Y-Mol
Collection
A Localized Web Tool Based on Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development. https://github.com/xiaomingaaa/Y-MOL
•
4 items
•
Updated
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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 1 new columns ({'system'})
This happened while the json dataset builder was generating data using
hf://datasets/Matthewmtf/Y-Mol-Instructions/Molecule_generation/train/train.json (at revision ce691dfa255c2d822449d5ff9aac8bfbda13188e)
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 643, 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
id: int64
system: string
instruction: string
input: string
output: string
history: list<item: null>
child 0, item: null
to
{'id': Value(dtype='string', id=None), 'instruction': Value(dtype='string', id=None), 'input': Value(dtype='string', id=None), 'output': Value(dtype='string', id=None), 'history': Sequence(feature=Value(dtype='null', 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 1436, 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 1053, 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 1 new columns ({'system'})
This happened while the json dataset builder was generating data using
hf://datasets/Matthewmtf/Y-Mol-Instructions/Molecule_generation/train/train.json (at revision ce691dfa255c2d822449d5ff9aac8bfbda13188e)
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 | instruction
string | input
string | output
string | history
sequence |
|---|---|---|---|---|
1
|
What is the nRig value of this molecule O=C(Nc1nc(-c2cc(F)ccc2F)cs1)C1=NN(C2CCS(=O)(=O)C2)C(=O)CC1?
|
22.
|
[] |
|
2
|
What is the nRig value of this molecule CC1CC(C)CC(NC(=O)NC(C(=O)O)C(C)C)C1?
|
14.
|
[] |
|
3
|
What is the nRig value of this molecule O=C(C1CCOc2ccccc21)N1CCN(Cc2ccccc2)CC1?
|
18.
|
[] |
|
4
|
What is the nRig value of this molecule O=C(CCCCOc1ccc2c(c1)CCCC2)NCCCO?
|
11.
|
[] |
|
5
|
What is the nRig value of this molecule COC(OO)c1ccccc1C(O)O?
|
9.
|
[] |
|
6
|
What is the nRig value of this molecule COc1ccc(OC)c(NC(=O)c2c(C)c(-c3ccc(Cl)cc3Cl)nc3ccccc23)c1?
|
23.
|
[] |
|
7
|
What is the nRig value of this molecule COc1cc(C#N)c(OC)c(N)c1C?
|
11.
|
[] |
|
8
|
What is the nRig value of this molecule C=CCOc1ccc(F)c(-c2nc(C(=O)Nc3cnccc3C3CC(C)C(O)C(N)C3)ccc2F)c1F?
|
26.
|
[] |
|
9
|
What is the nRig value of this molecule CCOc1ccc(C(=O)NC(C(=O)N2CCOCC2)C(C)C)cc1?
|
16.
|
[] |
|
10
|
What is the nRig value of this molecule Cc1cc(N2CCC3(CCCN(Cc4cccnc4)C3=O)C2)nc2ccccc12?
|
21.
|
[] |
|
11
|
What is the nRig value of this molecule Cc1ccc(S(=O)(=O)NC(CSSCC(NS(=O)(=O)c2ccc(C)cc2)C(=O)O)C(=O)O)cc1?
|
19.
|
[] |
|
12
|
What is the nRig value of this molecule CCCOP(=O)(O)OCCN(C)CC?
|
6.
|
[] |
|
13
|
What is the nRig value of this molecule O=C(NCC1=CCNCC1)c1cc(I)ccc1Br?
|
13.
|
[] |
|
14
|
What is the nRig value of this molecule CCN1c2ccc(C)cc2C=CC1C=Cc1ccc(O)c2ncccc12?
|
19.
|
[] |
|
15
|
What is the nRig value of this molecule CC(C)(C)CC(=O)NCC(=O)NC1CCCCCC1C(=O)O?
|
16.
|
[] |
|
16
|
What is the nRig value of this molecule COc1ccc2c(c1)C=CC1=NC(C(c3ccccc3)c3ccc(O)cc3)C(C)N12?
|
21.
|
[] |
|
17
|
What is the nRig value of this molecule COc1ccc(CC(=S)C(C)C2NC(=O)C2C(C)(O[Si](C)C)C(C)(C)C)c(OC)c1?
|
19.
