Message Passing Module by dario-coscia · Pull Request #516 · mathLab/PINA

dario-coscia · 2025-03-21T10:26:14Z

Description

This PR fixes #515.

Here a tentative RoadMap

InteractionNetworkBlock: implements the interaction network (See sec.2 of https://arxiv.org/pdf/1704.01212)
DeepTensorNetworkBlock: implements the Deep Tensor Neural Networks block (See sec.2 of https://arxiv.org/pdf/1704.01212)
EGNNBlock: implements the E(n) Equivariant Graph Neural Network block(See sec.3 of https://arxiv.org/pdf/2102.09844)
RadialFieldBlock: implements the radial field network block (See Tab1. of https://arxiv.org/pdf/2102.09844)
SchnetBlock: implements the schnet block (See Tab1. of https://arxiv.org/pdf/2102.09844)

Checklist

Code follows the project’s Code Style Guidelines
Tests have been added or updated
Documentation has been updated if necessary
Pull request is linked to an open issue

github-actions · 2025-03-21T10:32:06Z

Code Coverage Summary

Filename                                                       Stmts    Miss  Cover    Missing
-----------------------------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------
__init__.py                                                        7       0  100.00%
graph.py                                                         114      11  90.35%   99-100, 112, 124, 126, 142, 144, 166, 169, 182, 271
label_tensor.py                                                  251      32  87.25%   81, 121, 144-148, 165, 177, 182, 188-193, 273, 280, 332, 334, 348, 444-447, 490, 537, 629, 649-651, 664-673, 688, 710
operator.py                                                       72       5  93.06%   250-268, 459
operators.py                                                       6       6  0.00%    3-12
plotter.py                                                         1       1  0.00%    3
trainer.py                                                        75       6  92.00%   195-204, 293, 314, 318, 322
utils.py                                                          60       8  86.67%   113, 150, 153, 156, 192-195
adaptive_function/__init__.py                                      3       0  100.00%
adaptive_function/adaptive_function.py                            55       0  100.00%
adaptive_function/adaptive_function_interface.py                  51       6  88.24%   98, 141, 148-151
adaptive_functions/__init__.py                                     6       6  0.00%    3-12
callback/__init__.py                                               5       0  100.00%
callback/linear_weight_update_callback.py                         28       1  96.43%   63
callback/optimizer_callback.py                                    22       1  95.45%   34
callback/processing_callback.py                                   49       5  89.80%   42-43, 73, 168, 171
callback/refinement/__init__.py                                    3       0  100.00%
callback/refinement/r3_refinement.py                              28       1  96.43%   88
callback/refinement/refinement_interface.py                       50       5  90.00%   32, 59, 67, 72, 78
callbacks/__init__.py                                              6       6  0.00%    3-12
condition/__init__.py                                              7       0  100.00%
condition/condition.py                                            35       8  77.14%   23, 127-128, 131-132, 135-136, 151
condition/condition_interface.py                                  37       4  89.19%   31, 76, 100, 122
condition/data_condition.py                                       26       1  96.15%   56
condition/domain_equation_condition.py                            19       0  100.00%
condition/input_equation_condition.py                             44       1  97.73%   129
condition/input_target_condition.py                               44       1  97.73%   125
data/__init__.py                                                   3       0  100.00%
data/data_module.py                                              201      22  89.05%   41-52, 132, 172, 193, 232, 313-317, 323-327, 399, 466, 546, 637, 639
data/dataset.py                                                   85       7  91.76%   42, 123-126, 256, 307
domain/__init__.py                                                10       0  100.00%
domain/cartesian.py                                              112      10  91.07%   37, 47, 75-76, 92, 97, 103, 246, 256, 264
domain/difference_domain.py                                       25       2  92.00%   54, 87
domain/domain_interface.py                                        20       5  75.00%   37-41
domain/ellipsoid.py                                              104      24  76.92%   52, 56, 127, 250-257, 269-282, 286-287, 290, 295
domain/exclusion_domain.py                                        28       1  96.43%   86
domain/intersection_domain.py                                     28       1  96.43%   85
domain/operation_interface.py                                     26       1  96.15%   88
domain/simplex.py                                                 72      14  80.56%   62, 207-225, 246-247, 251, 256
domain/union_domain.py                                            25       1  96.00%   43
equation/__init__.py                                               4       0  100.00%
equation/equation.py                                              11       0  100.00%
equation/equation_factory.py                                      24      10  58.33%   37, 62-75, 97-110, 132-145
equation/equation_interface.py                                     4       0  100.00%
equation/system_equation.py                                       22       0  100.00%
geometry/__init__.py                                               7       7  0.00%    3-15
loss/__init__.py                                                   7       0  100.00%
loss/loss_interface.py                                            17       2  88.24%   45, 51
loss/lp_loss.py                                                   15       0  100.00%
loss/ntk_weighting.py                                             26       0  100.00%
loss/power_loss.py                                                15       0  100.00%
loss/scalar_weighting.py                                          16       0  100.00%
loss/weighting_interface.py                                        6       0  100.00%
model/__init__.py                                                 10       0  100.00%
model/average_neural_operator.py                                  31       2  93.55%   73, 82
model/deeponet.py                                                 93      13  86.02%   187-190, 209, 240, 283, 293, 303, 313, 323, 333, 488, 498
