Reconstruction algorithm - SbRP

.github/CODE_OF_CONDUCT.md

@@ -1,4 +1,4 @@
-# Code of Conduct for the Network Centrality Library Project
+# Code of Conduct for the Network Source Detection Library) Project
 
 ## Our Pledge
 

.github/CONTRIBUTING.md

@@ -22,19 +22,19 @@ We warmly welcome contributions to NSDLib! This document provides guidelines for
 
 ### Implementation Requirements
 
-- **Centrality Measures Implementation**:
-  - Each centrality measure must be implemented in a separate file within the `nsdlib/algorithms` directory.
-  - The file name should match the centrality measure's name.
-  - Each file must contain a single function, named after the centrality measure, that calculates this measure. This function should accept a NetworkX graph as input and return a dictionary mapping nodes to their centrality values.
-  - Each centrality measure function must be exposed in the `nsdlib/algorithms` package to be accessible for external use.
-  - Add an entry for the new centrality measure in the `Centrality` enum to ensure it's recognized and accessible through a standardized interface.
+- **Source Detection Method Implementation**:
+  - Each new method must be implemented in a separate file within the `nsdlib/algorithms` directory in appropriate package according to its intended purpose e.g. reconstruction algorithm should be placed in `reconstruction` package.
+  - The file name should match the method's name.
+  - Each file must contain a single function, named after the new method name.
+  - Each alg function must be exposed in the `nsdlib/algorithms` package to be accessible for external use.
+  - Add an entry for the new alg in the appropiate taxonomy class, e.g. for reconstruction algorithm new entry should be placed into `PropagationReconstructionAlgorithm` enum to ensure it's recognized and accessible through a standardized interface.
 
 - **Testing**:
   - Contributions must include tests covering the new functionality. We require at least 80% test coverage for changes.
   - Use the `pytest` framework for writing tests.
 
 - **Documentation**:
-  - Update the project documentation to reflect the addition of new centrality measures or any other significant changes.
+  - Update the project documentation to reflect the addition of new method or any other significant changes.
   - Ensure that examples, usage guides, and API documentation are clear and updated.
 
 ### Making Changes

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,6 +1,6 @@
 ---
 name: Bug Report
-about: Create a report to help us improve the network centrality library
+about: Create a report to help us improve the NSDLib
 title: "[BUG]"
 labels: bug
 assignees: ''

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,6 @@
 ---
 name: Feature Request
-about: Suggest an idea for the network centrality library
+about: Suggest an idea for the NSDLib
 title: "[FEATURE]"
 labels: enhancement
 assignees: ''

.gitignore

@@ -1,45 +1,7 @@
 ### JetBrains template
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
 # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
-
-# User-specific stuff
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
-.idea/**/dictionaries
-.idea/**/shelf
-
-# AWS User-specific
-.idea/**/aws.xml
-
-# Generated files
-.idea/**/contentModel.xml
-
-# Sensitive or high-churn files
-.idea/**/dataSources/
-.idea/**/dataSources.ids
-.idea/**/dataSources.local.xml
-.idea/**/sqlDataSources.xml
-.idea/**/dynamic.xml
-.idea/**/uiDesigner.xml
-.idea/**/dbnavigator.xml
-
-# Gradle
-.idea/**/gradle.xml
-.idea/**/libraries
-
-# Gradle and Maven with auto-import
-# When using Gradle or Maven with auto-import, you should exclude module files,
-# since they will be recreated, and may cause churn.  Uncomment if using
-# auto-import.
-# .idea/artifacts
-# .idea/compiler.xml
-# .idea/jarRepositories.xml
-# .idea/modules.xml
-# .idea/*.iml
-# .idea/modules
-# *.iml
-# *.ipr
+.idea
 
 # CMake
 cmake-build-*/

CHANGELOG.md

@@ -3,16 +3,6 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.2.1] - 2024-02-23
+## [0.1.0] - 2024-07-08
 ### Added
-- All common modules exported in `__init__.py` file
-
-## [0.2.0] - 2024-02-22
-### Added
-- new centrality measure - hubbell centrality has been added
-- updated maintenance related files
-- extended documentation
-
-## [0.1.1] - 2024-01-09
-### Added
-- nsdlib version 0.1.1 release
+- NSDlib version 0.1.0 release

README.md

@@ -1,22 +1,21 @@
 # NSDlib
 
-NSDlib (Network source detection library) is a tool to compute a wide range of centrality measures for a given network. The
-library is designed to work with Python Networkx library.
+NSDlib (Network source detection library) is a comprehensive library designed for detecting sources of propagation in networks. This library offers a variety of algorithms that help researchers and developers analyze and identify the origins of information (epidemic etc.) spread within networks.
 
