Duality Technology and Palisade

2022-11-29 23:05:02 -06:00 · 2022-11-29 23:05:02 -06:00 · 3947a74936
commit 3947a74936
parent 947bdb12c1
53 changed files with 24105 additions and 0 deletions
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/CMakeLists.txt
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/CMakeLists.txt
@ -0,0 +1,25 @@
+cmake_minimum_required (VERSION 3.5.1)
+  
+project(demo CXX)
+set(CMAKE_CXX_STANDARD 11)
+
+find_package(Palisade)
+
+set( CMAKE_CXX_FLAGS ${PALISADE_CXX_FLAGS} )
+set( CMAKE_EXE_LINKER_FLAGS ${PALISADE_EXE_LINKER_FLAGS} )
+
+include_directories( ${OPENMP_INCLUDES} )
+include_directories( ${PALISADE_INCLUDE} )
+include_directories( ${PALISADE_INCLUDE}/core )
+include_directories( ${PALISADE_INCLUDE}/pke )
+
+link_directories( ${PALISADE_LIBDIR} )
+link_directories( ${OPENMP_LIBRARIES} )
+link_libraries( ${PALISADE_LIBRARIES} )
+
+### ADD YOUR EXECUTABLE(s) HERE
+### add_executable( EXECUTABLE-NAME SOURCES )
+###
+### EXAMPLE: 
+add_executable( demo-logistic demo-logistic.cpp )
+add_executable( demo-chi2 demo-chi2.cpp )
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/LICENSE.md
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/LICENSE.md
@ -0,0 +1,108 @@
+Copyright (c) 2020 Duality Technologies, Inc.
+Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License <https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode>
+See the LICENSE file for the full text of the license.
+If you share the Licensed Material (including in modified form) you must include the above attribution in the copy you share.
+
+
+Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License
+By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
+
+Section 1 – Definitions.
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+Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License.
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+Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
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+For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.
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+Section 5 – Disclaimer of Warranties and Limitation of Liability.
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--- a/Code/Duality_Technologies/palisade-gwas-demos-master/PreLoad.cmake
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/PreLoad.cmake
@ -0,0 +1 @@
+set (CMAKE_GENERATOR "Unix Makefiles" CACHE INTERNAL "" FORCE)
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/README.md
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/README.md
@ -0,0 +1,49 @@
+GWAS Research Prototypes using Homomorphic Encryption
+=====================================
+
+This gitlab repository includes the implementation of Logistic Regression Approximation (LRA) and Chi-Square GWAS protocols described in
+"Secure large-scale genome-wide association studies using homomorphic encryption"
+by Marcelo Blatt, Alexander Gusev, Yuriy Polyakov, and Shafi Goldwasser.
+
+The repo includes the following files:
+* demo-logistic.cpp - research prototype for the LRA protocol.
+* demo-chi2.cpp - research prototype for the Chi-Square protocol.
+* data/random_sample.csv - an artificial random data set including 3 features, 200 individuals, and 16,384 SNPs (provided solely for demonstration purposes). 
+
+Notes on Compatibility with Different Versions of PALISADE
+=====================================
+The code in the master branch works in PALISADE v1.7 - 1.9. If you need to run this code in v1.10 and later, please use the branch called `updated-to-v1.10`.
+
+How to Build and Run the Prototypes
+=====================================
+
+1. Install PALISADE v1.7 - 1.9, e.g., v1.9.1 from [PALISADE Development Repository](https://gitlab.com/palisade/palisade-development/-/tree/release-v1.9.1). Follow the instructions provided in [README.md](https://gitlab.com/palisade/palisade-development/-/blob/release-v1.9.1/README.md).
+
+2. Clone this repository to a local directory and switch to this directory. 
+
+3. Create a directory where the binaries will be built. The typical choice is a subfolder "build". In this case, run the following commands:
+```
+mkdir build
+cd build
+cmake ..
+make
+```
+4. Run the following command to execute the LRA prototype (change sample size and number of SNPs as needed):
+```
+./demo-logistic --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
+```
+
+or
+
+Run the following command to execute the Chi-Square prototype (change sample size and number of SNPs as needed):
+```
+./demo-chi2 --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
+```
+
+5. The results will be written to the "data" folder. The following output files will be created for both prototypes:
+
+* pvalue.txt - p-values for each SNP
+* result.txt - runtime metrics
+
+Additional files with outputs of protocol-specific statistics will also be created.