model/feed_forward.py                                             89      11  87.64%   58, 195, 200, 278-292
model/fourier_neural_operator.py                                  78      10  87.18%   96-100, 110, 155-159, 218, 220, 242, 342
model/graph_neural_operator.py                                    40       2  95.00%   58, 60
model/kernel_neural_operator.py                                   34       6  82.35%   83-84, 103-104, 123-124
model/low_rank_neural_operator.py                                 27       2  92.59%   89, 98
model/multi_feed_forward.py                                       12       5  58.33%   25-31
model/spline.py                                                   89      37  58.43%   30, 41-66, 69, 128-132, 135, 159-177, 180
model/block/__init__.py                                           12       0  100.00%
model/block/average_neural_operator_block.py                      12       0  100.00%
model/block/convolution.py                                        64      13  79.69%   77, 81, 85, 91, 97, 111, 114, 151, 161, 171, 181, 191, 201
model/block/convolution_2d.py                                    146      27  81.51%   155, 162, 282, 314, 379-433, 456
model/block/embedding.py                                          48       7  85.42%   93, 143-146, 155, 168
model/block/fourier_block.py                                      31       0  100.00%
model/block/gno_block.py                                          22       4  81.82%   73-77, 87
model/block/integral.py                                           18       4  77.78%   22-25, 71
model/block/low_rank_block.py                                     24       0  100.00%
model/block/orthogonal.py                                         37       0  100.00%
model/block/pod_block.py                                          73      10  86.30%   55-58, 70, 83, 113, 148-153, 187, 212
model/block/rbf_block.py                                         179      25  86.03%   18, 42, 53, 64, 75, 86, 97, 223, 280, 282, 298, 301, 329, 335, 363, 367, 511-524
model/block/residual.py                                           46       0  100.00%
model/block/spectral.py                                           83       4  95.18%   132, 140, 262, 270
model/block/stride.py                                             28       7  75.00%   55, 58, 61, 67, 72-74
model/block/utils_convolution.py                                  22       3  86.36%   58-60
model/block/message_passing/__init__.py                            6       0  100.00%
model/block/message_passing/deep_tensor_network_block.py          21       0  100.00%
model/block/message_passing/en_equivariant_network_block.py       39       0  100.00%
model/block/message_passing/interaction_network_block.py          23       0  100.00%
model/block/message_passing/radial_field_network_block.py         20       0  100.00%
model/block/message_passing/schnet_block.py                       25       0  100.00%
model/layers/__init__.py                                           6       6  0.00%    3-12
optim/__init__.py                                                  5       0  100.00%
optim/optimizer_interface.py                                       7       0  100.00%
optim/scheduler_interface.py                                       7       0  100.00%
optim/torch_optimizer.py                                          14       0  100.00%
optim/torch_scheduler.py                                          19       2  89.47%   5-6
problem/__init__.py                                                6       0  100.00%
problem/abstract_problem.py                                      117      18  84.62%   39-40, 59-70, 115-120, 149, 161, 179, 253, 257, 286
problem/inverse_problem.py                                        22       0  100.00%
problem/parametric_problem.py                                      8       1  87.50%   29
problem/spatial_problem.py                                         8       0  100.00%
problem/time_dependent_problem.py                                  8       0  100.00%
problem/zoo/__init__.py                                            8       0  100.00%
problem/zoo/advection.py                                          33       7  78.79%   36-38, 52, 108-110
problem/zoo/allen_cahn.py                                         20       6  70.00%   20-22, 34-36
problem/zoo/diffusion_reaction.py                                 29       5  82.76%   94-104
problem/zoo/helmholtz.py                                          30       6  80.00%   36-42, 103-107
problem/zoo/inverse_poisson_2d_square.py                          31       0  100.00%
problem/zoo/poisson_2d_square.py                                  19       3  84.21%   65-70
problem/zoo/supervised_problem.py                                 11       0  100.00%
solver/__init__.py                                                 6       0  100.00%
solver/garom.py                                                  107       2  98.13%   129-130
solver/solver.py                                                 188      10  94.68%   192, 215, 287, 290-291, 350, 432, 515, 556, 562
solver/ensemble_solver/__init__.py                                 4       0  100.00%
solver/ensemble_solver/ensemble_pinn.py                           23       1  95.65%   104
solver/ensemble_solver/ensemble_solver_interface.py               27       0  100.00%
solver/ensemble_solver/ensemble_supervised.py                      9       0  100.00%
solver/physics_informed_solver/__init__.py                         8       0  100.00%
solver/physics_informed_solver/causal_pinn.py                     47       3  93.62%   157, 166-167
solver/physics_informed_solver/competitive_pinn.py                58       0  100.00%
solver/physics_informed_solver/gradient_pinn.py                   17       0  100.00%
solver/physics_informed_solver/pinn.py                            18       0  100.00%
solver/physics_informed_solver/pinn_interface.py                  47       1  97.87%   130
solver/physics_informed_solver/rba_pinn.py                        35       3  91.43%   155-158
solver/physics_informed_solver/self_adaptive_pinn.py              90       3  96.67%   315-318
solver/supervised_solver/__init__.py                               4       0  100.00%
solver/supervised_solver/reduced_order_model.py                   24       1  95.83%   137
solver/supervised_solver/supervised.py                             7       0  100.00%
solver/supervised_solver/supervised_solver_interface.py           25       0  100.00%
solvers/__init__.py                                                6       6  0.00%    3-12
solvers/pinns/__init__.py                                          6       6  0.00%    3-12
TOTAL                                                           4663     504  89.19%

