UVAE: Integration of Unpaired and Heterogeneous Clinical Flow Cytometry Data

UVAE: Integration of Unpaired and Heterogeneous Clinical Flow Cytometry Data This repository contains training data, metadata, and results for the above publication. 'data.zip' contains the subsampled flow cytometry data and clinical metadata for the lineage and chemokine panels. 'toy-data.zip' contains the synthetic data (in pickle and csv formats) used for benchmarks and the associated source flow file. 'data-cycombine-comp.zip' contains the processed DFCI and van Gassen datasets used for model comparison, the scripts used to obtain the .RDS files from raw flow data, the derived imputation datasets (created by splitting the data and hiding 5 markers from each panel), and the results of training imputation UVAE and cyCombine models. 'models-integration.zip' contains the trained UVAE models for lineage and chemokine panels, as well as imputed marker data. 'models-severity.zip' contains the trained COVID severity regression models, as well as their scores and gradient attribution plots. Note that 'models-integration' and 'models-severity' are trained on the entire CIRCO data (the severity models regression was performed on 4 held-out folds, but the initial integration and cluster definition were performed on the entire dataset). 'crossvalidation.zip' contains the models used to obtain test scores, which were trained by fully holding out the test data for each fold. Inside, there are 4 separate UVAE models for lineage (in 'lineage-split') and chemokine (in 'chemokine-split'). Each contains a separate embedding file containing both training and test data used to train the severity models. The severity models are in 'severity-reg-held' folder, with full results in 'scores/combined.csv'.UVAE：未配对异质性临床流式细胞术数据的整合 本仓库包含对应上述发表论文的训练数据、元数据与实验结果。 `data.zip` 包含用于谱系面板与趋化因子面板的下采样流式细胞术数据及临床元数据。 `toy-data.zip` 包含用于基准测试的合成数据（格式为pickle与csv）以及对应的原始流式文件。 `data-cycombine-comp.zip` 包含用于模型对比的已处理DFCI与van Gassen数据集、从原始流式数据获取.RDS文件的脚本、衍生插补数据集（通过拆分数据并隐藏每个面板中的5个标记物构建），以及训练插补UVAE与cyCombine模型的实验结果。 `models-integration.zip` 包含针对谱系面板与趋化因子面板训练得到的UVAE模型，以及插补后的标记物数据。 `models-severity.zip` 包含训练完成的新冠严重程度回归模型，及其评估分数与梯度归因图。请注意，`models-integration`与`models-severity`均基于完整CIRCO数据集进行训练：严重程度模型的回归实验在4个留出折上完成，但初始整合与聚类定义是在全数据集上执行的。 `crossvalidation.zip` 包含用于获取测试集分数的模型，此类模型通过完全留出每个交叉验证折的测试数据进行训练。该压缩包内包含4个独立的UVAE模型：谱系模型位于`lineage-split`文件夹，趋化因子模型位于`chemokine-split`文件夹。每个模型均附带独立的嵌入文件，其中包含用于训练严重程度模型的全部训练与测试数据。严重程度模型存于`severity-reg-held`文件夹，完整实验结果保存在`scores/combined.csv`中。