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phenixace
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S2-TOMG-Bench

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Instruction
stringlengths
31
131
carbon
int64
1
40
oxygen
int64
0
5
nitrogen
int64
0
5
sulfur
int64
0
5
fluorine
int64
0
5
chlorine
int64
0
5
bromine
int64
0
5
iodine
int64
0
5
phosphorus
int64
0
5
boron
int64
0
5
silicon
int64
0
5
selenium
int64
0
5
tellurium
int64
0
5
arsenic
int64
0
5
antimony
int64
0
5
bismuth
int64
0
5
polonium
int64
0
5
Please generate a molecule with 8 carbon atoms, 1 nitrogen atom, and 3 oxygen atoms.
8
3
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule composed of 35 carbon atoms and 1 oxygen atom.
35
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 15 carbon atoms and 2 bromine atoms.
15
0
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
There is a molecule with 35 carbon atoms.
35
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 38 carbon atoms, 2 oxygen atoms, and 1 tellurium atom.
38
2
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
The molecule has 10 carbon atoms, 2 sulfur atoms, 3 oxygen atoms, 1 nitrogen atom, and 5 antimony atoms.
10
3
1
2
0
0
0
0
0
0
0
0
0
0
5
0
0
Please generate a molecule composed of 25 carbon atoms and 2 tellurium atoms.
25
0
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
The molecule contains 24 carbon atoms.
24
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 5 carbon atoms and 5 silicon atoms.
5
0
0
0
0
0
0
0
0
0
5
0
0
0
0
0
0
Please generate a molecule composed of 15 carbon atoms.
15
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 30 carbon atoms.
30
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule has 23 carbon atoms and 2 phosphorus atoms.
23
0
0
0
0
0
0
0
2
0
0
0
0
0
0
0
0
The molecule contains 5 carbon atoms and 1 chlorine atom.
5
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 30 carbon atoms.
30
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule has 36 carbon atoms, 1 tellurium atom, and 2 boron atoms.
36
0
0
0
0
0
0
0
0
2
0
0
1
0
0
0
0
There is a molecule with 21 carbon atoms.
21
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 14 carbon atoms, 4 sulfur atoms, 1 phosphorus atom, and 2 fluorine atoms.
14
0
0
4
2
0
0
0
1
0
0
0
0
0
0
0
0
There is a molecule consisting of 16 carbon atoms and 1 boron atom.
16
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
There is a molecule with 38 carbon atoms.
38
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 9 carbon atoms and 3 silicon atoms.
9
0
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
Please generate a molecule consisting 10 carbon atoms, 1 fluorine atom, and 5 oxygen atoms.
10
5
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 34 carbon atoms, 2 arsenic atoms, 1 oxygen atom, 4 boron atoms, and 3 phosphorus atoms.
34
1
0
0
0
0
0
0
3
4
0
0
0
2
0
0
0
Please generate a molecule consisting 28 carbon atoms.
28
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 17 carbon atoms, 2 chlorine atoms, and 3 oxygen atoms.
17
3
0
0
0
2
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 33 carbon atoms.
33
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule consisting 24 carbon atoms and 2 silicon atoms.
24
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
0
The molecule contains 1 carbon atom.
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule composed of 2 carbon atoms and 3 arsenic atoms.
2
0
0
0
0
0
0
0
0
0
0
0
0
3
0
0
0
The molecule has 20 carbon atoms.
20
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule composed of 37 carbon atoms.
37
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule composed of 32 carbon atoms, 1 chlorine atom, 2 oxygen atoms, 4 boron atoms, and 5 bismuth atoms.
32
2
0
0
0
1
0
0
0
4
0
0
0
0
0
5
0
The molecule has 35 carbon atoms, 1 fluorine atom, and 5 phosphorus atoms.
35
0
0
0
1
0
0
0
5
0
0
0
0
0
0
0
0
Please generate a molecule composed of 29 carbon atoms.
29
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 5 carbon atoms.
5
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule has 36 carbon atoms and 2 oxygen atoms.
36
2
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule has 4 carbon atoms.
4
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 3 carbon atoms.
3
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 16 carbon atoms and 1 nitrogen atom.
16
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 37 carbon atoms and 3 silicon atoms.
37
0
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
Please generate a molecule composed of 13 carbon atoms.
13
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 28 carbon atoms.
28
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 30 carbon atoms and 1 polonium atom.
30
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
The molecule consists of 26 carbon atoms, 2 oxygen atoms, and 1 sulfur atom.
26
2
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 12 carbon atoms and 1 arsenic atom.
12
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
Please generate a molecule composed of 36 carbon atoms.
36
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 35 carbon atoms, 1 antimony atom, 2 selenium atoms, 3 oxygen atoms, and 4 bromine atoms.
35
3
0
0
0
0
4
0
0
0
0
2
0
0
1
0
0
The molecule is composed of 25 carbon atoms, 2 silicon atoms, 1 nitrogen atom, 3 phosphorus atoms, and 4 boron atoms.
25
0
1
0
0
0
0
0
3
4
2
0
0
0
0
0
0
Please generate a molecule with 14 carbon atoms and 2 bromine atoms.
14
0
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 4 carbon atoms and 3 chlorine atoms.
