Case Based Reasoning

The R package case-based-reasoning provides an R interface case based reasoning using machine learning.

Installation

CRAN

install.packages("CaseBasedReasoning")

GITHUB

install.packages("devtools")
devtools::install_github("sipemu/case-based-reasoning")

Features

This R package provides two methods case based reasoning by using an endpoint:

• Linear, logistic, and Cox regression

• Proximity and Depth Measure extracted from a fitted random forest (ranger package)

Besides the functionality of searching similar cases, some additional features are included:

• automatic validation of the key variables between the query and similar cases dataset

• checking proportional hazard assumption for the Cox Model

• C++-functions for distance calculation

Example: Cox-Beta-Model

Initialization

In the first example, we use the Cox-Model and the ovarian data set from the survival package. In the first step we initialize the R6 data object.

library(tidyverse)
library(survival)
library(CaseBasedReasoning)
ovarian$resid.ds <- factor(ovarian$resid.ds)
ovarian$rx <- factor(ovarian$rx)
ovarian$ecog.ps <- factor(ovarian$ecog.ps)

# initialize R6 object
coxBeta <- CoxBetaModel$new(Surv(futime, fustat) ~ age + resid.ds + rx + ecog.ps)

Similar Cases

After the initialization, we may want to get for each case in the query data the most similar case from the learning data.

n <- nrow(ovarian)
trainID <- sample(1:n, floor(0.8 * n), F)
testID <- (1:n)[-trainID]

# fit model 
ovarian[trainID, ] %>% 
  coxBeta$fit()
# get similar cases
ovarian[testID, ] %>%
  coxBeta$get_similar_cases(queryData = ovarian[testID, ], k = 3) -> matchedData

You may extract then the similar cases and the verum data and put them together:

Note 1: In the initialization step, we dropped all cases with missing values in the variables of data and endPoint. So, you need to make sure that NA handling is done by you.

Note 2: The data.table returned from coxBeta$get_similar_cases has four additional columns:

1. caseId: By this column you may map the similar cases to cases in data, e.g. if you had chosen k = 3, then the first three elements in the column caseId will be 1 (following three 2 and so on). This means that this three cases are the three most similar cases to case 0 in verum data.
2. scDist: The calculated distance
3. scCaseId: Grouping number of query with matched data
4. group: Grouping matched or query data

Distance Matrix

Alternatively, you may just be interested in the distance matrix, then you go this way:

ovarian %>%
  coxBeta$calc_distance_matrix() -> distMatrix

coxBeta$calc_distance_matrix() calculates the full distance matrix. This matrix the dimension: cases of data versus cases of query data. If the query dataset is bot available, this functions calculates a n times n distance matrix of all pairs in data. The distance matrix is saved internally in the cbrCoxModel object: coxBeta$distMat.

Example: RandomForest-Model

Initialization

In the second example, we present the Random Forest model for a distance measure approximation applied on the ovarian data set from the survival package. This package offers two ways for distance/similarity calculation (see documentation):

• proximity

• depth

Let's initialize the R6 data object.

library(tidyverse)
library(survival)
library(CaseBasedReasoning)
ovarian$resid.ds <- factor(ovarian$resid.ds)
ovarian$rx <- factor(ovarian$rx)
ovarian$ecog.ps <- factor(ovarian$ecog.ps)

# initialize R6 object
rfSC <- RFModel$new(Surv(futime, fustat) ~ age + resid.ds + rx + ecog.ps)

All cases with missing values in the learning and end point variables are dropped (na.omit) and the reduced data set without missing values is saved internally. You get a text output on how many cases were dropped. character variables will be transformed to factor.

Optionally, you may want to adjust some parameters in the fitting step of the random forest algorithm. Possible arguments are: , ntree, mtry, and splitrule. The documentation of this parameters can be found in the ranger R-package. Furthermore, you are able to choose the two distance measures:

• Proximity: the proximity matrix
• Depth (Default): Calculates the average edge length over all trees

This can be done by

rfSC$set_dist(distMethod = "Proximity")

All other steps (excluding checking for proportional hazard assumption are the same as for the Cox-Model).

Similar Cases:

n <- nrow(ovarian)
trainID <- sample(1:n, floor(0.8 * n), F)
testID <- (1:n)[-trainID]

# fit model 
ovarian[trainID, ] %>% 
  rfSC$fit()
# get similar cases
ovarian[trainID, ] %>%
  rfSC$get_similar_cases(queryData = ovarian[testID, ], k = 3) -> matchedData

Distance Matrix Calculation:

ovarian %>%
  rfSC$calc_distance_matrix() -> distMatrix

Contribution

Responsible for Mathematical Model Development and Programming

• PD Dr. Jürgen Dippon, Institut für Stochastik und Anwendungen, Universität Stuttgart

• Dr. Simon Müller, TTI GmbH - MUON-STAT

Medical Advisor

• Dr. Peter Fritz

• Professor Dr. Friedel

Funding

The work was funded by the Robert Bosch Foundation. Special thanks go to Professor Dr. Friedel (Thoraxchirugie - Klinik Schillerhöhe).

References

Main

• Dippon et al. A statistical approach to case based reasoning, with application to breast cancer data (2002),

• Friedel et al. Postoperative Survival of Lung Cancer Patients: Are There Predictors beyond TNM? (2012).

Other

• Englund and Verikas A novel approach to estimate proximity in a random forest: An exploratory study

• Stuart, E. et al. Matching methods for causal inference: Designing observational studies

• Defossez et al. Temporal representation of care trajectories of cancer patients using data from a regional information system: an application in breast cancer