Whether viewed as an expert or as a source of ‘knowledge hallucination’, the use of ChatGPT in medical practice has stirred ongoing debate. This study sought to evaluate ChatGPT's capabilities in the field of clinical genetics, focusing on tasks such as ‘Clinical genetics exams’, ‘Associations between genetic diseases and pathogenic genes’, and ‘Limitations and trends in clinical genetics’. Results indicated that ChatGPT performed exceptionally well in question-answering tasks, particularly in clinical genetics exams and diagnosing single-gene diseases. It also effectively outlined the current limitations and prospective trends in clinical genetics. However, ChatGPT struggled to provide comprehensive answers regarding multi-gene or epigenetic diseases, particularly with respect to genetic variations or chromosomal abnormalities. In terms of systematic summarization and inference, some randomness was evident in ChatGPT's responses. In summary, while ChatGPT possesses a foundational understanding of general knowledge in clinical genetics due to hyperparameter learning, it encounters significant challenges when delving into specialized knowledge and navigating the complexities of clinical genetics, particularly in mitigating ‘Knowledge Hallucination’. To optimize its performance and depth of expertise in clinical genetics, integration with specialized knowledge databases and knowledge graphs is imperative.

To accurately segment various clinical lesions from computed tomography(CT) images is a critical task for the diagnosis and treatment of many diseases. However, current segmentation frameworks are tailored to specific diseases, and limited frameworks can detect and segment different types of lesions. Besides, it is another challenging problem for current segmentation frameworks to segment visually inconspicuous and small-scale tumors (such as small intestinal stromal tumors and pancreatic tumors). Our proposed framework, CDI-NSTSEG, efficiently segments small non-salient tumors using multi-scale visual information and non-local target mining. CDI-NSTSEG follows the diagnostic process of clinicians, including preliminary screening, localization, refinement, and segmentation. Specifically, we first explore to extract the unique features at three different scales (1×, 0.5×, and 1.5×) based on the scale space theory. Our proposed scale fusion module (SFM) hierarchically fuses features to obtain a comprehensive representation, similar to preliminary screening in clinical diagnosis. The global localization module (GLM) is designed with a non-local attention mechanism. It captures the long-range semantic dependencies of channels and spatial locations from the fused features. GLM enables us to locate the tumor from a global perspective and output the initial prediction results. Finally, we design the layer focusing module (LFM) to gradually refine the initial results. LFM mainly conducts context exploration based on foreground and background features, focuses on suspicious areas layer-by-layer, and performs element-by-element addition and subtraction to eliminate errors. Our framework achieves state-of-the-art segmentation performance on small intestinal stromal tumor and pancreatic tumor datasets.

MOTIVATION: In the era of big data and precision medicine, accurate risk assessment is a prerequisite for the implementation of risk screening and preventive treatment. A large number of studies have focused on the risk of cancer, and related risk prediction models have been constructed, but there is a lack of effective resource integration for systematic comparison and personalized applications. Therefore, the establishment and analysis of the cancer risk prediction model knowledge base (CRPMKB) is of great significance. RESULTS: The current knowledge base contains 802 model data. The model comparison indicates that the accuracy of cancer risk prediction was greatly affected by regional differences, cancer types and model types. We divided the model variables into four categories: environment, behavioral lifestyle, biological genetics and clinical examination, and found that there are differences in the distribution of various variables among different cancer types. Taking 50 genes involved in the lung cancer risk prediction models as an example to perform pathway enrichment analyses and the results showed that these genes were significantly enriched in p53 Signaling and Aryl Hydrocarbon Receptor Signaling pathways which are associated with cancer and specific diseases. In addition, we verified the biological significance of overlapping lung cancer genes via STRING database. CRPMKB was established to provide researchers an online tool for the future personalized model application and developing. This study of CRPMKB suggests that developing more targeted models based on specific demographic characteristics and cancer types will further improve the accuracy of cancer risk model predictions. AVAILABILITY AND IMPLEMENTATION: CRPMKB is freely available at http://www.sysbio.org.cn/CRPMKB/. The data underlying this article are available in the article and in its online supplementary material. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Heart failure (HF) is a cardiovascular disease with a high incidence around the world. Accumulating studies have focused on the identification of biomarkers for HF precision medicine. To understand the HF heterogeneity and provide biomarker information for the personalized diagnosis and treatment of HF, a knowledge database collecting the distributed and multiple-level biomarker information is necessary. RESULTS: In this study, the HF biomarker knowledge database (HFBD) was established by manually collecting the data and knowledge from literature in PubMed. HFBD contains 2618 records and 868 HF biomarkers (731 single and 137 combined) extracted from 1237 original articles. The biomarkers were classified into proteins, RNAs, DNAs and the others at molecular, image, cellular and physiological levels. The biomarkers were annotated with biological, clinical and article information as well as the experimental methods used for the biomarker discovery. With its user-friendly interface, this knowledge database provides a unique resource for the systematic understanding of HF heterogeneity and personalized diagnosis and treatment of HF in the era of precision medicine. AVAILABILITY AND IMPLEMENTATION: The platform is openly available at http://sysbio.org.cn/HFBD/.