Medicine is a science of uncertainty but art of probability. The same symptoms may result from different diagnosis. The same diagnosis may need different treatment modalities. The same therapeutic maneuver may lead to different prognosis. The uncertainty of diagnosis, therapy and prognosis stems from that we do not understand the etiology and pathogenesis. It also arises from our incomplete enrollment of patient’s data. Take peptic ulcer as an example, stress and acid are considered the etiologic factors until the discovery of H. pylori. We cannot cure peptic ulcer by anxiolytics or acid-reducing agents but we can cure it by 2 weeks of antibiotics. The progress of genomic medicine was assumed to be the key for individual variability in manifeatation of diseases and the solution for precision medicine, especially in the diagnosis and management of malignant neoplasms. However, the gut microbiota, so-called secondary genome, can influence host’s health and disease treatment through bacteria-derived metabolites, immunity and gut-brain axis. Accordingly, investigation of host genomics and microbiomics simultaneously could lead to a better understanding of health and diseases. The big data analysis is mandatory for multiomics research. Therefore, machine learning or artificial intelligence becomes important research tools for precision or smart medicine. Deep phenotyping and deep learning are the root of deep medicine. Compared with current shallow medicine, deep medicine can provide a deeper insight into the etiology and pathogenesis through comprehensive data collection and analyses. Collectively, my planned courses will be “Paradigm shift of medicine: form shallow medicine to deep medicine”. The content will include (a)Evolution of etiology, pathogenesis, diagnosis and treatment of peptic ulcer and gastric cancer. (b)Methologic progress of molecular epidemiology, clinical trial, genomic medicine, microbiomics, big data analyses and artificial intelligence.
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