nico-curti / rfbp Goto Github PK

Replicated Focusing Belief Propagation algorithm

Home Page: https://nico-curti.github.io/rFBP

License: Other

C++ 83.20% Makefile 0.63% CMake 3.07% PowerShell 0.21% Shell 0.19% Python 12.12% Dockerfile 0.12% TeX 0.45%

belief-propagation deep-neural-networks spin-glass statistical-mechanics learning-algorithm machine-learning-algorithms python3 cpp17

rfbp's Introduction

Hi there, I'm Nico! 👋

Hi, I'm Nico Curti, a PhD at the Dept. of Physics and Astronomy of Bologna University (Italy).

Please feel free to clone projects, raise issues and submit PRs if you think something could be better.

💬 Ask me about anything
📫 You can contact me here

Happy Coding! 😊

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Latest pubblications

Implementation and optimization of algorithms in Biomedical Big Data Analytics.
A network approach for low-dimensional signatures from high-throughput data.
Prediction of vascular ageing based on smartphone acquired PPG signals.
rFBP: Replicated Focusing Belief Propagation algorithm.
plasticity: Unsupervised Neural Networks with biological-inspired learning rules.
COVID-19 Lung Segmentation.
Automated Prediction of the Response to Neoadjuvant Chemoradiotherapy in Patients Affected by Rectal Cancer.
Effectiveness of semi-supervised active learning in automated wound image segmentation.
Automated wound image segmentation: transfer learning from human to pet via active semi-supervised learning.
Characterization of pupillary light response features for the classification of patients with Optic Neuritis.

Top collaborators

_{Gianluca Carlini}	_{Riccardo Biondi}	_{Daniele Buschi}	_{Daniele Dall'Olio}	_{Enrico Giampieri}	_{Alessandro Fabbri}	_{Stefano Sinigardi}

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rfbp's Issues

Functionality Documentation

Hi,

during my review for JOSS (openjournals/joss-reviews#2663) I looked for what they call "functionality documentation". I was not able to find any API-Documentation on your GitHub page. Could you maybe add this?

Install from PyPI: numpy not found

Hi! This issue is related to the JOSS review (openjournals/joss-reviews#2663).

I tried to install the Python package from pip in a fresh venv and noticed that the requirements aren't installed as they should be.


~ pipenv install ReplicatedFocusingBeliefPropagation

Installing ReplicatedFocusingBeliefPropagation…
Error:  An error occurred while installing ReplicatedFocusingBeliefPropagation!
Error text: Collecting replicatedfocusingbeliefpropagation
  Downloading ReplicatedFocusingBeliefPropagation-1.0.1.tar.gz (417 kB)

    ERROR: Command errored out with exit status 1:
     command: /Users/lenzda/.local/share/virtualenvs/py-Ob9eXrK4/bin/python3.7m -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4x/6yrptfcn4kxdynxfy3qv1g20lmvv2v/T/pip-install-uu4qb3_7/replicatedfocusingbeliefpropagation/setup.py'"'"'; __file__='"'"'/private/var/folders/4x/6yrptfcn4kxdynxfy3qv1g20lmvv2v/T/pip-install-uu4qb3_7/replicatedfocusingbeliefpropagation/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/4x/6yrptfcn4kxdynxfy3qv1g20lmvv2v/T/pip-pip-egg-info-vplpgjcz
         cwd: /private/var/folders/4x/6yrptfcn4kxdynxfy3qv1g20lmvv2v/T/pip-install-uu4qb3_7/replicatedfocusingbeliefpropagation/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/4x/6yrptfcn4kxdynxfy3qv1g20lmvv2v/T/pip-install-uu4qb3_7/replicatedfocusingbeliefpropagation/setup.py", line 8, in <module>
        import numpy as np
    ModuleNotFoundError: No module named 'numpy'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

This is likely caused by a bug in ReplicatedFocusingBeliefPropagation. Report this to its maintainers.
✘ Installation Failed

I checked your travis config and noticed that you had to implement some workarounds because of a setuptools issue (pypa/setuptools#2352). Could you use this to patch the pip install accordingly?

Docstrings

During my review for JOSS (openjournals/joss-reviews#2663), I also found that for your C++ Code there are not always docstrings for functions. Could you maybe add these and while on it make sure they can be parsed from oxygen or whatever?

Also your Python Docstrings could be cleaned up a bit to be a bit more consistent regarding the parameter types. If you revisit them, make sure they follow the sphinx format (or some other but sphinx is really easy to use). If you want to, you could also remove the parameter types and replace them by Python's type annotations.

This is basically a preparation for #4

CONTRIBUTING.md doesn't exist

Hi! This issue is related to the JOSS review (openjournals/joss-reviews#2663).

I noted that towards the end of the README, you refer to the CONTRIBUTING.md for instructions on how to contribute to this project, but this file doesn't exist.

The same is true for the issue template and for the PR template.

LICENSE File

Hi,
first I want to thank you for this incredible work.

While reviewing for JOSS (openjournals/joss-reviews#2663), I noted that your license file is markdown and not a plain text file as required :)

nico-curti / rfbp Goto Github PK

rfbp's Introduction

Hi there, I'm Nico! 👋

Languages and Tools

Github groups

Latest pubblications

Top collaborators

Current works

rfbp's People

Contributors

Stargazers

Watchers

rfbp's Issues

Functionality Documentation

Install from PyPI: numpy not found

Docstrings

CONTRIBUTING.md doesn't exist

LICENSE File

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