|
[] |
|
18
|
What is the nRig value of this molecule CCOCC(NCc1cc(F)ccc1[N+](=O)[O-])C(C)C?
|
11.
|
[] |
|
19
|
What is the nRig value of this molecule CNc1ncnc(Oc2c(C)nn(C)c2C)c1C(C)C?
|
14.
|
[] |
|
20
|
What is the nRig value of this molecule COC(CNC(=O)NC(CC(C)C)C(=O)O)OC?
|
10.
|
[] |
|
21
|
What is the nRig value of this molecule CN(C(=O)CN1C(=O)NC(C)(c2ccc3c(c2)CCC3)C1=O)c1ccc([N+](=O)[O-])cc1?
|
22.
|
[] |
|
22
|
What is the nRig value of this molecule CCCCCCC(CCOC)CCOC(=O)CCCC(=O)OCCC?
|
8.
|
[] |
|
23
|
What is the nRig value of this molecule Cc1nc(-c2ncccn2)sc1C(=O)Nc1ccccc1NS(=O)(=O)c1ccccc1?
|
21.
|
[] |
|
24
|
What is the nRig value of this molecule Cc1cc(-c2c3ccccc3nc(C)[n+]2C)c(C)cc1F?
|
17.
|
[] |
|
25
|
What is the nRig value of this molecule Cc1cncn(CCNC(=O)Cn2cnc(-c3ccccc3)cc2=O)c1=O?
|
18.
|
[] |
|
26
|
What is the nRig value of this molecule CCCNC(=O)CC1CCC2C(COc3ccc(NC(=O)c4cscn4)cc3C(=O)N2C)O1?
|
23.
|
[] |
|
27
|
What is the nRig value of this molecule C=CC(C)=CC1CCCC2CCC(O)C12?
|
11.
|
[] |
|
28
|
What is the nRig value of this molecule COc1ccc(C(=O)CCCC(=O)NCc2ncc3ccccn23)cc1?
|
15.
|
[] |
|
29
|
What is the nRig value of this molecule O=C1NC(=S)C(=Cc2cccc(Cl)c2)S1?
|
12.
|
[] |
|
30
|
What is the nRig value of this molecule Cc1cc(-n2cncn2)c2cccc(OCc3c(Cl)ccc(N(C)C(=O)CNC(=O)C=Cc4ccc(C(=O)N(C)C)cc4)c3Cl)c2n1?
|
32.
|
[] |
|
31
|
What is the nRig value of this molecule c1cnc2ccc3nsnc3c2c1?
|
10.
|
[] |
|
32
|
What is the nRig value of this molecule O=C(NC(CC1CC1)B(O)O)C(Cc1ccccc1)CS(=O)(=O)c1ccc(Oc2ccc3c(c2)N=CC3)cc1?
|
22.
|
[] |
|
33
|
What is the nRig value of this molecule O=[N+]([O-])c1ccc(-c2ccc(C(F)(F)F)cc2)c(CO)c1?
|
16.
|
[] |
|
34
|
What is the nRig value of this molecule O=c1c2nnn(Cc3ccccc3Cl)c2ncn1Cc1ccc(F)cc1Cl?
|
19.
|
[] |
|
35
|
What is the nRig value of this molecule C=CC(=O)Oc1ccc(C(=O)Oc2ccc(OC(=O)c3ccc(OC(C)CC(C)(C)OC(=O)C=C)cc3)cc2CC)cc1?
|
27.
|
[] |
|
36
|
What is the nRig value of this molecule OCCc1nnc(CCc2ccc3c(c2)OCCO3)o1?
|
12.
|
[] |
|
37
|
What is the nRig value of this molecule O=C(NCc1cccc2c1OCCO2)c1sccc1S(=O)(=O)N1CCOCC1?
|
19.
|
[] |
|
38
|
What is the nRig value of this molecule CC1CCCCC1CNS(=O)(=O)Cc1ccccc1C#N?
|
14.
|
[] |
|
39
|
What is the nRig value of this molecule COC(=O)c1ccc(C2Oc3ccccc3C3=C2C(c2ccccc2F)n2ncnc2N3)cc1?
|
25.
