Topology learning

[levtelyatnikov]

Checklist

• My pull request has a clear and explanatory title.
• My pull request passes the Linting test.
• I added appropriate unit tests and I made sure the code passes all unit tests. (refer to comment below)
• My PR follows PEP8 guidelines. (refer to comment below)
• My code is properly documented, using numpy docs conventions, and I made sure the documentation renders properly.
• I linked to issues and PRs that are relevant to this PR.

Description

Issue

Additional context

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Codecov Report

Attention: Patch coverage is 54.81728% with 136 lines in your changes missing coverage. Please review.

Project coverage is 85.48%. Comparing base (6b5c349) to head (cf84728).
Report is 20 commits behind head on main.

Files with missing lines	Patch %	Lines
topobenchmarkx/nn/encoders/kdgm.py	13.79%	50 Missing ⚠️
topobenchmarkx/nn/encoders/alpha_dgm.py	8.57%	32 Missing ⚠️
topobenchmarkx/loss/model/DGMLoss.py	24.13%	22 Missing ⚠️
topobenchmarkx/nn/encoders/dgm_encoder.py	28.57%	20 Missing ⚠️
topobenchmarkx/loss/__init__.py	89.18%	4 Missing ⚠️
topobenchmarkx/loss/model/__init__.py	91.89%	3 Missing ⚠️
topobenchmarkx/loss/dataset/__init__.py	94.59%	2 Missing ⚠️
topobenchmarkx/nn/encoders/__init__.py	94.59%	2 Missing ⚠️
topobenchmarkx/nn/wrappers/graph/gnn_wrapper.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #114      +/-   ##
==========================================
- Coverage   88.29%   85.48%   -2.82%     
==========================================
  Files         122      126       +4     
  Lines        3289     3582     +293     
==========================================
+ Hits         2904     3062     +158     
- Misses        385      520     +135     

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