so4gp

Name	so4gp JSON
Version	0.6.7 JSON
	download
home_page	None
Summary	Some Python optimization algorithms for mining gradual patterns.
upload_time	2024-11-28 06:08:15
maintainer	None
docs_url	None
author	None
requires_python	>=3.9
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keywords	gradual patterns graank ant-colony-optimization data-mining swarm-intelligence
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**SO4GP** stands for: "Some Optimizations for Gradual Patterns". SO4GP applies optimizations such as swarm intelligence, HDF5 chunks, cluster analysis and many others in order to improve the efficiency of extracting gradual patterns. It provides Python algorithm implementations for these optimization techniques. The algorithm implementations include:

* (Classical) GRAANK algorithm for extracting GPs
* Ant Colony Optimization algorithm for extracting GPs
* Genetic Algorithm for extracting GPs
* Particle Swarm Optimization algorithm for extracting GPs
* Random Search algorithm for extracting GPs
* Local Search algorithm for extracting GPs
* Clustering-based algorithm for extracting GPs

A GP (Gradual Pattern) is a set of gradual items (GI) and its quality is measured by its computed support value. For example given a data set with 3 columns (age, salary, cars) and 10 objects. A GP may take the form: {age+, salary-} with a support of 0.8. This implies that 8 out of 10 objects have the values of column age 'increasing' and column 'salary' decreasing.

## Install Requirements
Before running **so4gp**, make sure you install the following ```Python Packages```:

```shell
pip3 install numpy>=1.23.2 pandas>=1.4.4 python-dateutil>=2.8.2 ypstruct>=0.0.2 scikit-learn>=1.1.2
```

## Usage
In order to run each algorithm for the purpose of extracting GPs, follow the instructions that follow.

First and foremost, import the **so4gp** python package via:

```python
import so4gp as sgp
```

### 1.  GRAdual rANKing Algorithm for GPs (GRAANK)

This is the classical approach (initially proposed by Anne Laurent) for mining gradual patterns. All the remaining algorithms are variants of this algorithm.

```python

mine_obj = sgp.GRAANK(data_source=f_path, min_sup=0.5, eq=False)
gp_json = mine_obj.discover()
print(gp_json)

```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **eq** - *[optional]* encode equal values as gradual ```default = False```


### 2. Ant Colony Optimization for GPs (ACO-GRAANK)
In this approach, it is assumed that every column can be converted into gradual item (GI). If the GI is valid (i.e. its computed support is greater than the minimum support threshold) then it is either increasing or decreasing (+ or -), otherwise it is irrelevant (x). Therefore, a pheromone matrix is built using the number of columns and the possible variations (increasing, decreasing, irrelevant) or (+, -, x). The algorithm starts by randomly generating GP candidates using the pheromone matrix, each candidate is validated by confirming that its computed support is greater or equal to the minimum support threshold. The valid GPs are used to update the pheromone levels and better candidates are generated.

```python

mine_obj = sgp.AntGRAANK(data_src)
gp_json = mine_obj.discover()
print(gp_json)
```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **max_iteration** - *[optional]* maximum number of iterations ```default = 1```
* **evaporation_factor** - *[optional]* evaporation factor ```default = 0.5```


### 3. Genetic Algorithm for GPs (GA-GRAANK)
In this approach, it is assumed that every GP candidate may be represented as a binary gene (or individual) that has a unique position and cost. The cost is derived from the computed support of that candidate, the higher the support value the lower the cost. The aim of the algorithm is search through a population of individuals (or candidates) and find those with the lowest cost as efficiently as possible.

```python

mine_obj = sgp.GeneticGRAANK(data_src)
gp_json = mine_obj.discover()
print(gp_json)
```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```
* **n_pop** - *[optional]* initial population ```default = 5```
* **pc** - *[optional]* offspring population multiple ```default = 0.5```
* **gamma** - *[optional]* crossover rate ```default = 1```
* **mu** - *[optional]* mutation rate ```default = 0.9```
* **sigma** - *[optional]* mutation rate ```default = 0.9```

### 4. Particle Swarm Optimization for GPs (PSO-GRAANK)
In this approach, it is assumed that every GP candidate may be represented as a particle that has a unique position and fitness. The fitness is derived from the computed support of that candidate, the higher the support value the higher the fitness. The aim of the algorithm is search through a population of particles (or candidates) and find those with the highest fitness as efficiently as possible.

```python

mine_obj = sgp.ParticleGRAANK(data_src)
gp_json = mine_obj.discover()
print(gp_json)
```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```
* **n_particles** - *[optional]* initial particle population ```default = 5```
* **velocity** - *[optional]* particle velocity ```default = 0.9```
* **coeff_p** - *[optional]* personal coefficient rate ```default = 0.01```
* **coeff_g** - *[optional]* global coefficient ```default = 0.9```