 ## Overview
 
-The goal of NSDlib is to offer a comprehensive repository for implementing a broad spectrum of centrality measures. Each
-year, new measures are introduced through scientific papers, often with only pseudo-code descriptions, making it
-difficult for researchers to evaluate and compare them with existing methods. While implementations of well-known
-centrality measures exist, recent innovations are frequently absent. NSDlib strives to bridge this gap. It references the
-renowned CentiServer portal for well-known centrality measures and their originating papers, aiming to encompass all
-these measures in the future.
+NSDLib is a complex library designed for easy integration into existing projects. It aims to be a comprehensive repository
+of source detection methods, outbreak detection techniques, and propagation graph reconstruction tools. Researchers worldwide are encouraged to contribute and utilize this library,
+facilitating the development of new techniques to combat misinformation and improve propagation analysis.
+Each  year, new techniques are introduced through scientific papers, often with only pseudo-code descriptions, making it
+difficult for researchers to evaluate and compare them with existing methods. NSDlib tries to bridge this gap and enhance researchers to put their implementations here.
 
 ## Code structure
 
-All custom implementations are provided under `nsdlib/algorithms` package. Each centrality measure is implemented in a separate file, named after the measure itself. Correspondingly, each file contains a function, named identically to the file, which calculates the centrality measure. This function accepts a NetworkX graph as input (and other params if applicable) and returns a dictionary, mapping nodes to their centrality values. Ultimately, every custom implementation is made available through the `nsdlib/algorithms` package.
-## Implemented centrality measures:
+All custom implementations are provided under `nsdlib/algorithms` package. Each method is implemented in a separate file, named after the method itself and in appropriate package according to its intended purpose e.g. reconstruction algorithm should be placed in `reconstruction` package. . Correspondingly, each file contains a function, named identically to the file, which does appropriate logic.  Ultimately, every custom implementation is made available through the `nsdlib/algorithms` package.
+## Implemented features:
 
+### Node evaluation algorithms
 - [Algebraic](https://www.centiserver.org/centrality/Algebraic_Centrality/)
 - [Average Distance](https://www.centiserver.org/centrality/Average_Distance/)
 - [Barycenter](https://www.centiserver.org/centrality/Barycenter_Centrality/)
@@ -58,6 +57,12 @@ All custom implementations are provided under `nsdlib/algorithms` package. Each
 - [Topological](https://www.centiserver.org/centrality/Topological_Coefficient/)
 - [Trophic Levels](https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.centrality.trophic_levels.html)
 
+### Outbreak detection algorithms
+- test
+
+### Graph reconstruction algorithms
+- SbRP
+
 ## How to use
 Library can be installed using pip:
 
@@ -69,31 +74,32 @@ pip install nsdlib
 
 Provided algorithms can be executed in the following ways:
 
-- by invoking a specific function from `nsdlib.algorithms` package, which computes a given centrality measure for a
-  given graph.
+- by utilizing 'SourceDetector' class and configuring it with 'SourceDetectionConfig' object. This approach allows for seamless source detection and result evaluation.
 
 ```python
 import networkx as nx
-import nsdlib as ncl
 
-# Create a graph
+from nsdlib.common.models import SourceDetectionConfig
+from nsdlib.source_detection import SourceDetector
+from nsdlib.taxonomies import NodeEvaluationAlgorithm
+
+
 G = nx.karate_club_graph()
 
-# Compute degree centrality
-degree_centrality = ncl.degree_centrality(G)
+config = SourceDetectionConfig(
+    node_evaluation_algorithm=NodeEvaluationAlgorithm.NETSLEUTH,
+)
+
+source_detector = SourceDetector(config)
 
-# Compute betweenness centrality
-betweenness_centrality = ncl.betweenness_centrality(G)
+result, evaluation = source_detector.detect_sources_and_evaluate(G=G,
+                                        IG=G, real_sources=[0,33])
+print(evaluation)
 
-# Compute closeness centrality
-closeness_centrality = ncl.closeness_centrality(G)
 
-# Compute eigenvector centrality
-eigenvector_centrality = ncl.eigenvector_centrality(G)
 ```
 
