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Background:  Parkinson’s disease (PD), Alzheimer’s disease (AD) are common neurodegenerative disease, while mild cognitive impairment (MCI) may be happened in the early stage of AD or PD. Blood biomarkers are considered to be less invasive, less cost and more convenient, and there is tremendous potential for the diagnosis and prediction of neurodegenerative diseases. As a recently mentioned field, artificial intelligence (AI) is often applied in biology and shows excellent results. In this article, we use AI to model PD, AD, MCI data and analyze the possible connections between them.   Method:  Human blood protein microarray profiles including 156 CT, 50 MCI, 132 PD, 50 AD samples are collected from Gene Expression Omnibus (GEO). First, we used bioinformatics methods and feature engineering in machine learning to screen important features, constructed artificial neural network (ANN) classifier models based on these features to distinguish samples, and evaluated the model’s performance with classification accuracy and Area Under Curve (AUC). Second, we used Ingenuity Pathway Analysis (IPA) methods to analyse the pathways and functions in early stage and late stage samples of different diseases, and potential targets for drug intervention by predicting upstream regulators.   Result:  We used different classifier to construct the model and finally found that ANN model would outperform the traditional machine learning model. In summary, three different classifiers were constructed to be used in different application scenarios, First, we incorporated 6 indicators, including EPHA2, MRPL19, SGK2, to build a diagnostic model for AD with a test set accuracy of up to 98.07%. Secondly, incorporated 15 indicators such as ERO1LB, FAM73B, IL1RN to build a diagnostic model for PD, with a test set accuracy of 97.05%. Then, 15 indicators such as XG, FGFR3 and CDC37 were incorporated to establish a four-category diagnostic model for both AD and PD, with a test set accuracy of 98.71%. All classifier models have an auc value greater than 0.95. Then, we verified that the constructed feature engineering filtered out fewer important features but contained more information, which helped to build a better model. In addition, by classifying the disease types more carefully into early and late stages of AD, MCI, and PD, respectively, we found that early PD may occur earlier than early MCI. Finally, there are 24 proteins that are both differentially expressed proteins and upstream regulators in the disease group versus the normal group, and these proteins may serve as potential therapeutic targets and targets for subsequent studies.   Conclusion:  The feature engineering we build allows better extraction of information while reducing the number of features, which may help in subsequent applications. Building a classifier based on blood protein profiles using deep learning methods can achieve better classification performance, and it can help us to diagnose the disease early. Overall, it is important for us to study neurodegenerative diseases from both diagnostic and interventional aspects.

Diagnostic AI Modeling and Pseudo Time Series Profiling of AD and PD Based on Individualized Serum Proteome Data