### 5. Local Search for GPs (LS-GRAANK)
In this approach, it is assumed that every GP candidate may be represented as a position that has a cost value associated with it. The cost is derived from the computed support of that candidate, the higher the support value the lower the cost. The aim of the algorithm is search through group of positions and find those with the lowest cost as efficiently as possible.

```python

mine_obj = sgp.HillClimbingGRAANK(data_src, min_sup)
gp_json = mine_obj.discover()
print(gp_json)
```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```
* **step_size** - *[optional]* step size ```default = 0.5```


### 6. Random Search for GPs (RS-GRAANK)
In this approach, it is assumed that every GP candidate may be represented as a position that has a cost value associated with it. The cost is derived from the computed support of that candidate, the higher the support value the lower the cost. The aim of the algorithm is search through group of positions and find those with the lowest cost as efficiently as possible.

```python
import so4gp as sgp

mine_obj = sgp.RandomGRAANK(data_src, min_sup)
gp_json = mine_obj.discover()
print(gp_json)
```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```


### 7. Clustering algorithm for GPs (Clu-BFS)
We borrow the net-win concept used in the work 'Clustering Using Pairwise Comparisons' proposed by R. Srikant to the problem of extracting gradual patterns (GPs). In order to mine for GPs, each feature yields 2 gradual items which we use to construct a bitmap matrix comparing each row to each other (i.e., (r1,r2), (r1,r3), (r1,r4), (r2,r3), (r2,r4), (r3,r4)).

In this approach, we convert the bitmap matrices into 'net-win vectors'. Finally, we apply spectral clustering to determine which gradual items belong to the same group based on the similarity of net-win vectors. Gradual items in the same cluster should have almost similar score vector.

```python
import so4gp as sgp

mine_obj = sgp.ClusterGP(data_source=data_src, min_sup=0.5, e_prob=0.1)
gp_json = mine_obj.discover()
print(gp_json)
```

where you specify the parameters as follows:

* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}
* **min_sup** - *[optional]* minimum support ```default = 0.5```
* **e_probability** - *[optional]* erasure probability ```default = 0.5```
* **max_iteration** - *[optional]* maximum iterations for estimating score vectors ```default = 10```


## Sample Output
The default output is the format of JSON:

```json
{
	"Algorithm": "RS-GRAANK",
	"Best Patterns": [
            [["Age+", "Salary+"], 0.6], 
            [["Expenses-", "Age+", "Salary+"], 0.6]
	],
	"Iterations": 20
}
```

### References
* Owuor, D., Runkler T., Laurent A., Menya E., Orero J (2021), Ant Colony Optimization for Mining Gradual Patterns. International Journal of Machine Learning and Cybernetics. https://doi.org/10.1007/s13042-021-01390-w
* Dickson Owuor, Anne Laurent, and Joseph Orero (2019). Mining Fuzzy-temporal Gradual Patterns. In the proceedings of the 2019 IEEE International Conference on Fuzzy Systems (FuzzIEEE). IEEE. https://doi.org/10.1109/FUZZ-IEEE.2019.8858883.
* Laurent A., Lesot MJ., Rifqi M. (2009) GRAANK: Exploiting Rank Correlations for Extracting Gradual Itemsets. In: Andreasen T., Yager R.R., Bulskov H., Christiansen H., Larsen H.L. (eds) Flexible Query Answering Systems. FQAS 2009. Lecture Notes in Computer Science, vol 5822. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04957-6_33

            