4
0
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 11 carbon atoms, 1 oxygen atom, 2 sulfur atoms, 5 phosphorus atoms, and 3 silicon atoms.
11
1
0
2
0
0
0
0
5
0
3
0
0
0
0
0
0
Please generate a molecule with 39 carbon atoms and 2 fluorine atoms.
39
0
0
0
2
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 34 carbon atoms, 2 nitrogen atoms, 1 boron atom, 3 sulfur atoms, and 5 chlorine atoms.
34
0
2
3
0
5
0
0
0
1
0
0
0
0
0
0
0
Please generate a molecule with 5 carbon atoms and 5 polonium atoms.
5
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
5
There is a molecule consisting of 5 carbon atoms.
5
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule consisting 17 carbon atoms, 3 arsenic atoms, 2 tellurium atoms, 1 sulfur atom, and 5 oxygen atoms.
17
5
0
1
0
0
0
0
0
0
0
0
2
3
0
0
0
Please generate a molecule with 34 carbon atoms and 4 bromine atoms.
34
0
0
0
0
0
4
0
0
0
0
0
0
0
0
0
0
Please generate a molecule consisting 7 carbon atoms.
7
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 7 carbon atoms.
7
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 19 carbon atoms.
19
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule has 22 carbon atoms, 1 tellurium atom, and 5 chlorine atoms.
22
0
0
0
0
5
0
0
0
0
0
0
1
0
0
0
0
Please generate a molecule composed of 4 carbon atoms and 1 tellurium atom.
4
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
Please generate a molecule consisting 22 carbon atoms and 2 nitrogen atoms.
22
0
2
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 36 carbon atoms and 4 oxygen atoms.
36
4
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 10 carbon atoms.
10
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 24 carbon atoms and 1 fluorine atom.
24
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 24 carbon atoms, 2 nitrogen atoms, 4 sulfur atoms, and 1 oxygen atom.
24
1
2
4
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule consisting 40 carbon atoms, 1 nitrogen atom, 2 oxygen atoms, 5 tellurium atoms, and 4 fluorine atoms.
40
2
1
0
4
0
0
0
0
0
0
0
5
0
0
0
0
The molecule has 27 carbon atoms.
27
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 7 carbon atoms, 1 arsenic atom, 2 nitrogen atoms, and 5 selenium atoms.
7
0
2
0
0
0
0
0
0
0
0
5
0
1
0
0
0
The molecule has 15 carbon atoms.
15
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 13 carbon atoms.
13
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 5 carbon atoms.
5
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 33 carbon atoms and 1 tellurium atom.
33
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
Please generate a molecule composed of 2 carbon atoms and 2 nitrogen atoms.
2
0
2
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 17 carbon atoms.
17
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 28 carbon atoms, 1 sulfur atom, and 2 iodine atoms.
28
0
0
1
0
0
0
2
0
0
0
0
0
0
0
0
0
The molecule has 37 carbon atoms.
37
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule with 28 carbon atoms and 2 selenium atoms.
28
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
The molecule consists of 13 carbon atoms.
13
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 22 carbon atoms.
22
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 8 carbon atoms and 1 iodine atom.
8
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 19 carbon atoms.
19
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 27 carbon atoms and 2 antimony atoms.
27
0
0
0
0
0
0
0
0
0
0
0
0
0
2
0
0
There is a molecule with 20 carbon atoms and 1 oxygen atom.
20
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 28 carbon atoms and 1 sulfur atom.
28
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule consisting of 14 carbon atoms and 3 antimony atoms.
14
0
0
0
0
0
0
0
0
0
0
0
0
0
3
0
0
Please generate a molecule composed of 11 carbon atoms.
11
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule consists of 40 carbon atoms.
40
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 16 carbon atoms.
16
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule consisting 13 carbon atoms.
13
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule composed of 16 carbon atoms and 1 silicon atom.
16
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
The molecule has 37 carbon atoms, 1 sulfur atom, and 3 fluorine atoms.
37
0
0
1
3
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule with 7 carbon atoms.
7
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
There is a molecule composed of 34 carbon atoms.
34
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Please generate a molecule composed of 16 carbon atoms and 2 selenium atoms.
16
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
The molecule contains 36 carbon atoms.
36
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule contains 29 carbon atoms, 4 arsenic atoms, and 1 fluorine atom.
29
0
0
0
1
0
0
0
0
0
0
0
0
4
0
0
0
There is a molecule composed of 11 carbon atoms.
11
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
The molecule is composed of 16 carbon atoms, 1 chlorine atom, and 2 iodine atoms.
16
0
0
0
0
1
0
2
0
0
0
0
0
0
0
0
0
The molecule has 19 carbon atoms.
19
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
End of preview. Expand in Data Studio

S^2-Bench Dataset (TOMG) (full version, 45k entries)

Official Huggingface Datasets for S^2-Bench: "Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation"

Please refer to our Github Repo for more usage and useful information.

