The objective of topic inference in research proposals aims to obtain the most suitable disciplinary division from the discipline system defined by a funding agency. The agency will subsequently find appropriate peer-review experts from their database based on this division. Automated topic inference can reduce human errors caused by manual topic filling, bridge the knowledge gap between funding agencies and project applicants, and improve system efficiency. Existing methods focus on modeling this as a hierarchical multi-label classification problem, using generative models to iteratively infer the most appropriate topic information. However, these methods overlook the gap in scale between interdisciplinary research proposals and non-interdisciplinary ones, leading to an unjust phenomenon where the automated inference system categorizes interdisciplinary proposals as non-interdisciplinary, causing unfairness during the expert assignment. How can we address this data imbalance issue under a complex discipline system and hence resolve this unfairness? In this article, we implement a topic label inference system based on a Transformer encoder–decoder architecture. Furthermore, we utilize interpolation techniques to create a series of pseudo-interdisciplinary proposals from non-interdisciplinary ones during training based on non-parametric indicators, such as cross-topic probabilities and topic occurrence probabilities. This approach aims to reduce the bias of the system during model training. Finally, we conduct extensive experiments on a real-world dataset to verify the effectiveness of the proposed method. The experimental results demonstrate that our training strategy can significantly mitigate the unfairness generated in the topic inference task. To improve the reproducibility of our research, we have released accompanying code by Dropbox. 1