|
[] |
|
40
|
What is the nRig value of this molecule CCOP(=O)(CC)OCCC(CON1C(=O)c2ccccc2C1=O)CO[Si](C)(C)C(C)(C)C?
|
18.
|
[] |
|
41
|
What is the nRig value of this molecule CCOC(=O)CC(=O)C1(OC)CCN(C(=O)OC(C)(C)C)CC1?
|
17.
|
[] |
|
42
|
What is the nRig value of this molecule CC1CN(c2c(CO[Si](c3ccccc3)(c3ccccc3)C(C)(C)C)cc(C(=O)c3ccccc3)c(F)c2F)CC(C)O1?
|
30.
|
[] |
|
43
|
What is the nRig value of this molecule CC(C)(O)C=NNC(N)=S?
|
8.
|
[] |
|
44
|
What is the nRig value of this molecule C=CCC(N)c1c(Br)cc(Br)c(O)c1Br?
|
11.
|
[] |
|
45
|
What is the nRig value of this molecule CCOc1cc(N)c(Cl)cc1C(=O)NCC1CN(CCCO)CCO1?
|
15.
|
[] |
|
46
|
What is the nRig value of this molecule CCN(CC)S(=O)(=O)c1ccc(C(=O)NCC(O)c2ccc(C(F)(F)F)cc2)cc1?
|
20.
|
[] |
|
47
|
What is the nRig value of this molecule CCC(C)(OC)c1nc2cccc(C(=O)O)c2o1?
|
12.
|
[] |
|
48
|
What is the nRig value of this molecule CCC(NC(=O)C1=NNC(=O)CC1)c1ncccc1C?
|
14.
|
[] |
|
49
|
What is the nRig value of this molecule CCCCCc1ccc(C(=O)N(Cc2cccc(C#CC(O)c3ccccc3)c2)C2CCN(CCC(C)C)CC2)cc1?
|
26.
|
[] |
|
50
|
What is the nRig value of this molecule CN(Cc1ccccc1Br)C(=O)C1CCCC1N?
|
13.
|
[] |
|
51
|
What is the nRig value of this molecule CC(C)(C)OC(=O)C(=CC(OC1CCCCC1)C(O)CO)CC[N+](=O)[O-]?
|
16.
|
[] |
|
52
|
What is the nRig value of this molecule CS(=O)(=O)N1CCC(Cc2ccc(Cl)nn2)C1?
|
12.
|
[] |
|
53
|
What is the nRig value of this molecule COc1cc(Br)cc(S(=O)(=O)NC2CCNC(C)C2)c1?
|
14.
|
[] |
|
54
|
What is the nRig value of this molecule COc1ccc2oc(C(=O)Nc3cc(Cl)ccc3OC)c(C)c2c1?
|
17.
|
[] |
|
55
|
What is the nRig value of this molecule CC(C)N(C)c1cc(NCC#N)ncn1?
|
10.
|
[] |
|
56
|
What is the nRig value of this molecule CCCCCCOC(=O)NC1(NC(=O)OCCCCCC)C=CC=CC1C?
|
14.
|
[] |
|
57
|
What is the nRig value of this molecule NC(CC(=O)Nc1ccccc1Cl)=NOCc1ccc(F)cc1?
|
15.
|
[] |
|
58
|
What is the nRig value of this molecule CC1CC1C(=O)N1CC2(C1)C(COc1ncccc1F)CCS2(=O)=O?
|
17.
|
[] |
|
59
|
What is the nRig value of this molecule CCC(O)c1ccc(Oc2c(F)cccc2[N+](=O)[O-])cn1?
|
14.
|
[] |
|
60
|
What is the nRig value of this molecule CC(=CCCNC1CC1)CC1CCCC1?
|
7.
|
[] |
|
61
|
What is the nRig value of this molecule COCC(C)Nc1ncnc(NNC(=O)c2ccccc2C)c1[N+](=O)[O-]?
|
16.
|
[] |
|
62
|
What is the nRig value of this molecule COCC(=O)Nc1ccc2c(c1)C(=O)N(C)C1CCC(CC(=O)NCC(F)(F)F)OC1CO2?
|
24.
|
[] |
|
63
|
What is the nRig value of this molecule Cc1c(C(=O)OC(C)C(=O)Nc2ccccc2C(F)(F)F)cccc1[N+](=O)[O-]?