Results for commit: fbc0382

Minimum allowed coverage is 80.123%

♻️ This comment has been updated with latest results

dario-coscia · 2025-04-10T16:58:47Z

Hi @AleDinve @GiovanniCanali ! How is it going with this?

GiovanniCanali · 2025-04-10T17:03:59Z

Hi @AleDinve @GiovanniCanali ! How is it going with this?

Hi @dario-coscia, I need to fix some minor issues with InteractionNetwork, and then I will fix EGNN. Also, tests will be implemented. @AleDinve agreed to take care of the remaining classes.

AleDinve · 2025-04-10T17:05:48Z

Hi @AleDinve @GiovanniCanali ! How is it going with this?

Hi @dario-coscia, I need to fix some minor issues with InteractionNetwork, and then I will fix EGNN. Also, tests will be implemented. @AleDinve agreed to take care of the remaining classes.

Yes, I confirm, I will have a tentative implementation of the classes assigned to me by the weekend.

dario-coscia

Very good @GiovanniCanali and @AleDinve ! I made few comments on the implementation of the various blocks.

I think we should think about inserting inside utils.py a simple function that checks integer types and values. For example (very minimalistic):

def check_values(value, positive=True, strict=True):
   if positive and strict:
       assert value >= 0
   .....

this would reduce a lot of lines of code inside the blocks.

