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README.md

ITR (Individualized Treatment Recommendation)

ITR is a library implementing the framework described in the paper Estimating Optimal Treatment Regimes via Subgroup Identification in Randomized Control Trials and Observational Studies by Haoda Fu, Jin Zhou, Douglas E. Faries.

The library is implemented in C++ and can be built with cmake version 3.12 or later. The library has been tested with gcc version 8.1.0 and clang version 9.1.0.

Installation

Assume the source code has been unpacked into directory /path/to/ITR, the following steps will build the library in /path/to/ITR-build and install the library in /path/to/ITR-install.

> cd /path/to/ITR-build
> cmake /path/to/ITR -DCMAKE_INSTALL_PREFIX=/path/to/ITR-install
> make
> make install

This will install header file ITR.h, Data.h, and SearchEngine.h to /path/to/ITR-install/include/itr and libitr.a to path/to/ITR-install/lib. One could also specify a particular compiler by prefixing CC=/path/to/c_compiler CXX=/path/to/cpp_compiler to the cmake configuration line.

Usage

The demo directory contains a simple example demo.cpp showing how to use the library. A simple digest of this example is given below.

To use the library, one needs to include the header file ITR.h.

Inside main, one first creates an ITR::ITR instance. The non-type parameter specifies the depth of the search, where the valid values are 1, 2, or 3. Additionally, the constructor takes two arguments: The first one is a std::string object specifying the path to the input csv file, and the second one is the number of threads used in the search. Here, one has the choice of running the search sequentially or in parallel by passing an unsigned integer nThreads to the method. If nThreads is 1, the search is done sequentially. If nThreads is greater than 1, the search is done in parallel.

For the csv input file, the first line must be a header. The first column is the subject identifier, followed by continuous variables (labeled as cont*), ordinal variables (labeled as ord*), nominal variables (nom*), actions (A*), responses (Y*), and condition probablity P(A = 1 | X). The ITR library is case insensitive to these labels. The constructor of ITR::ITR will throw an exception if the input file does not exist or the search depth is invalid.

Once the search completes, one can query the top n search results by calling the report method.

Generally, one needs to provide -I/path/to/ITR-install/include/itr and -L/path/to/ITR-install/lib -litr to the compile command. For the demo example, it can be built as follows

> cd /path/to/ITR-build/demo
> make demo
> ./demo

We add a few options to the demo program, which can be found by

> .demo
Usage: ./demo [OPTIONS]
--data=STRING  Path to input file, default is sample100.csv
--thread=NUM   Number of threads to use, default is 1
--best=NUM     Number of top results to display, default is 5

An sample output of the demo program looks like

> ./demo --thread=8
Loading input data ...
Creating search engine with depth 3
Searching 689048 choices ...
Completed in 5.079716e-03 seconds using 8 threads
Score = 6.884978e+01, rule =  X1 < 49.8351,  X2 >= 49.6823,  X7 not in {0, 2} 
Score = 6.787278e+01, rule =  X1 < 58.8109,  X6 not in {2, 3},  X7 not in {2, 3} 
Score = 6.744488e+01, rule =  X1 < 49.8351,  X7 not in {0, 2},  X8 not in {2} 
Score = 6.742991e+01, rule =  X1 < 42.1108,  X5 < 3,  X6 not in {2, 3} 
Score = 6.740870e+01, rule =  X1 < 49.8351,  X6 not in {0, 2},  X8 not in {2} 

Authors

Bo Zhang (zhang_bo3 at lilly.com)

Jie Xue (xue_jie at lilly.com)

Haoda Fu (fu_haoda at lilly.com)