Configurations

Each configuration represents a different task:

  • MolCustom_AtomNum: Molecular customized generation by atom number
  • MolCustom_BondNum: Molecular customized generation by bond number
  • MolCustom_FunctionalGroup: Molecular customized generation by functional group
  • MolEdit_AddComponent: Molecular editing - adding components
  • MolEdit_SubComponent: Molecular editing - substituting components
  • MolEdit_DelComponent: Molecular editing - deleting components
  • MolOpt_LogP: Molecular optimization for LogP
  • MolOpt_MR: Molecular optimization for MR
  • MolOpt_QED: Molecular optimization for QED

Usage 

from datasets import load_dataset

# Load a specific configuration
dataset = load_dataset("phenixace/S2-TOMG-Bench", "MolCustom_AtomNum")

# Or load all configurations
configs = ["MolCustom_AtomNum", "MolCustom_BondNum", "MolCustom_FunctionalGroup",
           "MolEdit_AddComponent", "MolEdit_SubComponent", "MolEdit_DelComponent",
           "MolOpt_LogP", "MolOpt_MR", "MolOpt_QED"]

datasets = {config: load_dataset("phenixace/S2-TOMG-Bench", config) for config in configs}

Citation

If you use our data, please cite us in the format below:

@article{li2024speak,
  title={Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation},
  author={Li, Jiatong and Li, Junxian and Liu, Yunqing and Zheng, Changmeng and Wei, Xiaoyong and Zhou, Dongzhan and Li, Qing},
  journal={arXiv preprint arXiv:2412.14642v3},
  year={2024}
}

Current Leaderboard

Rank Model #Parameters (B) $\overline{S!R}$ (%) $\overline{W!S!R} (%)$
1 Llama3.1-8B (OpenMolIns-xlarge) 8 58.79 39.33
2 Claude-3.5 - 51.10 35.92
3 Gemini-1.5-pro - 52.25 34.80
4 GPT-4-turbo - 50.74 34.23
5 GPT-4o - 49.08 32.29
6 Claude-3 - 46.14 30.47
7 Llama3.1-8B (OpenMolIns-large) 8 43.1 27.22
8 Galactica-125M (OpenMolIns-xlarge) 0.125 44.48 25.73
9 Llama3-70B-Instruct (Int4) 70 38.54 23.93
10 Galactica-125M (OpenMolIns-large) 0.125 39.28 23.42
11 Galactica-125M (OpenMolIns-medium) 0.125 34.54 19.89
12 GPT-3.5-turbo - 28.93 18.58
13 Galactica-125M (OpenMolIns-small) 0.125 24.17 15.18
14 Gemma3-12B 12 26.28 15.00
15 Deepseek-R1-distill-Qwen-7B 7 25.07 14.61
16 Llama3.1-8B-Instruct 8 26.26 14.09
17 Llama3-8B-Instruct 8 26.40 13.75
18 chatglm-9B 9 18.50 13.13(7)
19 Galactica-125M (OpenMolIns-light) 0.125 20.95 13.13(6)
20 ChemDFM-v1.5-8B 8 18.24 12.07
21 ChemLLM-20B 20 16.23 9.76
22 Llama3.2-1B (OpenMolIns-large) 1 14.11 8.10
23 yi-1.5-9B 9 14.10 7.32
24 Mistral-7B-Instruct-v0.2 7 11.17 4.81
25 BioT5-base 0.25 24.19 4.21
26 MolT5-large 0.78 23.11 2.89
27 Llama3.1-1B-Instruct 1 3.95 1.99
28 MolT5-base 0.25 11.11 1.30(0)
29 MolT5-small 0.08 11.55 1.29(9)
30 Qwen2-7B-Instruct 7 0.18 0.15

OpenMolIns

The instruction tuning datasets are also available at Hugging Face Datasets:

  1. OpenMolIns-light
  2. OpenMolIns-small
  3. OpenMolIns-medium
  4. OpenMolIns-large
  5. OpenMolIns-xlarge
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Paper for phenixace/S2-TOMG-Bench