+
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/build/CMakeCache.txt
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/build/CMakeCache.txt
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+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ < 800
+# define COMPILER_ID "VisualAge"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__NVCOMPILER)
+# define COMPILER_ID "NVHPC"
+# define COMPILER_VERSION_MAJOR DEC(__NVCOMPILER_MAJOR__)
+# define COMPILER_VERSION_MINOR DEC(__NVCOMPILER_MINOR__)
+# if defined(__NVCOMPILER_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__NVCOMPILER_PATCHLEVEL__)
+# endif
+
+#elif defined(__PGI)
+# define COMPILER_ID "PGI"
+# define COMPILER_VERSION_MAJOR DEC(__PGIC__)
+# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__)
+# if defined(__PGIC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__)
+# endif
+
+#elif defined(_CRAYC)
+# define COMPILER_ID "Cray"
+# define COMPILER_VERSION_MAJOR DEC(_RELEASE_MAJOR)
+# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR)
+
+#elif defined(__TI_COMPILER_VERSION__)
+# define COMPILER_ID "TI"
+  /* __TI_COMPILER_VERSION__ = VVVRRRPPP */
+# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000)
+# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000   % 1000)
+# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__        % 1000)
+
+#elif defined(__CLANG_FUJITSU)
+# define COMPILER_ID "FujitsuClang"
+# define COMPILER_VERSION_MAJOR DEC(__FCC_major__)
+# define COMPILER_VERSION_MINOR DEC(__FCC_minor__)
+# define COMPILER_VERSION_PATCH DEC(__FCC_patchlevel__)
+# define COMPILER_VERSION_INTERNAL_STR __clang_version__
+
+
+#elif defined(__FUJITSU)
+# define COMPILER_ID "Fujitsu"
+# if defined(__FCC_version__)
+#   define COMPILER_VERSION __FCC_version__
+# elif defined(__FCC_major__)
+#   define COMPILER_VERSION_MAJOR DEC(__FCC_major__)
+#   define COMPILER_VERSION_MINOR DEC(__FCC_minor__)
+#   define COMPILER_VERSION_PATCH DEC(__FCC_patchlevel__)
+# endif
+# if defined(__fcc_version)
+#   define COMPILER_VERSION_INTERNAL DEC(__fcc_version)
+# elif defined(__FCC_VERSION)
+#   define COMPILER_VERSION_INTERNAL DEC(__FCC_VERSION)
+# endif
+
+
+#elif defined(__ghs__)
+# define COMPILER_ID "GHS"
+/* __GHS_VERSION_NUMBER = VVVVRP */
+# ifdef __GHS_VERSION_NUMBER
+# define COMPILER_VERSION_MAJOR DEC(__GHS_VERSION_NUMBER / 100)
+# define COMPILER_VERSION_MINOR DEC(__GHS_VERSION_NUMBER / 10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__GHS_VERSION_NUMBER      % 10)
+# endif
+
+#elif defined(__TASKING__)
+# define COMPILER_ID "Tasking"
+  # define COMPILER_VERSION_MAJOR DEC(__VERSION__/1000)
+  # define COMPILER_VERSION_MINOR DEC(__VERSION__ % 100)
+# define COMPILER_VERSION_INTERNAL DEC(__VERSION__)
+
+#elif defined(__SCO_VERSION__)
+# define COMPILER_ID "SCO"
+
+#elif defined(__ARMCC_VERSION) && !defined(__clang__)
+# define COMPILER_ID "ARMCC"
+#if __ARMCC_VERSION >= 1000000
+  /* __ARMCC_VERSION = VRRPPPP */
+  # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/1000000)
+  # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 100)
+  # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION     % 10000)
+#else
+  /* __ARMCC_VERSION = VRPPPP */
+  # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/100000)
+  # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 10)
+  # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION    % 10000)
+#endif
+
+
+#elif defined(__clang__) && defined(__apple_build_version__)
+# define COMPILER_ID "AppleClang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__)
+
+#elif defined(__clang__) && defined(__ARMCOMPILER_VERSION)
+# define COMPILER_ID "ARMClang"
+  # define COMPILER_VERSION_MAJOR DEC(__ARMCOMPILER_VERSION/1000000)
+  # define COMPILER_VERSION_MINOR DEC(__ARMCOMPILER_VERSION/10000 % 100)
+  # define COMPILER_VERSION_PATCH DEC(__ARMCOMPILER_VERSION     % 10000)
+# define COMPILER_VERSION_INTERNAL DEC(__ARMCOMPILER_VERSION)
+
+#elif defined(__clang__)
+# define COMPILER_ID "Clang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+
+#elif defined(__LCC__) && (defined(__GNUC__) || defined(__GNUG__) || defined(__MCST__))
+# define COMPILER_ID "LCC"
+# define COMPILER_VERSION_MAJOR DEC(1)
+# if defined(__LCC__)
+#  define COMPILER_VERSION_MINOR DEC(__LCC__- 100)
+# endif
+# if defined(__LCC_MINOR__)
+#  define COMPILER_VERSION_PATCH DEC(__LCC_MINOR__)
+# endif
+# if defined(__GNUC__) && defined(__GNUC_MINOR__)
+#  define SIMULATE_ID "GNU"
+#  define SIMULATE_VERSION_MAJOR DEC(__GNUC__)
+#  define SIMULATE_VERSION_MINOR DEC(__GNUC_MINOR__)
+#  if defined(__GNUC_PATCHLEVEL__)
+#   define SIMULATE_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+#  endif
+# endif
+
+#elif defined(__GNUC__) || defined(__GNUG__)
+# define COMPILER_ID "GNU"
+# if defined(__GNUC__)
+#  define COMPILER_VERSION_MAJOR DEC(__GNUC__)
+# else
+#  define COMPILER_VERSION_MAJOR DEC(__GNUG__)
+# endif
+# if defined(__GNUC_MINOR__)
+#  define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__)
+# endif
+# if defined(__GNUC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(_MSC_VER)
+# define COMPILER_ID "MSVC"
+  /* _MSC_VER = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100)
+# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100)
+# if defined(_MSC_FULL_VER)
+#  if _MSC_VER >= 1400
+    /* _MSC_FULL_VER = VVRRPPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000)
+#  else
+    /* _MSC_FULL_VER = VVRRPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000)
+#  endif
+# endif
+# if defined(_MSC_BUILD)
+#  define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD)
+# endif
+
+#elif defined(_ADI_COMPILER)
+# define COMPILER_ID "ADSP"
+#if defined(__VERSIONNUM__)
+  /* __VERSIONNUM__ = 0xVVRRPPTT */
+#  define COMPILER_VERSION_MAJOR DEC(__VERSIONNUM__ >> 24 & 0xFF)
+#  define COMPILER_VERSION_MINOR DEC(__VERSIONNUM__ >> 16 & 0xFF)
+#  define COMPILER_VERSION_PATCH DEC(__VERSIONNUM__ >> 8 & 0xFF)
+#  define COMPILER_VERSION_TWEAK DEC(__VERSIONNUM__ & 0xFF)
+#endif
+
+#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC)
+# define COMPILER_ID "IAR"
