Order polytope improvements #319

lucaperju · 2024-07-12T07:44:00Z

Check that given DAG is acyclic when constructing a poset
Generator for random Order polytopes
Add possibility to generate Order Polytopes as Hpolytope class

* copy and replace lp_rlp.h * remove re-initialization of eta * update ubuntu version from 18 to 20 in R cran tests * minor improvements (explanatory comments) --------- Co-authored-by: Apostolos Chalkis <apostolos.chalkis@quantagonia.com>

* initialize nuts sampler class * implement the burnin of nuts sampler * add tests and resolve bugs * implement e0 estimation in burnin of nuts * optimize leapfrog * integrate nuts into the R interface * document random walk in sample_points.cpp in R interface * fix burnin for the non-truncated case * resolve bugs in hmc and nuts pipelines * improve the preprocess in burin step of nuts * split large lines in sample_points.cpp * Add NUTS C++ example and update CMake (GeomScale#29) * resolve PR comments * fix minor bug * fix compiler bug * fix error in building the C++ examples * resolve warnings in sample_points * fix lpsolve cran warning * fix cran warning on mac * improve lpsolve cmake for cran check * fix R warning in mac test * remove lpsolve header * resolve PR comments --------- Co-authored-by: Marios Papachristou <papachristoumarios@gmail.com> Co-authored-by: Apostolos Chalkis <apostolos.chalkis@quantagonia.com>

…iance parameter

…ce parameter, add define lp_solve guards to orderpolytope

Remove volesti4dingo branch

…_source Build only with lp-solve source code, no need for liblpsolve55.so files

* Enable c++17 support in tests and fix saxpy calls * Fix structure, code style and tests in autodiff

* correcting the includes to point the boost library directory * modifs to include only the include/ and external/ directories * modifs * Update CMakeLists.txt --------- Co-authored-by: Vissarion Fisikopoulos <fisikop@gmail.com> Co-authored-by: vfisikop <160006479+vfisikop@users.noreply.github.com>

…rent develop

Remove R interface

Refactor trigonometric_positive_intersect function for hpolytopes

update_position complexity improvement

* improve the implementation of maximum ellipsoid computation * minor fix in rounding unit-test * fix file copyrights * apply termination criterion after transformation in max ellipsoid rounding * resolve PR comments --------- Co-authored-by: Apostolos Chalkis <apostolos.chalkis@quantagonia.com>

…eomScale#310) * improve the implementation of maximum ellipsoid computation * minor fix in rounding unit-test * fix file copyrights * fix max_ball bug and create new unit test * fix max_ball bug and create new unit test * apply termination criterion after transformation in max ellipsoid rounding * imrpove skinny poly generator's interface * improve stopping criterion and seed setting * complete unit tests implementations * implement Newton method to compute the analytic center * minor changes * resolve PR comments * complete analytic center computation * resolve conflicts * minor changes * minor changes * minor changes * improve new unit tests * resolve PR comments --------- Co-authored-by: Apostolos Chalkis <apostolos.chalkis@quantagonia.com>

* Position Nudging after Position Update * Complexity improvements and Polytope Normalization * HPolytope Normalization Flag * Polytope normalization within Walk Constructor * Alias HPolytope Normalization for Nudging inside Gaussian HMC * Polytope Normalization in ComputeInner Ball Fixed * Polytope Normalization Style change * Nudge in function within Gaussian HMC, and restore Hpoly file * More efficient Nudge in Process

…ocessing routines (GeomScale#312) * generalize rounding loop * support sparse cholesky operator * complete sparse support in max_inscribed_ball * complete sparse support in preprocesing * add sparse tests * change main rounding function name * improve explaining comments * resolve PR comments * changing the dates in copyrights * use if constexpr instead of SNIFAE * update the examples to cpp17 * update to cpp17 order polytope example * fix templating in mat_computational_operators * fix templating errors and change header file to mat_computational_operators --------- Co-authored-by: Apostolos Chalkis <apostolos.chalkis@quantagonia.com>

* new function is_correlation_matrix * update example function call this example calls the is_correlation_matrix() function that is present in include/matrix_operations/EigenvaluesProblems.h * remove blank line * remove blank line * fix spaces, add function parameter

* generalize rounding loop * support sparse cholesky operator * complete sparse support in max_inscribed_ball * complete sparse support in preprocesing * add sparse tests * change main rounding function name * improve explaining comments * resolve PR comments * changing the dates in copyrights * use if constexpr instead of SNIFAE * update the examples to cpp17 * update to cpp17 order polytope example * fix templating in mat_computational_operators * fix templating errors and change header file to mat_computational_operators * first implementation of the volumetric barrier ellipsoid * add criterion for step_iter * restructure code that computes barriers' centers * remove unused comments * resolve PR comments * remove NT typename from max_step() --------- Co-authored-by: Apostolos Chalkis <apostolos.chalkis@quantagonia.com>

…lesti into order_polytope_improvements

vfisikop

Great, thanks! Could you also add one or two unit tests to test the functionality?

vfisikop · 2024-07-12T09:55:38Z

include/generators/order_polytope_generator.h

+// generates a Polytope from a poset
+/// @tparam Polytope Type of returned polytope
+template <class Polytope>
+Polytope get_orderpoly(Poset &poset) {


poset is not changed so why not passing it as a const reference?