Raw data

            {
    "_id": null,
    "home_page": null,
    "name": "so4gp",
    "maintainer": null,
    "docs_url": null,
    "requires_python": ">=3.9",
    "maintainer_email": "Dickson Owuor <owuordickson@gmail.com>",
    "keywords": "gradual patterns, GRAANK, ant-colony-optimization, data-mining, swarm-intelligence",
    "author": null,
    "author_email": "Dickson Owuor <owuordickson@gmail.com>, Anne Laurent <laurent@lirmm.fr>",
    "download_url": "https://files.pythonhosted.org/packages/cb/90/9032d30e5addd119b3591871a716e02618a7725e0069345a5dce94e09e71/so4gp-0.6.7.tar.gz",
    "platform": null,
    "description": "\r\n**SO4GP** stands for: \"Some Optimizations for Gradual Patterns\". SO4GP applies optimizations such as swarm intelligence, HDF5 chunks, cluster analysis and many others in order to improve the efficiency of extracting gradual patterns. It provides Python algorithm implementations for these optimization techniques. The algorithm implementations include:\r\n\r\n* (Classical) GRAANK algorithm for extracting GPs\r\n* Ant Colony Optimization algorithm for extracting GPs\r\n* Genetic Algorithm for extracting GPs\r\n* Particle Swarm Optimization algorithm for extracting GPs\r\n* Random Search algorithm for extracting GPs\r\n* Local Search algorithm for extracting GPs\r\n* Clustering-based algorithm for extracting GPs\r\n\r\nA GP (Gradual Pattern) is a set of gradual items (GI) and its quality is measured by its computed support value. For example given a data set with 3 columns (age, salary, cars) and 10 objects. A GP may take the form: {age+, salary-} with a support of 0.8. This implies that 8 out of 10 objects have the values of column age 'increasing' and column 'salary' decreasing.\r\n\r\n## Install Requirements\r\nBefore running **so4gp**, make sure you install the following ```Python Packages```:\r\n\r\n```shell\r\npip3 install numpy>=1.23.2 pandas>=1.4.4 python-dateutil>=2.8.2 ypstruct>=0.0.2 scikit-learn>=1.1.2\r\n```\r\n\r\n## Usage\r\nIn order to run each algorithm for the purpose of extracting GPs, follow the instructions that follow.\r\n\r\nFirst and foremost, import the **so4gp** python package via:\r\n\r\n```python\r\nimport so4gp as sgp\r\n```\r\n\r\n### 1.  GRAdual rANKing Algorithm for GPs (GRAANK)\r\n\r\nThis is the classical approach (initially proposed by Anne Laurent) for mining gradual patterns. All the remaining algorithms are variants of this algorithm.\r\n\r\n```python\r\n\r\nmine_obj = sgp.GRAANK(data_source=f_path, min_sup=0.5, eq=False)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **eq** - *[optional]* encode equal values as gradual ```default = False```\r\n\r\n\r\n### 2. Ant Colony Optimization for GPs (ACO-GRAANK)\r\nIn this approach, it is assumed that every column can be converted into gradual item (GI). If the GI is valid (i.e. its computed support is greater than the minimum support threshold) then it is either increasing or decreasing (+ or -), otherwise it is irrelevant (x). Therefore, a pheromone matrix is built using the number of columns and the possible variations (increasing, decreasing, irrelevant) or (+, -, x). The algorithm starts by randomly generating GP candidates using the pheromone matrix, each candidate is validated by confirming that its computed support is greater or equal to the minimum support threshold. The valid GPs are used to update the pheromone levels and better candidates are generated.\r\n\r\n```python\r\n\r\nmine_obj = sgp.AntGRAANK(data_src)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **max_iteration** - *[optional]* maximum number of iterations ```default = 1```\r\n* **evaporation_factor** - *[optional]* evaporation factor ```default = 0.5```\r\n\r\n\r\n### 3. Genetic Algorithm for GPs (GA-GRAANK)\r\nIn this approach, it is assumed that every GP candidate may be represented as a binary gene (or individual) that has a unique position and cost. The cost is derived from the computed support of that candidate, the higher the support value the lower the cost. The aim of the algorithm is search through a population of individuals (or candidates) and find those with the lowest cost as efficiently as possible.\r\n\r\n```python\r\n\r\nmine_obj = sgp.GeneticGRAANK(data_src)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```\r\n* **n_pop** - *[optional]* initial population ```default = 5```\r\n* **pc** - *[optional]* offspring population multiple ```default = 0.5```\r\n* **gamma** - *[optional]* crossover rate ```default = 1```\r\n* **mu** - *[optional]* mutation rate ```default = 0.9```\r\n* **sigma** - *[optional]* mutation rate ```default = 0.9```\r\n\r\n### 4. Particle Swarm Optimization for GPs (PSO-GRAANK)\r\nIn this approach, it is assumed that every GP candidate may be represented as a particle that has a unique position and fitness. The fitness is derived from the computed support of that candidate, the higher the support value the higher the fitness. The aim of the algorithm is search through a population of particles (or candidates) and find those with the highest fitness as efficiently as possible.