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validation_pct: The proportion of the data samples used as validation data. For GLM this is the proportion of the rows in the training data. For GBM it is the proportion of the samples in the training data.
validation_frame_size: The number of data samples (in rows) to use as validation samples. For GLM this is the number of rows in the training data. For GBM it is the number of samples in the training data.
validation_frame_index: The position of the validation data in the validation_frame list. If x and y are not provided, the first and last validation data are used. For example, if the first and last validation data are not present, -1 and 1 are used, respectively.
validation_frame_test_index: The position of the test data in the validation_frame list. If x and y are not provided, the first and last test data are used. For example, if the first and last test data are not present, -1 and 1 are used, respectively.
Note: The function to predict HLA class I based on sequence data is supported by Chimera [ ]; the function to predict KRAS mutation is supported by Gephi [ ], and Nyan [ ]. The function to predict TCR is supported by TCRseqFlow [ ].
We have performed additional performance evaluation of leukocyte subtypes stratified by cell surface marker expression. In particular, we have used our test data to benchmark commonly used leukocyte subpopulation markers in isolation of each other, and have evaluated the relative performance of these markers in isolation, with several subtype-specific markers. We have also compared the performance of our newly developed technique (tSNE + tSNE + DNN) to that of other existing algorithms (tSNE + tSNE + SVM, tSNE + SVM + DNN).
validation_frame: Used to select the best lambda based on the validation data. If available, cross-validation performance takes precedence. If no validation data is available, the best lambda is selected based on training data performance and is therefore guaranteed to always be the minimal lambda computed since GLM cannot overfit on a training dataset.
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One of the drawbacks to this approach was that we needed to recompile every time we made even a small change to the code. This slowed everything else we were doing down and because we couldn't always have someone waiting for the application to finish building. 827ec27edc