Small immunological clocks identified by Deep Learning and Gradient Boosting
Frontiers in Immunology(2023)
摘要
Background The aging process affects all systems of the human body, and the observed increase in inflammatory components affecting the immune system in old age can lead to the development of age-associated diseases and systemic inflammation.
Results We propose a small clock model SImAge based on a limited number of immunological biomarkers. To regress the chronological age from cytokine data, we first use a baseline Elastic Net model, gradient-boosted decision trees models, and several deep neural network architectures. For the full dataset of 46 immunological parameters, DANet, SAINT, FT-Transformer and TabNet models showed the best results for the test dataset. Dimensionality reduction of these models with SHAP values revealed the 10 most age-associated immunological parameters, taken to construct the SImAge small immunological clock. The best result of the SImAge model shown by the FT-Transformer deep neural network model has mean absolute error of 6.94 years and Pearson ρ = 0.939 on the independent test dataset. Explainable artificial intelligence methods allow for explaining the model solution for each individual participant.
Conclusions We developed an approach to construct a model of immunological age based on just 10 immunological parameters, coined SImAge, for which the FT-Transformer deep neural network model had proved to be the best choice. The model shows competitive results compared to the published studies on immunological profiles, and takes a smaller number of features as an input. Neural network architectures outperformed gradient-boosted decision trees, and can be recommended in the further analysis of immunological profiles.
### Competing Interest Statement
The authors have declared no competing interest.
* AI
: Artificial Intelligence
AutoInt
: Automatic Feature Interaction Learning via Self-Attentive Neural Network
CatBoost
: Categorical Boosting
CI
: Confidence Interval
CKD
: Chronic Kidney Disease
DANet
: Deep Abstract Network
DNA
: Deoxyribonucleic Acid
DNN
: Deep Neural Network
ESRD
: End-Stage Renal Disease
FDR
: False Discovery Rate
FT-Transformer
: Feature Tokenizer and Transformer
GBDT
: Gradient-Boosted Decision Tree
GLU
: Gated Linear Unit
GOSS
: Gradient-based One-Side Sampling
LightGBM
: Light Gradient Boosting Machine
MAE
: Mean Absolute Error
MLP
: Multilayer Perceptron
MVS
: Minimal Variance Sampling
NAM
: Neural Additive Model
NODE
: Neural Oblivious Decision Ensemble
ODT
: Oblivious Decision Tree
OOR
: Out Of Range
RMSE
: Root Mean Squared Error
SAINT
: Self-Attention and Intersample Attention Transformer
SGB
: Stochastic Gradient Boosting
SHAP
: Shapley Additive Explanations
STD
: Standard Deviation
TPE
: Tree-structured Parzen Estimator
XAI
: Explainable Artificial Intelligence
XGBoost
: eXtreme Gradient Boosting
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