\r\n\r\n```python\r\n\r\nmine_obj = sgp.ParticleGRAANK(data_src)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```\r\n* **n_particles** - *[optional]* initial particle population ```default = 5```\r\n* **velocity** - *[optional]* particle velocity ```default = 0.9```\r\n* **coeff_p** - *[optional]* personal coefficient rate ```default = 0.01```\r\n* **coeff_g** - *[optional]* global coefficient ```default = 0.9```\r\n\r\n### 5. Local Search for GPs (LS-GRAANK)\r\nIn this approach, it is assumed that every GP candidate may be represented as a position that has a cost value associated with it. The cost is derived from the computed support of that candidate, the higher the support value the lower the cost. The aim of the algorithm is search through group of positions and find those with the lowest cost as efficiently as possible.\r\n\r\n```python\r\n\r\nmine_obj = sgp.HillClimbingGRAANK(data_src, min_sup)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```\r\n* **step_size** - *[optional]* step size ```default = 0.5```\r\n\r\n\r\n### 6. Random Search for GPs (RS-GRAANK)\r\nIn this approach, it is assumed that every GP candidate may be represented as a position that has a cost value associated with it. The cost is derived from the computed support of that candidate, the higher the support value the lower the cost. The aim of the algorithm is search through group of positions and find those with the lowest cost as efficiently as possible.\r\n\r\n```python\r\nimport so4gp as sgp\r\n\r\nmine_obj = sgp.RandomGRAANK(data_src, min_sup)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **max_iteration** - *[optional]* maximum number of algorithm iterations ```default = 1```\r\n\r\n\r\n### 7. Clustering algorithm for GPs (Clu-BFS)\r\nWe borrow the net-win concept used in the work 'Clustering Using Pairwise Comparisons' proposed by R. Srikant to the problem of extracting gradual patterns (GPs). In order to mine for GPs, each feature yields 2 gradual items which we use to construct a bitmap matrix comparing each row to each other (i.e., (r1,r2), (r1,r3), (r1,r4), (r2,r3), (r2,r4), (r3,r4)).\r\n\r\nIn this approach, we convert the bitmap matrices into 'net-win vectors'. Finally, we apply spectral clustering to determine which gradual items belong to the same group based on the similarity of net-win vectors. Gradual items in the same cluster should have almost similar score vector.\r\n\r\n```python\r\nimport so4gp as sgp\r\n\r\nmine_obj = sgp.ClusterGP(data_source=data_src, min_sup=0.5, e_prob=0.1)\r\ngp_json = mine_obj.discover()\r\nprint(gp_json)\r\n```\r\n\r\nwhere you specify the parameters as follows:\r\n\r\n* **data_src** - *[required]* data source {either a ```file in csv format``` or a ```Pandas DataFrame```}\r\n* **min_sup** - *[optional]* minimum support ```default = 0.5```\r\n* **e_probability** - *[optional]* erasure probability ```default = 0.5```\r\n* **max_iteration** - *[optional]* maximum iterations for estimating score vectors ```default = 10```\r\n\r\n\r\n## Sample Output\r\nThe default output is the format of JSON:\r\n\r\n```json\r\n{\r\n\t\"Algorithm\": \"RS-GRAANK\",\r\n\t\"Best Patterns\": [\r\n            [[\"Age+\", \"Salary+\"], 0.6], \r\n            [[\"Expenses-\", \"Age+\", \"Salary+\"], 0.6]\r\n\t],\r\n\t\"Iterations\": 20\r\n}\r\n```\r\n\r\n### References\r\n* Owuor, D., Runkler T., Laurent A., Menya E., Orero J (2021), Ant Colony Optimization for Mining Gradual Patterns. International Journal of Machine Learning and Cybernetics. https://doi.org/10.1007/s13042-021-01390-w\r\n* Dickson Owuor, Anne Laurent, and Joseph Orero (2019). Mining Fuzzy-temporal Gradual Patterns. In the proceedings of the 2019 IEEE International Conference on Fuzzy Systems (FuzzIEEE). IEEE. https://doi.org/10.1109/FUZZ-IEEE.2019.8858883.\r\n* Laurent A., Lesot MJ., Rifqi M. (2009) GRAANK: Exploiting Rank Correlations for Extracting Gradual Itemsets. In: Andreasen T., Yager R.R., Bulskov H., Christiansen H., Larsen H.L. (eds) Flexible Query Answering Systems. FQAS 2009. Lecture Notes in Computer Science, vol 5822. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04957-6_33\r\n",
    "bugtrack_url": null,
    "license": "GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007  Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.  Preamble  The GNU General Public License is a free, copyleft license for software and other kinds of works.  The licenses for most software and other practical works are designed to take away your freedom to share and change the works.  By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users.  We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors.  You can apply it to your programs, too.  When we speak of free software, we are referring to freedom, not price.  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