Copilot

Pull Request Overview

This PR adds implementations of various message-passing neural network blocks, a new utility for validating integer inputs, and corresponding tests.

Implements five blocks: InteractionNetworkBlock, DeepTensorNetworkBlock, EnEquivariantNetworkBlock, RadialFieldNetworkBlock, SchnetBlock.
Introduces check_positive_integer in pina/utils.py and adds tests in tests/test_utils.py.
Expands the test suite under tests/test_messagepassing to cover constructor, forward, and backward behavior for each block.

Reviewed Changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
tests/test_utils.py	Reorganized imports; added `test_check_positive_integer`.
tests/test_messagepassing/test_schnet_block.py	Added constructor, forward, and backward tests for `SchnetBlock`.
tests/test_messagepassing/test_radial_field_network_block.py	Added constructor, forward, and backward tests for `RadialFieldNetworkBlock`.
tests/test_messagepassing/test_interaction_network_block.py	Added constructor, forward, and backward tests for `InteractionNetworkBlock`.
tests/test_messagepassing/test_equivariant_network_block.py	Added constructor, forward, and backward tests for `EnEquivariantNetworkBlock`.
tests/test_messagepassing/test_deep_tensor_network_block.py	Added constructor, forward, and backward tests for `DeepTensorNetworkBlock`.
pina/utils.py	Added `check_positive_integer` utility.
pina/model/block/message_passing/schnet_block.py	Implemented `SchnetBlock`.
pina/model/block/message_passing/radial_field_network_block.py	Implemented `RadialFieldNetworkBlock`.
pina/model/block/message_passing/interaction_network_block.py	Implemented `InteractionNetworkBlock`.
pina/model/block/message_passing/egnn_block.py	Implemented `EnEquivariantNetworkBlock`.
pina/model/block/message_passing/deep_tensor_network_block.py	Implemented `DeepTensorNetworkBlock`.
pina/model/block/message_passing/init.py	Updated `__all__` to include new blocks.

dario-coscia

Very nice overall! I think the PR is almost ready.

I left few comments because I find some differences in EGNN and ShNet implementation wrt the paper.

Also I wanted to ask, should we test invariance and Equiv. in tests? I think we should

GiovanniCanali · 2025-05-30T12:26:36Z

@dario-coscia loops and hyperlinks have been fixed.

There are two last things left:

fix the forward of the Equivariant Network. I will take care of it asap.
implement equivariance tests for the very same model.

GiovanniCanali · 2025-06-01T08:40:20Z

Fixed EGNN and added equivariance test. Ready for final review @dario-coscia.

dario-coscia

For me everything is great now!

I made a simple fix in EGNN to avoid self.message... to be more pyg compliant. I also added invariance tests for SchNEt and Equivariance for RBF following what @GiovanniCanali did for EGNN!

AleDinve · 2025-06-01T11:35:24Z

❤️

Co-authored-by: Dario Coscia <dariocos99@gmail.com>

* Fix adaptive refinement (#571) --------- Co-authored-by: Dario Coscia <93731561+dario-coscia@users.noreply.github.com> * Remove collector * Fixes * Fixes * rm unnecessary comment * fix advection (#581) * Fix tutorial .html link (#580) * fix problem data collection for v0.1 (#584) * Message Passing Module (#516) * add deep tensor network block * add interaction network block * add radial field network block * add schnet block * add equivariant network block * fix + tests + doc files * fix egnn + equivariance/invariance tests Co-authored-by: Dario Coscia <dariocos99@gmail.com> --------- Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it> * add type checker (#527) --------- Co-authored-by: Filippo Olivo <filippo@filippoolivo.com> Co-authored-by: Giovanni Canali <115086358+GiovanniCanali@users.noreply.github.com> Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it>