-- invoking `compute_centrality` method of `CentralityService` class, which allows to compute centrality for a given
-  centrality measure.
+- by importing and using specific method:
 
 ```python
 from typing import Any

src/aa.py

@@ -1,22 +1,18 @@
 import networkx as nx
-import netcenlib as ncl
+
 from nsdlib.common.models import SourceDetectionConfig
 from nsdlib.source_detection import SourceDetector
-from nsdlib.taxonomies import OutbreaksDetectionAlgorithm
+from nsdlib.taxonomies import NodeEvaluationAlgorithm
 
-# Create a graph
 G = nx.karate_club_graph()
 
 config = SourceDetectionConfig(
-    selection_threshold=None,
-    outbreaks_detection_algorithm=OutbreaksDetectionAlgorithm.LEIDEN,
+    node_evaluation_algorithm=NodeEvaluationAlgorithm.NETSLEUTH,
 )
 
 source_detector = SourceDetector(config)
 
-result, evaluation = source_detector.detect_sources_and_evaluate(G=G,
-                                        IG=G, real_sources=[0,33])
+result, evaluation = source_detector.detect_sources_and_evaluate(
+    G=G, IG=G, real_sources=[0, 33]
+)
 print(result.global_scores)
-print(ncl.degree_centrality(G))
-
-print(evaluation)

src/nsdlib/algorithms/__init__.py

@@ -0,0 +1,91 @@
+# flake8: noq
+
+from nsdlib.algorithms.outbreaks_detection import (
+    CPM_Bipartite as outbreaks_detection_CPM_Bipartite,
+    agdl as outbreaks_detection_agdl,
+    angel as outbreaks_detection_angel,
+    aslpaw as outbreaks_detection_aslpaw,
+    async_fluid as outbreaks_detection_async_fluid,
+    attribute_clustering as outbreaks_detection_attribute_clustering,
+    bayan as outbreaks_detection_bayan,
+    belief as outbreaks_detection_belief,
+    bimlpa as outbreaks_detection_bimlpa,
+    bipartite_clustering as outbreaks_detection_bipartite_clustering,
+    coach as outbreaks_detection_coach,
+    condor as outbreaks_detection_condor,
+    conga as outbreaks_detection_conga,
+    congo as outbreaks_detection_congo,
+    core_expansion as outbreaks_detection_core_expansion,
+    cpm as outbreaks_detection_cpm,
+    crisp_partition as outbreaks_detection_crisp_partition,
+    dcs as outbreaks_detection_dcs,
+    demon as outbreaks_detection_demon,
+    der as outbreaks_detection_der,
+    dpclus as outbreaks_detection_dpclus,
+    ebgc as outbreaks_detection_ebgc,
+    edge_clustering as outbreaks_detection_edge_clustering,
+    ego_networks as outbreaks_detection_ego_networks,
+    eigenvector as outbreaks_detection_eigenvector,
+    em as outbreaks_detection_em,
+    endntm as outbreaks_detection_endntm,
+    eva as outbreaks_detection_eva,
+    frc_fgsn as outbreaks_detection_frc_fgsn,
+    ga as outbreaks_detection_ga,
+    gdmp2 as outbreaks_detection_gdmp2,
+    girvan_newman as outbreaks_detection_girvan_newman,
+    graph_entropy as outbreaks_detection_graph_entropy,
+    greedy_modularity as outbreaks_detection_greedy_modularity,
+    head_tail as outbreaks_detection_head_tail,
+    hierarchical_link_community as outbreaks_detection_hierarchical_link_community,
+    ilouvain as outbreaks_detection_ilouvain,
+    infomap as outbreaks_detection_infomap,
+    infomap_bipartite as outbreaks_detection_infomap_bipartite,
+    internal as outbreaks_detection_internal,
+    internal_dcd as outbreaks_detection_internal_dcd,
+    ipca as outbreaks_detection_ipca,
+    kclique as outbreaks_detection_kclique,
+    kcut as outbreaks_detection_kcut,
+    label_propagation as outbreaks_detection_label_propagation,
+    lais2 as outbreaks_detection_lais2,
+    leiden as outbreaks_detection_leiden,
+    lemon as outbreaks_detection_lemon,
+    lfm as outbreaks_detection_lfm,
+    louvain as outbreaks_detection_louvain,
+    lpam as outbreaks_detection_lpam,
+    lpanni as outbreaks_detection_lpanni,
+    lswl as outbreaks_detection_lswl,
+    lswl_plus as outbreaks_detection_lswl_plus,
+    markov_clustering as outbreaks_detection_markov_clustering,
+    mcode as outbreaks_detection_mcode,
+    mod_m as outbreaks_detection_mod_m,
+    mod_r as outbreaks_detection_mod_r,
+    multicom as outbreaks_detection_multicom,
+    node_perception as outbreaks_detection_node_perception,
+    overlapping_partition as outbreaks_detection_overlapping_partition,
+    overlapping_seed_set_expansion as outbreaks_detection_overlapping_seed_set_expansion,
+    paris as outbreaks_detection_paris,
+    percomvc as outbreaks_detection_percomvc,
+    principled_clustering as outbreaks_detection_principled_clustering,
+    pycombo as outbreaks_detection_pycombo,
+    r_spectral_clustering as outbreaks_detection_r_spectral_clustering,
+    rb_pots as outbreaks_detection_rb_pots,
+    rber_pots as outbreaks_detection_rber_pots,
+    ricci_community as outbreaks_detection_ricci_community,
+    sbm_dl as outbreaks_detection_sbm_dl,
+    sbm_dl_nested as outbreaks_detection_sbm_dl_nested,
+    scan as outbreaks_detection_scan,
+    siblinarity_antichain as outbreaks_detection_siblinarity_antichain,
+    significance_communities as outbreaks_detection_significance_communities,
+    slpa as outbreaks_detection_slpa,
+    spectral as outbreaks_detection_spectral,
+    spinglass as outbreaks_detection_spinglass,
+    surprise_communities as outbreaks_detection_surprise_communities,
+    temporal_partition as outbreaks_detection_temporal_partition,
+    threshold_clustering as outbreaks_detection_threshold_clustering,
+    tiles as outbreaks_detection_tiles,
+    umstmo as outbreaks_detection_umstmo,
+    walkscan as outbreaks_detection_walkscan,
+    walktrap as outbreaks_detection_walktrap,
+    wCommunity as outbreaks_detection_wCommunity,
+)
+from nsdlib.algorithms.reconstruction import sbrp as reconstruction_sbrp