|
21.
|
[] |
|
64
|
What is the nRig value of this molecule [H]CC([H])COc1c(C)cc(-c2noc(-c3cc(C)nc(N(CC)CC)c3)n2)cc1C?
|
18.
|
[] |
|
65
|
What is the nRig value of this molecule C=C(Cl)CN1CCCOC(CN)C1?
|
9.
|
[] |
|
66
|
What is the nRig value of this molecule CCOc1ccccc1NC(=O)C([NH2+]CC1COc2ccccc2O1)c1ccccc1?
|
19.
|
[] |
|
67
|
What is the nRig value of this molecule CCOC(=O)C=NOc1cncs1?
|
8.
|
[] |
|
68
|
What is the nRig value of this molecule CCN(CCCc1ccccc1)CCCc1cc(=O)n(C)c(=O)n1C?
|
14.
|
[] |
|
69
|
What is the nRig value of this molecule CN(CC1CCCC1O)C(=O)Nc1nc2c(s1)CCCCCC2?
|
17.
|
[] |
|
70
|
What is the nRig value of this molecule COc1ccc(CS(=O)(=O)C(C#N)=Cc2ccc(OC)c(OC)c2)cc1?
|
17.
|
[] |
|
71
|
What is the nRig value of this molecule Clc1ccc(Cn2cc(CN=Nc3nc(-c4ccc(Cl)cc4Cl)cs3)c3ccccc32)c(Cl)c1?
|
23.
|
[] |
|
72
|
What is the nRig value of this molecule COCC1(C)CNc2c(C#N)cc(-c3ccnc(Cl)n3)cc21?
|
16.
|
[] |
|
73
|
What is the nRig value of this molecule CCOc1ccc(N(CC(=O)N(Cc2ccccc2C)C(C)C(=O)NC2CCCC2)S(=O)(=O)c2ccc(C)cc2)cc1?
|
26.
|
[] |
|
74
|
What is the nRig value of this molecule CCCCCCCCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCCCCCCCC)c1ccc(-c2ccc(C=Cc3ccc([N+](=O)[O-])c(C#N)c3)cc2)cc1?
|
20.
|
[] |
|
75
|
What is the nRig value of this molecule CCc1cc(C(=O)N2CCOC(c3ccncc3)C2)no1?
|
15.
|
[] |
|
76
|
What is the nRig value of this molecule COc1ccc2c(c1)CCC1C2CCC2(C)C(O)CCC12O?
|
17.
|
[] |
|
77
|
What is the nRig value of this molecule CC(C)c1cnc(-c2cccc(N)c2)nc1?
|
12.
|
[] |
|
78
|
What is the nRig value of this molecule CC(C)CC(=O)OC(C(C)C)C1CC(C)CC2(CC(C)CC(C)O2)O1?
|
18.
|
[] |
|
79
|
What is the nRig value of this molecule Cc1ccc(C(=O)CC(OCc2ccccc2)C(OCc2ccccc2)C2COC(C)(C)O2)cc1?
|
20.
|
[] |
|
80
|
What is the nRig value of this molecule O=C1CCC(C(=O)NC2(c3ccc(F)cc3)CCC2)N1?
|
14.
|
[] |
|
81
|
What is the nRig value of this molecule C=CS1(F)n2c(C)cc(C)c2C(c2cc(-c3cccc4c3oc3ccccc34)cc(-c3cccc4c3oc3ccccc34)c2)=C2C(C)CC(C)=[N+]21?
|
37.
|
[] |
|
82
|
What is the nRig value of this molecule COCCN1CCC(n2cc(Nc3ncc4nnn(-c5ccnc(OC)c5)c4n3)cn2)CC1?
|
20.
|
[] |
|
83
|
What is the nRig value of this molecule CCCc1c(C=Cc2ccccc2F)oc2ccc(C(=O)O)cc2c1=O?
|
18.
|
[] |
|
84
|
What is the nRig value of this molecule CCCCCCCCC=CCCCCCCCCC(O)(O)C(C)=O?
|
7.
|
[] |
|
85
|
What is the nRig value of this molecule O=C(Nc1ccccc1SCc1ccc(Cl)cc1)C1CCN(Cc2nc(-c3cccs3)no2)CC1?