+# if defined(__VER__) && defined(__ICCARM__)
+#  define COMPILER_VERSION_MAJOR DEC((__VER__) / 1000000)
+#  define COMPILER_VERSION_MINOR DEC(((__VER__) / 1000) % 1000)
+#  define COMPILER_VERSION_PATCH DEC((__VER__) % 1000)
+#  define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__)
+# elif defined(__VER__) && (defined(__ICCAVR__) || defined(__ICCRX__) || defined(__ICCRH850__) || defined(__ICCRL78__) || defined(__ICC430__) || defined(__ICCRISCV__) || defined(__ICCV850__) || defined(__ICC8051__) || defined(__ICCSTM8__))
+#  define COMPILER_VERSION_MAJOR DEC((__VER__) / 100)
+#  define COMPILER_VERSION_MINOR DEC((__VER__) - (((__VER__) / 100)*100))
+#  define COMPILER_VERSION_PATCH DEC(__SUBVERSION__)
+#  define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__)
+# endif
+
+
+/* These compilers are either not known or too old to define an
+  identification macro.  Try to identify the platform and guess that
+  it is the native compiler.  */
+#elif defined(__hpux) || defined(__hpua)
+# define COMPILER_ID "HP"
+
+#else /* unknown compiler */
+# define COMPILER_ID ""
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]";
+#ifdef SIMULATE_ID
+char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]";
+#endif
+
+#ifdef __QNXNTO__
+char const* qnxnto = "INFO" ":" "qnxnto[]";
+#endif
+
+#if defined(__CRAYXT_COMPUTE_LINUX_TARGET)
+char const *info_cray = "INFO" ":" "compiler_wrapper[CrayPrgEnv]";
+#endif
+
+#define STRINGIFY_HELPER(X) #X
+#define STRINGIFY(X) STRINGIFY_HELPER(X)
+
+/* Identify known platforms by name.  */
+#if defined(__linux) || defined(__linux__) || defined(linux)
+# define PLATFORM_ID "Linux"
+
+#elif defined(__MSYS__)
+# define PLATFORM_ID "MSYS"
+
+#elif defined(__CYGWIN__)
+# define PLATFORM_ID "Cygwin"
+
+#elif defined(__MINGW32__)
+# define PLATFORM_ID "MinGW"
+
+#elif defined(__APPLE__)
+# define PLATFORM_ID "Darwin"
+
+#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+# define PLATFORM_ID "Windows"
+
+#elif defined(__FreeBSD__) || defined(__FreeBSD)
+# define PLATFORM_ID "FreeBSD"
+
+#elif defined(__NetBSD__) || defined(__NetBSD)
+# define PLATFORM_ID "NetBSD"
+
+#elif defined(__OpenBSD__) || defined(__OPENBSD)
+# define PLATFORM_ID "OpenBSD"
+
+#elif defined(__sun) || defined(sun)
+# define PLATFORM_ID "SunOS"
+
+#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__)
+# define PLATFORM_ID "AIX"
+
+#elif defined(__hpux) || defined(__hpux__)
+# define PLATFORM_ID "HP-UX"
+
+#elif defined(__HAIKU__)
+# define PLATFORM_ID "Haiku"
+
+#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS)
+# define PLATFORM_ID "BeOS"
+
+#elif defined(__QNX__) || defined(__QNXNTO__)
+# define PLATFORM_ID "QNX"
+
+#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__)
+# define PLATFORM_ID "Tru64"
+
+#elif defined(__riscos) || defined(__riscos__)
+# define PLATFORM_ID "RISCos"
+
+#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__)
+# define PLATFORM_ID "SINIX"
+
+#elif defined(__UNIX_SV__)
+# define PLATFORM_ID "UNIX_SV"
+
+#elif defined(__bsdos__)
+# define PLATFORM_ID "BSDOS"
+
+#elif defined(_MPRAS) || defined(MPRAS)
+# define PLATFORM_ID "MP-RAS"
+
+#elif defined(__osf) || defined(__osf__)
+# define PLATFORM_ID "OSF1"
+
+#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv)
+# define PLATFORM_ID "SCO_SV"
+
+#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX)
+# define PLATFORM_ID "ULTRIX"
+
+#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX)
+# define PLATFORM_ID "Xenix"
+
+#elif defined(__WATCOMC__)
+# if defined(__LINUX__)
+#  define PLATFORM_ID "Linux"
+
+# elif defined(__DOS__)
+#  define PLATFORM_ID "DOS"
+
+# elif defined(__OS2__)
+#  define PLATFORM_ID "OS2"
+
+# elif defined(__WINDOWS__)
+#  define PLATFORM_ID "Windows3x"
+
+# elif defined(__VXWORKS__)
+#  define PLATFORM_ID "VxWorks"
+
+# else /* unknown platform */
+#  define PLATFORM_ID
+# endif
+
+#elif defined(__INTEGRITY)
+# if defined(INT_178B)
+#  define PLATFORM_ID "Integrity178"
+
+# else /* regular Integrity */
+#  define PLATFORM_ID "Integrity"
+# endif
+
+# elif defined(_ADI_COMPILER)
+#  define PLATFORM_ID "ADSP"
+
+#else /* unknown platform */
+# define PLATFORM_ID
+
+#endif
+
+/* For windows compilers MSVC and Intel we can determine
+   the architecture of the compiler being used.  This is because
+   the compilers do not have flags that can change the architecture,
+   but rather depend on which compiler is being used
+*/
+#if defined(_WIN32) && defined(_MSC_VER)
+# if defined(_M_IA64)
+#  define ARCHITECTURE_ID "IA64"
+
+# elif defined(_M_ARM64EC)
+#  define ARCHITECTURE_ID "ARM64EC"
+
+# elif defined(_M_X64) || defined(_M_AMD64)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# elif defined(_M_ARM64)
+#  define ARCHITECTURE_ID "ARM64"
+
+# elif defined(_M_ARM)
+#  if _M_ARM == 4
+#   define ARCHITECTURE_ID "ARMV4I"
+#  elif _M_ARM == 5
+#   define ARCHITECTURE_ID "ARMV5I"
+#  else
+#   define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM)
+#  endif
+
+# elif defined(_M_MIPS)
+#  define ARCHITECTURE_ID "MIPS"
+
+# elif defined(_M_SH)
+#  define ARCHITECTURE_ID "SHx"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__WATCOMC__)
+# if defined(_M_I86)
+#  define ARCHITECTURE_ID "I86"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC)
+# if defined(__ICCARM__)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(__ICCRX__)
+#  define ARCHITECTURE_ID "RX"
+
+# elif defined(__ICCRH850__)
+#  define ARCHITECTURE_ID "RH850"
+
+# elif defined(__ICCRL78__)
+#  define ARCHITECTURE_ID "RL78"
+
+# elif defined(__ICCRISCV__)
+#  define ARCHITECTURE_ID "RISCV"
+
+# elif defined(__ICCAVR__)
+#  define ARCHITECTURE_ID "AVR"
+
+# elif defined(__ICC430__)
+#  define ARCHITECTURE_ID "MSP430"
+
+# elif defined(__ICCV850__)
+#  define ARCHITECTURE_ID "V850"
+
+# elif defined(__ICC8051__)
+#  define ARCHITECTURE_ID "8051"
+
+# elif defined(__ICCSTM8__)
+#  define ARCHITECTURE_ID "STM8"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__ghs__)
+# if defined(__PPC64__)
+#  define ARCHITECTURE_ID "PPC64"
+
+# elif defined(__ppc__)
+#  define ARCHITECTURE_ID "PPC"
+
