README.md

USPTO-LLM

Introduction about USPTO-LLM

USPTO-LLM is an information-enriched chemical reaction dataset that provides more side information (reaction conditions and reaction steps division) for developing new reaction prediction and retrosynthesis methods and inspires new problems, such as reaction condition prediction.

The dataset comprises over 247K chemical reactions extracted from the patent documents of USPTO (United States Patent and Trademark Office), encompassing abundant information on reaction conditions. 

We employ large language models to expedite the data collection procedures automatically with a reliable quality control process. The extracted chemical reactions are organized as heterogeneous directed graphs, allowing us to formulate a series of prediction tasks, such as reaction prediction, retrosynthesis, and reaction condition prediction, in a unified graph-filling framework.

The chemical reactions are organized as heterogeneous directed graphs along with their reaction condition information, such as:

id	class	rs>>ps	solvents	catalyst	temperature	time
20160114-US20160007601A1-0113	-1	[Cl-].C(C)N=C=NCCC[NH+](C)C.C1(=CC=CC=C1)CCC(=O)O.CC(\C=C/C)O>>C1(=CC=CC=C1)C#CC(=O)OC(C)\C=C/C	['C(Cl)Cl']	['CN(C)C=1C=CN=CC1']	['room temperature']	['25200']

About this repository

This repository contains the code for generating the USPTO-LLM dataset.

Code

In 'USPTO-LLM/Code', there are several python files and jupyter notebooks.

1. api_request_parallel_processor.py is used to call the API to generate the heterogeneous directed graph of USPTO-LLM. Our default API is gpt-4-1106-preview.

2. generate_request.py is used to generate the json file uspto_request.json for each API submission based on the reaction data in uspto_full.json and the FIXED_PROMPT.

3. extract_api_outcome.ipynb is used to extract the reaction data from the result_uspto_request.json generated by the API, including the "pattern repair" technique mentioned in the paper.

4. prompt_to_json.py is used to convert the written prompt into json format and store it in the string variable FIXED_PROMPT.

The running order is: prompt_to_json.py → generate_request.py → api_request_parallel_processor.py → extract_api_outcome.ipynb

Prompt

Prompt is used to guide the large language model to generate the standardized heterogeneous directed graph of USPTO-LLM. The prompt is stored in the Prompt folder, including the .txt and .json versions of the prompt.

Supplement

In the Supplement folder, annotation_process.pdf provides the detailed annotation process of the USPTO-LLM dataset, including the detailed design of prompt, the process of the pattern repair technique, and the mechanism of our two-round generation strategy.

Training_Info

The following table shows the performance of different large language models used in this work to generate heterogeneous directed graphs in the USPTO-LLM dataset.

LLM Type	gpt-4-0613	gpt-4-1106-preview	gpt-4-0125-preview	gpt-3.5-turbo-0125
	Dataset	USPTO_full	USPTO_full	USPTO_full
	Reactions per Request	3	3	3
1st-round	API calls	1030	2000	2000
	Success Rate (Before Pattern Repair)	0.67	0.65	0.66
	Success Rate (After Pattern Repair)	0.88	0.84	0.86
	Valid HeteroGraphs per API call (Before Pattern Repair)	2.00	1.94	1.98
	Valid HeteroGraphs per API call (After Pattern Repair)	2.64	2.53	2.57
2nd-round	API calls	434	233	285
	Success Rate (Before Pattern Repair)	0.26	0.20	0.24
	Success Rate (After Pattern Repair)	0.51	0.31	0.32
	Valid HeteroGraphs per API call (Before Pattern Repair)	0.78	0.59	0.71
	Valid HeteroGraphs per API call (After Pattern Repair)	1.54	0.92	0.95
Total	API calls	1464	2233	2285
	Success Rate (Before Pattern Repair)	0.78	0.67	0.70
	Success Rate (After Pattern Repair)	0.88	0.90	0.90
	Valid HeteroGraphs per API call (Before Pattern Repair)	1.64	1.80	1.83
	Valid HeteroGraphs per API call (After Pattern Repair)	1.86	2.42	2.37