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Chemical reaction data has existed and still largely exists in unstructured forms. But curating such information into datasets suitable for tasks such as yield and reaction outcome prediction is impractical via manual curation and not possible to automate through programmatic means alone. Large language models (LLMs) have emerged as potent tools, showcasing remarkable capabilities in processing textual information and therefore could be extremely useful in automating this process. To address the challenge of unstructured data, we manually curated a dataset of structured chemical reaction data to fine-tune and evaluate LLMs. We propose a paradigm that leverages prompt-tuning, fine-tuning techniques, and a verifier to check the extracted information. We evaluate the capabilities of various LLMs, including LLAMA-2 and GPT models with different parameter counts, on the data extraction task. Our results show that prompt tuning of GPT-4 yields the best accuracy and evaluation results. Fine-tuning LLAMA-2 models with hundreds of samples does enable them and organize scientific material according to user-defined schemas better though. This workflow shows an adaptable approach for chemical reaction data extraction but also highlights the challenges associated with nuance in chemical information. We open-sourced our code at GitHub. 

Inverse molecular generation is an essential task for drug discovery, and generative models offer a very promising avenue, especially when diffusion models are used. Despite their great success, existing methods are inherently limited by the lack of a semantic latent space that can not be navigated and perform targeted exploration to generate molecules with desired properties. Here, we present a property-guided diffusion model for generating desired molecules, which incorporates a sophisticated diffusion process capturing intricate interactions of nodes and edges within molecular graphs and leverages a time-dependent molecular property classifier to integrate desired properties into the diffusion sampling process. Furthermore, we extend our model to a multi-property-guided paradigm. Experimental results underscore the competitiveness of our approach in molecular generation, highlighting its superiority in generating desired molecules without the need for additional optimization steps. 

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved considerable progress, especially in methods based on deep molecular graph learning. In this survey, we systematically review these graph-based molecular representation techniques, especially the methods incorporating chemical domain knowledge. Specifically, we first introduce the features of 2D and 3D molecular graphs. Then we summarize and categorize MRL methods into three groups based on their input. Furthermore, we discuss some typical chemical applications supported by MRL. To facilitate studies in this fast-developing area, we also list the benchmarks and commonly used datasets in the paper. Finally, we share our thoughts on future research directions.

 

Graph representation learning has attracted tremendous attention due to its remarkable performance in many real-world applications. However, prevailing supervised graph representation learning models for specific tasks often suffer from label sparsity issue as data labeling is always time and resource consuming. In light of this, few-shot learning on graphs (FSLG), which combines the strengths of graph representation learning and few-shot learning together, has been proposed to tackle the performance degradation in face of limited annotated data challenge. There have been many studies working on FSLG recently. In this paper, we comprehensively survey these work in the form of a series of methods and applications. Specifically, we first introduce FSLG challenges and bases, then categorize and summarize existing work of FSLG in terms of three major graph mining tasks at different granularity levels, i.e., node, edge, and graph. Finally, we share our thoughts on some future research directions of FSLG. The authors of this survey have contributed significantly to the AI literature on FSLG over the last few years.