|
22.
|
[] |
|
86
|
What is the nRig value of this molecule CC1C(c2nc(SCc3ccc(CN)cc3)n[nH]2)CC(O)N1S(=O)(=O)N1CCC(O)C1?
|
20.
|
[] |
|
87
|
What is the nRig value of this molecule COc1cc2nc(-c3cccc(NCCNC(=O)N4CCOCC4)c3)nc(N)c2cc1OC?
|
22.
|
[] |
|
88
|
What is the nRig value of this molecule O=C1CCCCN1[O-]?
|
7.
|
[] |
|
89
|
What is the nRig value of this molecule CC(C)(C)OC(=O)N1CCN(c2ccc(Nc3ncc4c(=O)n(-c5c(Cl)cccc5Cl)ccc4n3)cc2CO)CC1?
|
31.
|
[] |
|
90
|
What is the nRig value of this molecule CCOc1ccc(NC(=O)CCC(=O)c2ccc(Cl)s2)cc1S(=O)(=O)N(C)C?
|
17.
|
[] |
|
91
|
What is the nRig value of this molecule CC(Oc1ccccc1)C(=O)N(c1ccc(Br)cc1)C1C=CS(=O)(=O)C1?
|
18.
|
[] |
|
92
|
What is the nRig value of this molecule CCc1ccc2nc(N(CCN3CCOCC3)C(=O)c3ccnn3CC)sc2c1?
|
18.
|
[] |
|
93
|
What is the nRig value of this molecule OC(c1cccc(F)c1Cl)c1occc1Br?
|
12.
|
[] |
|
94
|
What is the nRig value of this molecule O=NN(c1ccc(CC2CCC(C(O)c3ccccc3)N2)cc1)C1CCc2cccc(=O)n21?
|
21.
|
[] |
|
95
|
What is the nRig value of this molecule Cc1ccc(N=C(N)c2ccccc2)c(O)c1?
|
13.
|
[] |
|
96
|
What is the nRig value of this molecule CCCCOC(=O)C1=C(C)NC(=O)NC1c1ccc(OC)c(Br)c1?
|
16.
|
[] |
|
97
|
What is the nRig value of this molecule CC(C)(C)OC(=O)NC(Cc1c(F)c(F)c(F)c(F)c1F)C(=O)Nc1n[nH]c(=S)s1?
|
23.
|
[] |
|
98
|
What is the nRig value of this molecule CC(C)C1CN(c2nc3ccccc3o2)CCN1C(=S)Nc1cccc2c1CCN(C(=O)OCc1ccccc1)C2?
|
30.
|
[] |
|
99
|
What is the nRig value of this molecule COc1cccc(Sc2nc(C)cc(C)c2C(N)=NO)c1?
|
15.
|
[] |
|
100
|
What is the nRig value of this molecule NCCCC(=O)Nc1cc(NC(=O)c2ccncc2)ccc1Cl?
|
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This dataset is constructed for supervised fine-tuning (SFT) of Y-Mol, a multimodal foundation model for drug discovery. It contains high-quality instruction–response pairs that span a wide range of drug-related tasks, designed to align the model with expert-like capabilities in molecular reasoning and decision-making.
The dataset covers four key tasks:
- Molecular Property Prediction
Synthetic instruction–response pairs are generated using expert tools (e.g., ADMETlab, SwissADME) to simulate predictions of pharmacokinetic and physicochemical properties such as solubility, permeability, toxicity, and metabolic stability.
- Molecule Generation
Includes prompts and reference outputs for generating novel molecular structures conditioned on specific constraints such as bioactivity profiles, physicochemical rules, or scaffold constraints.
- Drug–Target Interaction (DTI) Prediction
Contains natural language prompts describing candidate drugs and targets, paired with binary or affinity-based interaction labels sourced or simulated from public databases and predictive models.
- Drug–Drug Interaction (DDI) Prediction
Captures interactions between drug pairs with both mechanistic and effect-level annotations, aiming to train the model to reason about combinatorial effects or contraindications.
Each instruction–response pair is designed to be LLM-friendly and structured to encourage step-by-step reasoning, enabling Y-Mol to generalize across multiple biomedical and cheminformatics tasks.
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