Drug-target interaction prediction (DTI) is essential in various applications including drug discovery and clinical application. There are two perspectives of input data widely used in DTI prediction: Intrinsic data represents how drugs or targets are constructed, and extrinsic data represents how drugs or targets are related to other biological entities. However, any of the two perspectives of input data can be scarce for some drugs or targets, especially for those unpopular or newly discovered. Furthermore, ground-truth labels for specific interaction types can also be scarce. Therefore, we propose the first method to tackle DTI prediction under input data and/or label scarcity. To make our model functional when only one perspective of input data is available, we design two separate experts to process intrinsic and extrinsic data respectively and fuse them adaptively according to different samples. Furthermore, to make the two perspectives complement each other and remedy label scarcity, two experts synergize with each other in a mutually supervised way to exploit the enormous unlabeled data. Extensive experiments on 3 real-world datasets under different extents of input data scarcity and/or label scarcity demonstrate our model outperforms states of the art significantly and steadily, with a maximum improvement of 53.53%. We also test our model without any data scarcity and it still outperforms current methods.

Large language models (LLMs) have demonstrated their strong capabilities in various domains, and have been recently integrated for graph analysis as graph language models (GLMs). With LLMs as the predictor, some GLMs can interpret unseen tasks described by natural language, and learn from a few examples in the prompts without parameter tuning, known as in-context learning (ICL). Another subset of GLMs utilizes abundant training labels to enhance model performance, known as instruction tuning. However, we argue that ICL on graphs has effectiveness issues due to fixed parameters and efficiency issues due to long context. Meanwhile, the large amount of labeled data required for instruction tuning can be difficult to obtain in real-world scenarios. To this end, we aim to introduce an extra parameter adaptation stage that can efficiently tailor GLMs to an unseen graph and task with only a few labeled examples, in exchange for better prediction accuracy and faster inference speed. For implementation, in this paper we propose GraphLAMA method, with its model backbone and learning schemes specialized for efficient tuning and inference. Specifically, for the model backbone, we use a graph neural network (GNN) with several well-designed components (e.g., hop encodings, gating modules) to transform nodes into the representation space of LLM tokens. Task instructions can then be represented as a mixture of node and language tokens. In the pre-training stage, all model parameters except for the LLM will be trained with different tasks (i.e., node matching, node classification, and link prediction) to capture general knowledge. In the adaptation stage, only a few pre-trained parameters will be updated based on few-shot examples. Extensive experiments on few/zero-shot node classification and summary generation show that our proposed GraphLAMA achieves state-of-the-art (SOTA) performance with 4.91% absolute improvement in accuracy. Compared with ICL, our inference speed can be 10 times faster under 5-shot setting. Our code is available on GitHub at https://github.com/BUPT-GAMMA/GraphLAMA.

Yuxia Wu, Shujie Li, Yuan Fang, Chuan Shi. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers). 2025.