* Fix adaptive refinement (mathLab#571) --------- Co-authored-by: Dario Coscia <93731561+dario-coscia@users.noreply.github.com> * Remove collector * Fixes * Fixes * rm unnecessary comment * fix advection (mathLab#581) * Fix tutorial .html link (mathLab#580) * fix problem data collection for v0.1 (mathLab#584) * Message Passing Module (mathLab#516) * add deep tensor network block * add interaction network block * add radial field network block * add schnet block * add equivariant network block * fix + tests + doc files * fix egnn + equivariance/invariance tests Co-authored-by: Dario Coscia <dariocos99@gmail.com> --------- Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it> * add type checker (mathLab#527) --------- Co-authored-by: Filippo Olivo <filippo@filippoolivo.com> Co-authored-by: Giovanni Canali <115086358+GiovanniCanali@users.noreply.github.com> Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it>

dario-coscia assigned dario-coscia and GiovanniCanali Mar 21, 2025

dario-coscia added enhancement New feature or request pr-to-fix Label for PR that needs modification labels Mar 21, 2025

dario-coscia linked an issue Mar 21, 2025 that may be closed by this pull request

Message Passing Module #515

Closed

dario-coscia assigned AleDinve Apr 4, 2025

dario-coscia force-pushed the dev branch from de34a02 to 4e16d0a Compare April 8, 2025 08:19

GiovanniCanali force-pushed the messagepassing branch from b17fd16 to 23b3560 Compare April 9, 2025 13:07

GiovanniCanali force-pushed the messagepassing branch 2 times, most recently from 5727bcc to 426da3e Compare April 11, 2025 08:59

dario-coscia force-pushed the dev branch from a84b105 to a2b6c1f Compare April 14, 2025 09:44

dario-coscia force-pushed the dev branch from d0d8577 to d10c525 Compare April 23, 2025 16:57

dario-coscia and others added 3 commits April 25, 2025 13:14

add buggy egnn block

5a4fc44

add deep tensor network block

a7c8c35

add interaction network block

9a09821

dario-coscia force-pushed the messagepassing branch from f38ccbd to 1c6bef4 Compare April 25, 2025 11:15

dario-coscia commented Apr 25, 2025

View reviewed changes

dario-coscia assigned dario-coscia and unassigned dario-coscia Apr 25, 2025

AleDinve added 3 commits May 29, 2025 23:17

add radial field network block

0ba352c

add schnet block

cbf4e80

add equivariant network block

f13a5f3

GiovanniCanali force-pushed the messagepassing branch 3 times, most recently from 5b7a708 to 1525549 Compare May 29, 2025 21:28

GiovanniCanali unassigned dario-coscia May 30, 2025

Copilot AI reviewed May 30, 2025

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dario-coscia added pr-to-fix Label for PR that needs modification and removed pr-to-review Label for PR that are ready to been reviewed labels May 30, 2025

GiovanniCanali force-pushed the messagepassing branch from 4d814a6 to 4110851 Compare May 30, 2025 09:15

GiovanniCanali approved these changes May 30, 2025

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GiovanniCanali added pr-to-review Label for PR that are ready to been reviewed and removed pr-to-fix Label for PR that needs modification labels May 30, 2025

dario-coscia commented May 30, 2025

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GiovanniCanali added pr-to-fix Label for PR that needs modification pr-to-review Label for PR that are ready to been reviewed and removed pr-to-review Label for PR that are ready to been reviewed pr-to-fix Label for PR that needs modification labels May 30, 2025

dario-coscia commented Jun 1, 2025

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dario-coscia force-pushed the messagepassing branch 2 times, most recently from a3e7f9f to 104c639 Compare June 1, 2025 11:44

GiovanniCanali self-requested a review June 1, 2025 11:50

fix + tests + doc files

2cd5a5e

GiovanniCanali force-pushed the messagepassing branch from 383a92a to c7bf7d9 Compare June 1, 2025 12:29

fix egnn + equivariance/invariance tests

fbc0382

Co-authored-by: Dario Coscia <dariocos99@gmail.com>

GiovanniCanali force-pushed the messagepassing branch from c7bf7d9 to fbc0382 Compare June 1, 2025 13:07

GiovanniCanali approved these changes Jun 1, 2025

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dario-coscia merged commit 2101d79 into dev Jun 1, 2025
18 checks passed

GiovanniCanali deleted the messagepassing branch June 14, 2025 09:02

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