+# elif defined(__ARM__)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(__x86_64__)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(__i386__)
+#  define ARCHITECTURE_ID "X86"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__TI_COMPILER_VERSION__)
+# if defined(__TI_ARM__)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(__MSP430__)
+#  define ARCHITECTURE_ID "MSP430"
+
+# elif defined(__TMS320C28XX__)
+#  define ARCHITECTURE_ID "TMS320C28x"
+
+# elif defined(__TMS320C6X__) || defined(_TMS320C6X)
+#  define ARCHITECTURE_ID "TMS320C6x"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+# elif defined(__ADSPSHARC__)
+#  define ARCHITECTURE_ID "SHARC"
+
+# elif defined(__ADSPBLACKFIN__)
+#  define ARCHITECTURE_ID "Blackfin"
+
+#elif defined(__TASKING__)
+
+# if defined(__CTC__) || defined(__CPTC__)
+#  define ARCHITECTURE_ID "TriCore"
+
+# elif defined(__CMCS__)
+#  define ARCHITECTURE_ID "MCS"
+
+# elif defined(__CARM__)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(__CARC__)
+#  define ARCHITECTURE_ID "ARC"
+
+# elif defined(__C51__)
+#  define ARCHITECTURE_ID "8051"
+
+# elif defined(__CPCP__)
+#  define ARCHITECTURE_ID "PCP"
+
+# else
+#  define ARCHITECTURE_ID ""
+# endif
+
+#else
+#  define ARCHITECTURE_ID
+#endif
+
+/* Convert integer to decimal digit literals.  */
+#define DEC(n)                   \
+  ('0' + (((n) / 10000000)%10)), \
+  ('0' + (((n) / 1000000)%10)),  \
+  ('0' + (((n) / 100000)%10)),   \
+  ('0' + (((n) / 10000)%10)),    \
+  ('0' + (((n) / 1000)%10)),     \
+  ('0' + (((n) / 100)%10)),      \
+  ('0' + (((n) / 10)%10)),       \
+  ('0' +  ((n) % 10))
+
+/* Convert integer to hex digit literals.  */
+#define HEX(n)             \
+  ('0' + ((n)>>28 & 0xF)), \
+  ('0' + ((n)>>24 & 0xF)), \
+  ('0' + ((n)>>20 & 0xF)), \
+  ('0' + ((n)>>16 & 0xF)), \
+  ('0' + ((n)>>12 & 0xF)), \
+  ('0' + ((n)>>8  & 0xF)), \
+  ('0' + ((n)>>4  & 0xF)), \
+  ('0' + ((n)     & 0xF))
+
+/* Construct a string literal encoding the version number. */
+#ifdef COMPILER_VERSION
+char const* info_version = "INFO" ":" "compiler_version[" COMPILER_VERSION "]";
+
+/* Construct a string literal encoding the version number components. */
+#elif defined(COMPILER_VERSION_MAJOR)
+char const info_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[',
+  COMPILER_VERSION_MAJOR,
+# ifdef COMPILER_VERSION_MINOR
+  '.', COMPILER_VERSION_MINOR,
+#  ifdef COMPILER_VERSION_PATCH
+   '.', COMPILER_VERSION_PATCH,
+#   ifdef COMPILER_VERSION_TWEAK
+    '.', COMPILER_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct a string literal encoding the internal version number. */
+#ifdef COMPILER_VERSION_INTERNAL
+char const info_version_internal[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_',
+  'i','n','t','e','r','n','a','l','[',
+  COMPILER_VERSION_INTERNAL,']','\0'};
+#elif defined(COMPILER_VERSION_INTERNAL_STR)
+char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]";
+#endif
+
+/* Construct a string literal encoding the version number components. */
+#ifdef SIMULATE_VERSION_MAJOR
+char const info_simulate_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[',
+  SIMULATE_VERSION_MAJOR,
+# ifdef SIMULATE_VERSION_MINOR
+  '.', SIMULATE_VERSION_MINOR,
+#  ifdef SIMULATE_VERSION_PATCH
+   '.', SIMULATE_VERSION_PATCH,
+#   ifdef SIMULATE_VERSION_TWEAK
+    '.', SIMULATE_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]";
+char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]";
+
+
+
+#if defined(__INTEL_COMPILER) && defined(_MSVC_LANG) && _MSVC_LANG < 201403L
+#  if defined(__INTEL_CXX11_MODE__)
+#    if defined(__cpp_aggregate_nsdmi)
+#      define CXX_STD 201402L
+#    else
+#      define CXX_STD 201103L
+#    endif
+#  else
+#    define CXX_STD 199711L
+#  endif
+#elif defined(_MSC_VER) && defined(_MSVC_LANG)
+#  define CXX_STD _MSVC_LANG
+#else
+#  define CXX_STD __cplusplus
+#endif
+
+const char* info_language_standard_default = "INFO" ":" "standard_default["
+#if CXX_STD > 202002L
+  "23"
+#elif CXX_STD > 201703L
+  "20"
+#elif CXX_STD >= 201703L
+  "17"
+#elif CXX_STD >= 201402L
+  "14"
+#elif CXX_STD >= 201103L
+  "11"
+#else
+  "98"
+#endif
+"]";
+
+const char* info_language_extensions_default = "INFO" ":" "extensions_default["
+#if (defined(__clang__) || defined(__GNUC__) || defined(__xlC__) ||           \
+     defined(__TI_COMPILER_VERSION__)) &&                                     \
+  !defined(__STRICT_ANSI__)
+  "ON"
+#else
+  "OFF"
+#endif
+"]";
+
+/*--------------------------------------------------------------------------*/
+
+int main(int argc, char* argv[])
+{
+  int require = 0;
+  require += info_compiler[argc];
+  require += info_platform[argc];
+  require += info_arch[argc];
+#ifdef COMPILER_VERSION_MAJOR
+  require += info_version[argc];
+#endif
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+# Help Target
+help:
+	@echo "The following are some of the valid targets for this Makefile:"
+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... edit_cache"
+	@echo "... rebuild_cache"
+	@echo "... demo-chi2"
+	@echo "... demo-logistic"
+	@echo "... demo-chi2.o"
+	@echo "... demo-chi2.i"
+	@echo "... demo-chi2.s"
+	@echo "... demo-logistic.o"
+	@echo "... demo-logistic.i"
+	@echo "... demo-logistic.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
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+.PHONY : cmake_check_build_system
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+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/build/cmake_install.cmake
@ -0,0 +1,54 @@
+# Install script for directory: /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/palisade-gwas-demos-master
+
+# Set the install prefix
+if(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  set(CMAKE_INSTALL_PREFIX "/usr/local")
+endif()
+string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  if(BUILD_TYPE)
+    string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  else()
+    set(CMAKE_INSTALL_CONFIG_NAME "")
+  endif()
+  message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+endif()
+
+# Set the component getting installed.
