Dongsheng Li

Xinnan Dai, Caihua Shan, Jie Zheng et al.

Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks to provide biological insights for humans due to their black-box nature. Recently, some works integrated biological knowledge with neural networks to improve the transparency and performance of their models. However, these methods can only incorporate partial biological knowledge, leading to suboptimal performance. In this paper, we propose the Biological Factor Regulatory Neural Network (BFReg-NN), a generic framework to model relations among biological factors in cell systems. BFReg-NN starts from gene expression data and is capable of merging most existing biological knowledge into the model, including the regulatory relations among genes or proteins (e.g., gene regulatory networks (GRN), protein-protein interaction networks (PPI)) and the hierarchical relations among genes, proteins and pathways (e.g., several genes/proteins are contained in a pathway). Moreover, BFReg-NN also has the ability to provide new biologically meaningful insights because of its white-box characteristics. Experimental results on different gene expression-based tasks verify the superiority of BFReg-NN compared with baselines. Our case studies also show that the key insights found by BFReg-NN are consistent with the biological literature.

Zhuoxuan Jiang, Haoyuan Peng, Shanshan Feng et al.

Self-correction is emerging as a promising approach to mitigate the issue of hallucination in Large Language Models (LLMs). To facilitate effective self-correction, recent research has proposed mistake detection as its initial step. However, current literature suggests that LLMs often struggle with reliably identifying reasoning mistakes when using simplistic prompting strategies. To address this challenge, we introduce a unique prompting strategy, termed the Pedagogical Chain-of-Thought (PedCoT), which is specifically designed to guide the identification of reasoning mistakes, particularly mathematical reasoning mistakes. PedCoT consists of pedagogical principles for prompts (PPP) design, two-stage interaction process (TIP) and grounded PedCoT prompts, all inspired by the educational theory of the Bloom Cognitive Model (BCM). We evaluate our approach on two public datasets featuring math problems of varying difficulty levels. The experiments demonstrate that our zero-shot prompting strategy significantly outperforms strong baselines. The proposed method can achieve the goal of reliable mathematical mistake identification and provide a foundation for automatic math answer grading. The results underscore the significance of educational theory, serving as domain knowledge, in guiding prompting strategy design for addressing challenging tasks with LLMs effectively.