the sample’s text that are not included in the ground-truth annotation (i.e., not a target entity).
Corrupted OOD Text: We replace the entity mentions in the text with random OOD English words.
Corrupted OOD Text and Label: Similar to Corrupted OOD Text, but we replace ground-truth labels as well, such that the entities in the text and label match.
Corrupted and Shuffled OOD Text, Corrupted and Shuffled OOD Text and Label: Same as their non-shuffled counterpart, but with randomly shuffling the words of the sentence.

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