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+  if(COMPONENT)
+    message(STATUS "Install component: \"${COMPONENT}\"")
+    set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  else()
+    set(CMAKE_INSTALL_COMPONENT)
+  endif()
+endif()
+
+# Install shared libraries without execute permission?
+if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+  set(CMAKE_INSTALL_SO_NO_EXE "0")
+endif()
+
+# Is this installation the result of a crosscompile?
+if(NOT DEFINED CMAKE_CROSSCOMPILING)
+  set(CMAKE_CROSSCOMPILING "FALSE")
+endif()
+
+# Set default install directory permissions.
+if(NOT DEFINED CMAKE_OBJDUMP)
+  set(CMAKE_OBJDUMP "/usr/bin/objdump")
+endif()
+
+if(CMAKE_INSTALL_COMPONENT)
+  set(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
+else()
+  set(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
+endif()
+
+string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
+       "${CMAKE_INSTALL_MANIFEST_FILES}")
+file(WRITE "/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/palisade-gwas-demos-master/build/${CMAKE_INSTALL_MANIFEST}"
+     "${CMAKE_INSTALL_MANIFEST_CONTENT}")
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/build/demo-chi2
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/build/demo-chi2
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/build/demo-logistic
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/build/demo-logistic
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/data/chi2.txt
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/data/chi2.txt
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/data/odds.txt
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/data/odds.txt
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/data/pvalue.txt
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/data/pvalue.txt
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/data/random_sample.csv
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/data/random_sample.csv
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/data/result.txt
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/data/result.txt
@ -0,0 +1,5 @@
+Key Generation Time: 		0.021 s
+Encoding and Encryption Time: 	5.168 s
+Computation Time: 		1.487 s
+Decryption & Decoding Time: 	0.098 s
+End-to-end Runtime: 		6.941 s
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/demo-chi2.cpp
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/demo-chi2.cpp
@ -0,0 +1,550 @@
+/***
+ * Copyright (c) 2020 Duality Technologies, Inc.
+ * Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License <https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode>
+ * See the LICENSE.md file for the full text of the license.
+ * If you share the Licensed Material (including in modified form) you must include the above attribution in the copy you share.
+ ***/
+/*
+
+Implementation for the Chi-Square GWAS solution described in
+"Secure large-scale genome-wide association studies using homomorphic encryption"
+by Marcelo Blatt, Alexander Gusev, Yuriy Polyakov, and Shafi Goldwasser
+
+Command to execute the prototype
+./demo-chi2 --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
+
+*/
+
+#include <getopt.h>
+#include <numeric>
+#include <cmath>
+
+#include "palisade.h"
+
+using namespace std;
+using namespace lbcrypto;
+
+const double EPSILON = 1.0E-08;
+
+void RunChi2(const string &SNPDir, const string &SNPFileName,
+		const string &pValue, const string &Runtime, const string &SampleSize, const string &SNPs);
+
+Ciphertext<DCRTPoly> BinaryTreeAdd(std::vector<Ciphertext<DCRTPoly>> &vector);
+
+void ReadSNPFile(vector<string>& headers, std::vector<std::vector<double>> & dataColumns, std::vector<double> &y, string dataFileName, size_t N, size_t M);
+
+double BS(double z) {
+	double y = exp(-z*z/2);
+	return sqrt(1-y) * (31*y/200 - 341*y*y/8000) / sqrt(M_PI);
+}
+
+double normalCFD(double value) { return 0.5 * erfc(-value * M_SQRT1_2); }
+
+double sf(double value) { return 1 - normalCFD(value); }
+
+static bool Equal(double a, double b) {   return (EPSILON > fabs(a-b)); }
+
+static bool Less(double a, double b) {  return ((a-b) < (-EPSILON)); }
+
+static bool Greater(double a, double b) {   return ((a-b) > EPSILON); }
+
+double IncompleteGamma(double val, double p);
+
+int main(int argc, char **argv) {
+
+	int opt;
+
+	PalisadeParallelControls.Enable();
+
+	static struct option long_options[] =
+	  {
+		/* These options dont set a flag.