vfisikop · 2024-07-12T09:59:21Z

include/generators/order_polytope_generator.h

+    OrderPolytope<Point> OP(poset);
+    if constexpr (std::is_same< Polytope, OrderPolytope<Point> >::value ) {
+        return OP;
+    } else {


Here you assume that Polytope type is either OrderPolytope or HPolytope but is could be of other type as well and this is not handled by this function. You could create an else statement with a static assert.

vfisikop · 2024-07-12T10:03:54Z

include/misc/poset.h

@@ -25,6 +25,36 @@ class Poset {
    unsigned int n;  // elements will be from 0 to n-1
    RV order_relations;     // pairs of form a <= b

+    static void sorted_list(std::vector<unsigned int> &res, const unsigned int &n, const RV &relations)


I think it is more readable if you reorder parameters such that input parameters are first and output second, i.e., const unsigned int & n, const RV &relations, std::vector<unsigned int> &res

vfisikop · 2024-07-12T11:57:07Z

include/generators/order_polytope_generator.h

+        Polytope HP(OP.dimension(), OP.get_full_mat(), OP.get_vec());
+        return HP;
+    } else {
+        // TODO: implement functionality for more polytope types


A side note here: creating a V-polytope from an H-polytope representation of an order polytope is a hard problem (and cannot be approximated as volume computation) thus it is realistic to just remove that TODO ;)

…lesti into order_polytope_improvements

This reverts commit 0b97f7e.

TolisChal and others added 30 commits October 16, 2023 16:09

Use of SIMD computation in CRHMC walk [fixed] (GeomScale#286)

c31e98b

Update CODE_OF_CONDUCT.md

e767f46

Add define lp_solve guards to orderpolytope

c9fb177

Rename LinearProgramFunctor to ExponentialFunctor and add inverse var…

f91d4a9

…iance parameter

Rename LinearProgramFunctor to ExponentialFunctor, add inverse varian…

b15c9d8

…ce parameter, add define lp_solve guards to orderpolytope

Remove C11 flags from cran

1ae6a45

Merge pull request GeomScale#289 from vfisikop/remove_volesti4dingo

ad049d5

Remove volesti4dingo branch

Build only with lp-solve source code, no need for liblpsolve55.so files

432b967

Update tests and some examples to buid with lp solve from sources

7da53c4

Upgrade boost from 1.76 to 1.84

f8db05c

Fix ambiguous call to pow for clang, and disable LoadableBlasLib

1703e69

Merge pull request GeomScale#290 from vfisikop/fix/lpsolve_build_from…

93bbc50

…_source Build only with lp-solve source code, no need for liblpsolve55.so files

Update requirements.txt

5bf9188

Autopoint (GeomScale#256)

b2b5c06

Enable c++17 support in tests and fix saxpy calls (GeomScale#292)

bf1ebd0

* Enable c++17 support in tests and fix saxpy calls * Fix structure, code style and tests in autodiff

Remove R interface and update CI to test Rvolesti repository with cur…

8f7a9f2

…rent develop

Fix includes of header files

8724a73

Fix windows CI tests

4c6bcc3

Remove unused header files

4ee5374

Merge pull request GeomScale#293 from vfisikop/remove_R_interface

795e948

Remove R interface

Update and simplify documentation

9114f37

Refactor trigonometric_positive_intersect function for hpolytopes

742eb01

Merge pull request GeomScale#299 from vfisikop/trigonometric_intersect

6a5a17e

Refactor trigonometric_positive_intersect function for hpolytopes

update_position complexity improvement

9c32d0b

Merge pull request GeomScale#307 from vgnecula/refinements

3129f7b

update_position complexity improvement

Feature/spectra correlations (GeomScale#306)

e484865

TolisChal and others added 11 commits June 21, 2024 11:47

Order Polytopes generation

348aab4

minor changes for PR

65056ed

Merge branch 'GeomScale:develop' into order_polytope_improvements

c44355b

remove space and comment

f533e95

Merge branch 'order_polytope_improvements' of github.com:lucaperju/vo…

3ca6ab1

…lesti into order_polytope_improvements

remove bug

3087d98

vfisikop approved these changes Jul 12, 2024

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Unit test for Random Order Polytope, and minor changes

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vfisikop reviewed Jul 12, 2024

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remove comment

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TolisChal approved these changes Jul 17, 2024

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TolisChal force-pushed the develop branch from 992d203 to 7a0be2d Compare July 17, 2024 03:38

lucaperju added 9 commits July 17, 2024 15:28

Order Polytopes generation

12c1f8a

minor changes for PR

cff93cb

remove space and comment

634d3cc

remove bug

e388d43

Unit test for Random Order Polytope, and minor changes

d67be4b

remove comment

81aeb51

Merge branch 'order_polytope_improvements' of github.com:lucaperju/vo…

1dba5e5

…lesti into order_polytope_improvements

fix rebase bugs

fee9579

remove accidental line

e764a69

TolisChal approved these changes Jul 17, 2024

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TolisChal merged commit 0b97f7e into GeomScale:develop Jul 17, 2024
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TolisChal added a commit that referenced this pull request Jul 17, 2024

Revert "Order polytope improvements (#319)"

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This reverts commit 0b97f7e.

lucaperju deleted the order_polytope_improvements branch August 31, 2024 18:09

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Order polytope improvements #319

Order polytope improvements #319

lucaperju commented Jul 12, 2024

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Order polytope improvements #319

Order polytope improvements #319

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