Description Details Author(s) References Examples
Implement surrogate-assisted feature extraction (SAFE) and common machine learning approaches to train and validate phenotyping models. Background and details about the methods can be found at Zhang et al. (2019) <doi:10.1038/s41596-019-0227-6>, Yu et al. (2017) <doi:10.1093/jamia/ocw135>, and Liao et al. (2015) <doi:10.1136/bmj.h1885>.
The DESCRIPTION file:
This package was not yet installed at build time.
Index: This package was not yet installed at build time.
PheCAP provides a straightforward interface for conducting
phenotyping on eletronic health records. One can specify the
data via PhecapData
, define surrogate using
PhecapSurrogate
. Next, one may run
surrogate-assisted feature extraction (SAFE) by calling
phecap_run_feature_extraction
, and then
train and validate phenotyping models via
phecap_train_phenotyping_model
and
phecap_validate_phenotyping_model
.
The predictive performance can be visualized using
phecap_plot_roc_curves
.
Predicted phenotype is provided by
phecap_predict_phenotype
.
Yichi Zhang [aut], Chuan Hong [aut], Tianxi Cai [aut], PARSE LTD [aut, cre]
Maintainer: PARSE LTD <software@parse-health.org>
Yu, S., Chakrabortty, A., Liao, K. P., Cai, T., Ananthakrishnan, A. N., Gainer, V. S., ... & Cai, T. (2016). Surrogate-assisted feature extraction for high-throughput phenotyping. Journal of the American Medical Informatics Association, 24(e1), e143-e149.
Liao, K. P., Cai, T., Savova, G. K., Murphy, S. N., Karlson, E. W., Ananthakrishnan, A. N., ... & Churchill, S. (2015). Development of phenotype algorithms using electronic medical records and incorporating natural language processing. bmj, 350, h1885.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 | # Simulate an EHR dataset
size <- 2000
latent <- rgamma(size, 0.3)
latent2 <- rgamma(size, 0.3)
ehr_data <- data.frame(
ICD1 = rpois(size, 7 * (rgamma(size, 0.2) + latent) / 0.5),
ICD2 = rpois(size, 6 * (rgamma(size, 0.8) + latent) / 1.1),
ICD3 = rpois(size, 1 * rgamma(size, 0.5 + latent2) / 0.5),
ICD4 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
NLP1 = rpois(size, 8 * (rgamma(size, 0.2) + latent) / 0.6),
NLP2 = rpois(size, 2 * (rgamma(size, 1.1) + latent) / 1.5),
NLP3 = rpois(size, 5 * (rgamma(size, 0.1) + latent) / 0.5),
NLP4 = rpois(size, 11 * rgamma(size, 1.9 + latent) / 1.9),
NLP5 = rpois(size, 3 * rgamma(size, 0.5 + latent2) / 0.5),
NLP6 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
NLP7 = rpois(size, 1 * rgamma(size, 0.5) / 0.5),
HU = rpois(size, 30 * rgamma(size, 0.1) / 0.1),
label = NA)
ii <- sample.int(size, 400)
ehr_data[ii, "label"] <- with(
ehr_data[ii, ], rbinom(400, 1, plogis(
-5 + 1.5 * log1p(ICD1) + log1p(NLP1) +
0.8 * log1p(NLP3) - 0.5 * log1p(HU))))
# Define features and labels used for phenotyping.
data <- PhecapData(ehr_data, "HU", "label", validation = 0.4)
data
# Specify the surrogate used for
# surrogate-assisted feature extraction (SAFE).
# The typical way is to specify a main ICD code, a main NLP CUI,
# as well as their combination.
# The default lower_cutoff is 1, and the default upper_cutoff is 10.
# In some cases one may want to define surrogate through lab test.
# Feel free to change the cutoffs based on domain knowledge.
surrogates <- list(
PhecapSurrogate(
variable_names = "ICD1",
lower_cutoff = 1, upper_cutoff = 10),
PhecapSurrogate(
variable_names = "NLP1",
lower_cutoff = 1, upper_cutoff = 10))
# Run surrogate-assisted feature extraction (SAFE)
# and show result.
feature_selected <- phecap_run_feature_extraction(
data, surrogates, num_subsamples = 50, subsample_size = 200)
feature_selected
# Train phenotyping model and show the fitted model,
# with the AUC on the training set as well as random splits.
model <- phecap_train_phenotyping_model(
data, surrogates, feature_selected, num_splits = 100)
model
# Validate phenotyping model using validation label,
# and show the AUC and ROC.
validation <- phecap_validate_phenotyping_model(data, model)
validation
phecap_plot_roc_curves(validation)
# Apply the model to all the patients to obtain predicted phenotype.
phenotype <- phecap_predict_phenotype(data, model)
# A more complicated example
# Load Data.
data(ehr_data)
data <- PhecapData(ehr_data, "healthcare_utilization", "label", 0.4)
data
# Specify the surrogate used for
# surrogate-assisted feature extraction (SAFE).
# The typical way is to specify a main ICD code, a main NLP CUI,
# as well as their combination.
# In some cases one may want to define surrogate through lab test.
# The default lower_cutoff is 1, and the default upper_cutoff is 10.
# Feel free to change the cutoffs based on domain knowledge.
surrogates <- list(
PhecapSurrogate(
variable_names = "main_ICD",
lower_cutoff = 1, upper_cutoff = 10),
PhecapSurrogate(
variable_names = "main_NLP",
lower_cutoff = 1, upper_cutoff = 10),
PhecapSurrogate(
variable_names = c("main_ICD", "main_NLP"),
lower_cutoff = 1, upper_cutoff = 10))
# Run surrogate-assisted feature extraction (SAFE)
# and show result.
feature_selected <- phecap_run_feature_extraction(data, surrogates)
feature_selected
# Train phenotyping model and show the fitted model,
# with the AUC on the training set as well as random splits
model <- phecap_train_phenotyping_model(data, surrogates, feature_selected)
model
# Validate phenotyping model using validation label,
# and show the AUC and ROC
validation <- phecap_validate_phenotyping_model(data, model)
validation
phecap_plot_roc_curves(validation)
# Apply the model to all the patients to obtain predicted phenotype.
phenotype <- phecap_predict_phenotype(data, model)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.