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---
license: apache-2.0
tags:
- chemistry
- biology
- molecule
- instructions
---
This repo contains a low-rank adapter for [LLaMA2-7b-chat](https://huggingface.co/meta-llama/Llama-2-7b-chat), trained on the 🔬 **molecule-oriented instructions** from the 🧪 [Mol-Instructions](https://huggingface.co/datasets/zjunlp/Mol-Instructions) dataset.
Instructions for running it can be found at https://github.com/zjunlp/Mol-Instructions.
> Please refer to our [paper](https://arxiv.org/abs/2306.08018) for more details.
<h3> 🔬 Tasks</h3>
<details>
<summary><b>Molecule description generation</b></summary>
- *Please give me some details about this molecule:*
[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][=Branch1][C][=O][O][C@H1][Branch2][Ring1][=Branch1][C][O][C][=Branch1][C][=O][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][O][P][=Branch1][C][=O][Branch1][C][O][O][C][C@@H1][Branch1][=Branch1][C][=Branch1][C][=O][O][N]
```
The molecule is a 3-sn-phosphatidyl-L-serine in which the phosphatidyl acyl groups at positions 1 and 2 are specified as stearoyl and arachidonoyl respectively.
It is functionally related to an arachidonic acid and an octadecanoic acid.
```
</details>
<details>
<summary><b>Description-guided molecule design</b></summary>
- *Create a molecule with the structure as the one described:*
The molecule is a primary arylamine in which an amino functional group is substituted for one of the benzene hydrogens. It is a primary arylamine and a member of anilines.
```
[N][C][=C][C][=C][C][=C][Ring1][=Branch1]
```
</details>
<details>
<summary><b>Forward reaction prediction</b></summary>
- *With the provided reactants and reagents, propose a potential product:*
[O][=N+1][Branch1][C][O-1][C][=C][N][=C][Branch1][C][Cl][C][Branch1][C][I][=C][Ring1][Branch2].[Fe]
```
[N][C][=C][N][=C][Branch1][C][Cl][C][Branch1][C][I][=C][Ring1][Branch2]
```
</details>
<details>
<summary><b>Retrosynthesis</b></summary>
- *Please suggest potential reactants used in the synthesis of the provided product:*
[C][=C][C][C][N][C][=Branch1][C][=O][O][C][Branch1][C][C][Branch1][C][C][C]
```
[C][=C][C][C][N].[C][C][Branch1][C][C][Branch1][C][C][O][C][=Branch1][C][=O][O][C][=Branch1][C][=O][O][C][Branch1][C][C][Branch1][C][C][C]
```
</details>
<details>
<summary><b>Reagent prediction</b></summary>
- *Please provide possible reagents based on the following chemical reaction:*
[C][C][=C][C][=C][Branch1][C][N][C][=N][Ring1][#Branch1].[O][=C][Branch1][C][Cl][C][Cl]>>[C][C][=C][C][=C][Branch1][Branch2][N][C][=Branch1][C][=O][C][Cl][C][=N][Ring1][O]
```
[C][C][C][O][C][Ring1][Branch1].[C][C][N][Branch1][Ring1][C][C][C][C].[O]
```
</details>
<details>
<summary><b>Property prediction</b></summary>
- *Please provide the HOMO energy value for this molecule:*
[C][C][O][C][C][Branch1][C][C][C][Branch1][C][C][C]
```
-0.2482
```
</details>
<h3> 📝 Demo</h3>
As illustrated in [our repository](https://github.com/zjunlp/Mol-Instructions/tree/main/demo), we provide an example to perform generation.
```shell
>> python generate.py \
--CLI True \
--protein False\
--load_8bit \
--base_model $BASE_MODEL_PATH \
--lora_weights $FINETUNED_MODEL_PATH \
```
Please download [Llama-2-7b-chat](https://huggingface.co/meta-llama/Llama-2-7b-chat) to obtain the pre-training weights of LlamA-2-7b-chat, refine the `--base_model` to point towards the location where the model weights are saved.
For model fine-tuned on **molecule-oriented** instructions, set `$FINETUNED_MODEL_PATH` to `'zjunlp/llama2-molinst-molecule-7b'`.
<h3> 🚨 Limitations</h3>
The current state of the model, obtained via instruction tuning, is a preliminary demonstration. Its capacity to handle real-world, production-grade tasks remains limited.
<h3> 📚 References</h3>
If you use our repository, please cite the following related paper:
```
@inproceedings{fang2023mol,
author = {Yin Fang and
Xiaozhuan Liang and
Ningyu Zhang and
Kangwei Liu and
Rui Huang and
Zhuo Chen and
Xiaohui Fan and
Huajun Chen},
title = {Mol-Instructions: {A} Large-Scale Biomolecular Instruction Dataset
for Large Language Models},
booktitle = {{ICLR}},
publisher = {OpenReview.net},
year = {2024},
url = {https://openreview.net/pdf?id=Tlsdsb6l9n}
}
```
<h3> 🫱🏻🫲🏾 Acknowledgements</h3>
We appreciate [LLaMA-2](https://ai.meta.com/llama), [LLaMA](https://github.com/facebookresearch/llama), [Huggingface Transformers Llama](https://github.com/huggingface/transformers/tree/main/src/transformers/models/llama), [Alpaca](https://crfm.stanford.edu/2023/03/13/alpaca.html), [Alpaca-LoRA](https://github.com/tloen/alpaca-lora), [Chatbot Service](https://github.com/deep-diver/LLM-As-Chatbot) and many other related works for their open-source contributions. |