+		   We distinguish them by their indices. */
+		{"SNPdir",  	required_argument, 			0, 'S'},
+		{"SNPfilename",  	required_argument, 			0, 's'},
+		{"pvalue",  	required_argument, 			0, 'p'},
+		{"runtime",  	required_argument, 			0, 'r'},
+		{"samplesize",  	required_argument, 			0, 'N'},
+		{"snps",  	required_argument, 			0, 'M'},
+		{0, 0, 0, 0}
+	  };
+
+	/* getopt_long stores the option index here. */
+	int option_index = 0;
+
+	string SNPDir;
+	string SNPFileName;
+	string pValue;
+	string Runtime;
+	string SampleSize;
+	string SNPs;
+
+	while ((opt = getopt_long(argc, argv, "S:s:p:r:N:M", long_options, &option_index)) != -1) {
+		switch (opt)
+		{
+			case 'S':
+				SNPDir = optarg;
+				break;
+			case 's':
+				SNPFileName = optarg;
+				break;
+			case 'p':
+				pValue = optarg;
+				break;
+			case 'r':
+				Runtime = optarg;
+				break;
+			case 'N':
+				SampleSize = optarg;
+				break;
+			case 'M':
+				SNPs = optarg;
+				break;
+			default: /* '?' */
+			  std::cerr<< "Usage: "<<argv[0]<<" <arguments> " <<std::endl
+				   << "arguments:" <<std::endl
+				   << "  -S --SNPdir SNP file directory"  <<std::endl
+				   << "  -s --SNPfilename SNP file name"  <<std::endl
+				   << "  -o --pvalue p-values file"  <<std::endl
+				   << "  -r --runtime runtime output file name"  <<std::endl
+				   << "  -N --samplesize number of individuals"  <<std::endl
+			   	   << "  -M --snps number of SNPs"  <<std::endl;
+			  exit(EXIT_FAILURE);
+		}
+	}
+
+	RunChi2(SNPDir, SNPFileName, pValue, Runtime, SampleSize, SNPs);
+
+	return 0;
+
+}
+
+void RunChi2(const string &SNPDir,
+		const string &SNPFileName, const string &pValue, const string &Runtime, const string &SampleSize, const string &SNPs) {
+
+	TimeVar t;
+	TimeVar tAll;
+
+	TIC(tAll);
+
+	double keyGenTime(0.0);
+	double encryptionTime(0.0);
+	double computationTime(0.0);
+	double decryptionTime(0.0);
+	double endToEndTime(0.0);
+
+	std::cout << "\n======CHI-SQUARE SOLUTION========\n" << std::endl;
+
+	vector<string> headers1;
+	vector<string> headersS;
+
+	std::vector<double> yData;
+	std::vector<std::vector<double>> sData;
+
+	size_t N = std::stoi(SampleSize);
+	size_t M = std::stoi(SNPs);
+
+	ReadSNPFile(headersS,sData,yData,SNPDir + "/" + SNPFileName,N,M);
+
+	//usint m = 16384;
+	usint m = 65536;
+	usint init_size = 4;
+	usint dcrtBits = 54;
+
+	double scalingFactor = 2.5e-6;
+
+	CryptoContext<DCRTPoly> cc =
+		CryptoContextFactory<DCRTPoly>::genCryptoContextCKKS(
+			   init_size-1,
+			   dcrtBits,
+			   0,
+			   HEStd_128_classic,
+			   m/2, /*ringDimension*/
+			   APPROXRESCALE,
+			   BV,
+			   3, /*numLargeDigits*/
+			   2, /*maxDepth*/
+			   dcrtBits, /*firstMod*/
+			   0,
+			   OPTIMIZED);
+
+	cc->Enable(ENCRYPTION);
+	cc->Enable(SHE);
+	cc->Enable(LEVELEDSHE);
+
+	std::cout << "\nNumber of Individuals = " << sData.size() << std::endl;
+	std::cout << "Number of SNPs = " << sData[0].size() << std::endl;
+
+	TIC(t);
+
+	auto keyPair = cc->KeyGen();
+
+	keyGenTime = TOC(t);
+
+	TIC(t);
+
+	size_t sizeS = (size_t)std::ceil((double)sData[0].size()/(m/4));
+
+	std::vector<std::vector<std::vector<std::complex<double>>>> sDataArray(sizeS);
+
+	for(size_t s = 0; s < sizeS; s++)
+		sDataArray[s] = std::vector<std::vector<std::complex<double>>>(sData.size());
+
+	for (size_t i=0; i < sData.size(); i++){
+
+		for(size_t s = 0; s < sizeS; s++)
+			sDataArray[s][i] = std::vector<std::complex<double>>(sData[i].size());
+
+		size_t counter = 0;
+
+		for (size_t j=0; j<sData[i].size(); j++) {
+			if ((j>0) && (j%(m/4)==0))
+				counter++;
+			sDataArray[counter][i][j%(m/4)] = sData[i][j];
+		}
+	}
+
+	//std::cerr << " sData = " << sDataArray << std::endl;
+
+	std::vector<std::vector<Ciphertext<DCRTPoly>>> S(sizeS);
+	std::vector<Ciphertext<DCRTPoly>> Y(N);
+
+	for (size_t i = 0; i < sizeS; i++)
+		S[i] = std::vector<Ciphertext<DCRTPoly>>(N);
+
+	//Encryption of single-integer ciphertexts
+#pragma omp parallel for
+	for (size_t i=0; i<N; i++){
+		for (size_t s=0; s < sizeS; s++){
+			Plaintext sTemp = cc->MakeCKKSPackedPlaintext(sDataArray[s][i]);
+			S[s][i] = cc->Encrypt(keyPair.publicKey, sTemp);
+		}
+		Plaintext sTemp2 = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,yData[i]));
+		Y[i] = cc->Encrypt(keyPair.publicKey, sTemp2);
+	}
+
+	encryptionTime = TOC(t);
+
+	TIC(t);
+
+	Plaintext d = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,2*N));
+	d->SetFormat(EVALUATION);
+
+	Plaintext dScaled = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,2*N*scalingFactor));
+	dScaled->SetFormat(EVALUATION);
+
+	std::vector<Ciphertext<DCRTPoly>> ySum = Y;
+
+	auto yU = BinaryTreeAdd(ySum);
