MedFact: Benchmarking the Fact-Checking Capabilities of Large Language Models on Chinese Medical Texts

The increasing deployment of Large Language Models (LLMs) in healthcare necessitates a rigorous evaluation of their factual reliability. However, existing benchmarks are often limited by narrow domains of data, failing to capture the complexity of real-world medical information. To address this critical gap, we introduce MedFact, a new and challenging benchmark for Chinese medical fact-checking. MedFact comprises 2,116 expert-annotated instances curated from diverse real-world texts, spanning 13 medical specialties, 8 fine-grained error types, 4 writing styles, and multiple difficulty levels. Its construction employs a hybrid AI-human framework where iterative expert feedback refines an AI-driven, multi-criteria filtering process, ensuring both high data quality and difficulty. We conduct a comprehensive evaluation of 20 leading LLMs, benchmarking their performance on veracity classification and error localization against a human expert baseline. Our results reveal that while models can often determine if a text contains an error, precisely localizing it remains a substantial challenge, with even top-performing models falling short of human performance. Furthermore, our analysis uncovers a frequent ``over-criticism'' phenomenon, a tendency for models to misidentify correct information as erroneous, which is exacerbated by advanced reasoning techniques such as multi-agent collaboration and inference-time scaling. By highlighting these critical challenges for deploying LLMs in medical applications, MedFact provides a robust resource to drive the development of more factually reliable and medically aware models.

BrainNPT: Pre-training of Transformer networks for brain network classification

Deep learning methods have advanced quickly in brain imaging analysis over the past few years, but they are usually restricted by the limited labeled data. Pre-trained model on unlabeled data has presented promising improvement in feature learning in many domains, including natural language processing and computer vision. However, this technique is under-explored in brain network analysis. In this paper, we focused on pre-training methods with Transformer networks to leverage existing unlabeled data for brain functional network classification. First, we proposed a Transformer-based neural network, named as BrainNPT, for brain functional network classification. The proposed method leveraged <cls> token as a classification embedding vector for the Transformer model to effectively capture the representation of brain network. Second, We proposed a pre-training architecture with two pre-training strategies for BrainNPT model to leverage unlabeled brain network data to learn the structure information of brain networks. The results of classification experiments demonstrated the BrainNPT model without pre-training achieved the best performance with the state-of-the-art models, and the BrainNPT model with pre-training strongly outperformed the state-of-the-art models. The pre-training BrainNPT model improved 8.75% of accuracy compared with the model without pre-training. We further compared the pre-training strategies, analyzed the influence of the parameters of the model, and interpreted the fine-tuned model.

Transformer and Snowball Graph Convolution Learning for Biomedical Graph Classification

Graph or network has been widely used for describing and modeling complex systems in biomedicine. Deep learning methods, especially graph neural networks (GNNs), have been developed to learn and predict with such structured data. In this paper, we proposed a novel transformer and snowball encoding networks (TSEN) for biomedical graph classification, which introduced transformer architecture with graph snowball connection into GNNs for learning whole-graph representation. TSEN combined graph snowball connection with graph transformer by snowball encoding layers, which enhanced the power to capture multi-scale information and global patterns to learn the whole-graph features. On the other hand, TSEN also used snowball graph convolution as position embedding in transformer structure, which was a simple yet effective method for capturing local patterns naturally. Results of experiments using four graph classification datasets demonstrated that TSEN outperformed the state-of-the-art typical GNN models and the graph-transformer based GNN models.