+
+	std::vector<Ciphertext<DCRTPoly>> chiD(sizeS);
+	std::vector<Ciphertext<DCRTPoly>> chiN(sizeS);
+
+	std::vector<Ciphertext<DCRTPoly>> orD(sizeS);
+	std::vector<Ciphertext<DCRTPoly>> orN(sizeS);
+
+	for (size_t s = 0; s < sizeS; s++) {
+
+		std::vector<Ciphertext<DCRTPoly>> ySMult(N);
+
+#pragma omp parallel for
+		for(size_t i = 0; i < N; i++) {
+			ySMult[i] = cc->EvalMultNoRelin(S[s][i],Y[i]);
+		}
+
+		auto n11 = BinaryTreeAdd(ySMult);
+
+		n11 = cc->ModReduce(n11);
+
+		auto c1 = BinaryTreeAdd(S[s]);
+
+		auto r1 = cc->EvalAdd(yU,yU);
+
+		auto r1Scaled = cc->EvalMult(r1,scalingFactor);
+		r1Scaled = cc->ModReduce(r1Scaled);
+
+		auto c1Scaled = cc->EvalMult(c1,scalingFactor);
+		c1Scaled = cc->ModReduce(c1Scaled);
+
+		r1 = cc->LevelReduce(r1,nullptr);
+		c1 = cc->LevelReduce(c1,nullptr);
+
+		// Chi2 computation
+
+		// numerator
+
+		auto mult1 = cc->EvalMult(n11,dScaled);
+		auto mult2 = cc->EvalMultNoRelin(c1,r1Scaled);
+
+		auto chiN1 = cc->EvalSub(mult1,mult2);
+		chiN1 = cc->ModReduce(chiN1);
+
+		chiN[s] = cc->EvalMultNoRelin(chiN1,chiN1);
+
+		// denominator
+
+		auto chiD1 = cc->EvalMultNoRelin(c1,cc->EvalSub(dScaled,c1Scaled));
+		chiD1 = cc->ModReduce(chiD1);
+
+		auto chiD2 = cc->EvalMultNoRelin(r1,cc->EvalSub(dScaled,r1Scaled));
+		chiD2 = cc->ModReduce(chiD2);
+
+		chiD[s] = cc->EvalMultNoRelin(chiD1,chiD2);
+
+		// Odds Ratio Computation
+
+		auto n11Scaled = cc->EvalMult(n11,scalingFactor);
+		n11Scaled = cc->ModReduce(n11Scaled);
+
+		// denominator
+
+		auto or2 = cc->EvalSub(c1,n11);
+		or2 = cc->LevelReduce(or2,nullptr);
+
+		r1Scaled = cc->LevelReduce(r1Scaled,nullptr);
+		auto or3 = cc->EvalSub(r1Scaled,n11Scaled);
+
+		orD[s] = cc->EvalMultNoRelin(or2,or3);
+
+		// numerator
+
+		auto or1 = cc->EvalSub(n11Scaled,r1Scaled);
+		c1Scaled = cc->LevelReduce(c1Scaled,nullptr);
+		or1 = cc->EvalSub(or1,c1Scaled);
+		or1 = cc->EvalAdd(or1,dScaled);
+
+		n11 = cc->LevelReduce(n11,nullptr);
+		orN[s] = cc->EvalMultNoRelin(n11,or1);
+
+	}
+
+	computationTime = TOC(t);
+
+	TIC(t);
+
+	std::vector<Plaintext> pN(sizeS);
+	std::vector<Plaintext> pD(sizeS);
+	std::vector<Plaintext> oddN(sizeS);
+	std::vector<Plaintext> oddD(sizeS);
+
+	for (size_t s = 0; s < sizeS; s++) {
+		cc->Decrypt(keyPair.secretKey, chiN[s] , &(pN[s]));
+		cc->Decrypt(keyPair.secretKey, chiD[s] , &(pD[s]));
+		cc->Decrypt(keyPair.secretKey, orN[s] , &(oddN[s]));
+		cc->Decrypt(keyPair.secretKey, orD[s] , &(oddD[s]));
+	}
+
+	decryptionTime = TOC(t);
+
+	std::vector<double> chival(headersS.size());
+	std::vector<double> pval(headersS.size());
+	std::vector<double> odds(headersS.size());
+
+	for (size_t s = 0; s < sizeS; s++) {
+		for (size_t i = 0; i < m/4; i++) {
+			if (s*m/4 + i < headersS.size()) {
+
+				chival[s*m/4 + i] = pN[s]->GetCKKSPackedValue()[i].real()*2*N/pD[s]->GetCKKSPackedValue()[i].real();
+				if (chival[s*m/4 + i] < 0)
+					chival[s*m/4 + i] = 0;
+				pval[s*m/4 + i] = (double)1-IncompleteGamma(chival[s*m/4 + i]/2,0.5);
+				if (pval[s*m/4 + i] < 0)
+					pval[s*m/4 + i] = 1e-15;
+				else
+					if (pval[s*m/4 + i]==0)
+						pval[s*m/4 + i] = BS(sqrt(chival[s*m/4 + i]));
+
+				odds[s*m/4 + i] = oddN[s]->GetCKKSPackedValue()[i].real()/oddD[s]->GetCKKSPackedValue()[i].real();
+
+			}
+		}
+	}
+
+    ofstream myfile;
+    myfile.open(SNPDir + "/" + pValue);
+    myfile.precision(10);
+    for(uint32_t i = 0; i < headersS.size(); i++) {
+    	myfile << headersS[i] << "\t" << pval[i] << std::endl;
+    }
+    myfile.close();
+
+    ofstream myfile2;
+    myfile2.open(SNPDir + "/" + "odds.txt");
+    myfile2.precision(10);
+    for(uint32_t i = 0; i < headersS.size(); i++) {
+    	myfile2 << headersS[i] << "\t" << odds[i] << std::endl;
+    }
+    myfile2.close();
+
+    ofstream myfile3;
+    myfile3.open(SNPDir + "/" + "chi2.txt");
+    myfile3.precision(10);
+    for(uint32_t i = 0; i < headersS.size(); i++) {
+    	myfile3 << headersS[i] << "\t" << chival[i] << std::endl;
+    }
+    myfile3.close();
+
+	std::cout << "\nKey Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
+	std::cout << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
+	std::cout << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
+	std::cout << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
+
+	endToEndTime = TOC(tAll);
+
+    std::cout << "\nEnd-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl;
+
+    ofstream myfileRuntime;
+    myfileRuntime.open(SNPDir + "/" + Runtime);
+    myfileRuntime << "Key Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
+    myfileRuntime << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
+    myfileRuntime << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
+    myfileRuntime << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
+    myfileRuntime << "End-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl;
+    myfileRuntime.close();
+
+}
+
+Ciphertext<DCRTPoly> BinaryTreeAdd(std::vector<Ciphertext<DCRTPoly>> &vector) {
+
+	auto cc = vector[0]->GetCryptoContext();
+
+	for(size_t j = 1; j < vector.size(); j=j*2) {
+		for(size_t i = 0; i<vector.size(); i = i + 2*j) {
+			if ((i+j)<vector.size())
+				vector[i] = cc->EvalAdd(vector[i],vector[i+j]);
+		}
+	}
+
+	Ciphertext<DCRTPoly> result(new CiphertextImpl<DCRTPoly>(*(vector[0])));
+
+	return result;
+
+}
+
+double IncompleteGamma(double val, double p)
+{
+    if( !Greater(val, 0) || !Greater(p, 0) )
+        return 0;
+
+    double expValue = p*log(val) - val - lgamma(p);
+    if( Less(expValue, log(1.0E-37)) ) // undeflow
+        return 0;
+
+    double factor = exp(expValue);
+    if( !Greater(val, 1) || Less(val, p) )
+    {
+        double igamma = 1;
+        double term = 1;
+
+        for( int i = 1; Greater(term, EPSILON); ++i )
+        {
+            term *= (val/(p+i));
+            igamma += term;
+        }
+
+        return (igamma*factor/p);
+    }
+
+    double pn[6] = { 1, val, val+1, val*(2+val-p) };
+    double upperIncGamma = pn[2]/pn[3];
+
+    for( int j = 1; ; ++j )
+    {
+        double a = (j+1)*2 + val- p;
+        double b = (1 + j - p)*j;
+        pn[4] = a*pn[2] - b*pn[0];
+        pn[5] = a*pn[3] - b*pn[1];
+
+        if( !Equal(pn[5], 0) )
+        {
+            double rn = pn[4]/pn[5];
+            double diff = fabs(upperIncGamma - rn);
+            if( !Greater(diff, EPSILON) && !Greater(diff, (EPSILON*rn)) )
+                return (1 - factor*upperIncGamma);
+
+            upperIncGamma = rn;
+        }
+
+        for( int i = 0; i < 4; i++ )
+            pn[i] = pn[i+2];
+
+        if( !Greater(1.0E+37, fabs(pn[4])) ) // overflow
+        {
+            for( int i = 0; i < 4; i++ )
+                pn[i] = pn[i] / 1.0E+37;
+        }
+    }
+
+    return 0;
+}
+
+void ReadSNPFile(vector<string>& headers, std::vector<std::vector<double>> & dataColumns, std::vector<double> &y,
+                 string dataFileName, size_t N, size_t M)
+{
+
+	uint32_t cols = 0;
+
+	string fileName = dataFileName + ".csv";
+
+	std::cerr << "file name = " << fileName << std::endl;
+
+	ifstream file(fileName);
+	string line, value;
+
+	if(file.good()) {
+
+		getline(file, line);
+		cols = std::count(line.begin(), line.end(), ',') + 1;
+		stringstream ss(line);
+		vector<string> result;
+
+		size_t tempcounter = 0;
+
+		for(uint32_t i = 0; i < cols; i++) {
+			string substr;
+			getline(ss, substr, ',');
+			if ((substr != "") && (i>4) && (i<M+5)) {
+				headers.push_back(substr);
+				tempcounter++;
+			}
+		}
+
+		cols = tempcounter;
+
+	}
+
+	size_t counter = 0;
+	while((file.good()) && (counter < N)) {
+		getline(file, line);
+		uint32_t curCols = std::count(line.begin(), line.end(), ',') + 1;
+		if (curCols > 2) {
+			stringstream ss(line);
+			for(uint32_t i = 0; i < 5; i++) {
+				string substr;
+				getline(ss, substr, ',');
+				if ((i==1))
+					y.push_back(std::stod(substr));
+			}
+			std::vector<double> row(cols);
+			for(uint32_t i = 5; i < cols + 5; i++) {
+				string substr;
+				getline(ss, substr, ',');
+				if (i < M+5)
+				{
+					double val;
+					val = std::stod(substr);
+					row[i-5] = val;
+				}
+			}
+			dataColumns.push_back(row);
+		}
+		counter++;
+	}
+
+	file.close();
+
+    std::cout << "Read in data: ";
+	std::cout << dataFileName << std::endl;
+}
+
+
--- a/Code/Duality_Technologies/palisade-gwas-demos-master/demo-logistic.cpp
+++ b/Code/Duality_Technologies/palisade-gwas-demos-master/demo-logistic.cpp
--- a/Code/Duality_Technologies/palisade/palisade-development
+++ b/Code/Duality_Technologies/palisade/palisade-development
@ -0,0 +1 @@
+Subproject commit 622be46e44b7fac1c0ff1906fa4edda0629be438
				`@ -0,0 +1 @@`
				`set (CMAKE_GENERATOR "Unix Makefiles" CACHE INTERNAL "" FORCE)`
				`@ -0,0 +1 @@`
				`# This file is generated by cmake for dependency checking of the CMakeCache.txt file`
				`@ -0,0 +1 @@`
				`/usr/bin/c++ -Wall -Werror -O3 -DPALISADE_VERSION=1.11.8 -Wno-parentheses -DMATHBACKEND=2 -fopenmp -fopenmp "CMakeFiles/demo-chi2.dir/demo-chi2.cpp.o" -o demo-chi2 -L/usr/local/lib -Wl,-rpath,/usr/local/lib /usr/local/lib/libPALISADEpke.so.1.11.8 /usr/local/lib/libPALISADEbinfhe.so.1.11.8 -fopenmp /usr/local/lib/libPALISADEcore.so.1.11.8 -fopenmp`
				`@ -0,0 +1 @@`
				`Subproject commit 622be46e44b7fac1c0ff1906fa4edda0629be438`