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biclustpy-0.2
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مشاهده بیشترتوضیحات
bi-cluster editing library
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biclustpy-0.2 |
| نام | biclustpy |
| نسخه کتابخانه | 0.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | David B. Blumenthal |
| ایمیل نویسنده | david.blumenthal@wzw.tum.de |
| آدرس صفحه اصلی | http://github.com/dbblumenthal/biclustpy |
| آدرس اینترنتی | https://pypi.org/project/biclustpy/ |
| مجوز | LGPL |
# biclustpy
A Python library for bi-cluster editing.
## The Bi-Cluster Editing Problem
- Task: Given a matrix `weights` with positive and negative weights, transform the bipartite graph induced by `weights` into a disjoint collection of bi-cliques (bi-clusters) via edge insertions and deletions, such that the overall transformation cost is minimal.
- The node sets of the bipartite graph induced by `weights` are the sets of rows and columns. There is an edge between row `i` and column `k` if and only if `weights[i,k] > 0`.
- Deleting an existing edge `(i,k)` incurs cost `weights[i,k]`.
- Inserting a non-existing edge `(i,k)` incurs cost `-weights[i,k]`.
## Installation
1. Download and install [Gurobi](https://www.gurobi.com/) and obtain a license by following the instructions in the installation guide for [Linux](https://www.gurobi.com/documentation/8.0/quickstart_linux/software_installation_guid.html#section:Installation), [Mac OS](https://www.gurobi.com/documentation/8.0/quickstart_mac/software_installation_guid.html#section:Installation), or [Windows](https://www.gurobi.com/documentation/8.0/quickstart_windows/software_installation_guid.html#section:Installation).
2. Open a shell and execute `pip install biclustpy`.
## Library Usage
After installation, `import biclustpy as bp` into your Python application. Then use it as follows:
- `bp.Algorithm`: Use this class to select the algorithm you want to employ.
- `bp.Algorithm.algorithm_name`: String you can use to select the algorithm you want to employ. Default: `"ILP"`.
- Set to `"ILP"` if you want to use Gurobi to solve the ILP formulation suggested in [G. F. de Sousa Filho et al (2017): New heuristics for the bicluster editing problem](https://doi.org/10.1007/s10479-016-2261-x).
- Set to `"CH"` if you want to use the constructive heuristic suggested in [G. F. de Sousa Filho et al (2017): New heuristics for the bicluster editing problem](https://doi.org/10.1007/s10479-016-2261-x).
- More algorithms are following soon.
- `bp.Algorithm.ilp_time_limit`: Integer that specifies a time limit in seconds for the optimization and the tuning phase of the algorithm `"ILP"`. Default: `60`.
- `bp.Algorithm.ilp_tune`: Boolean flag that indicates whether or not `"ILP"` should be tuned before being optimized. Default: `False`.
- `bp.compute_bi_clusters(weights, algorithm)`: Use this function to solve a bi-cluster editing problem.
- `weights`: The problem instance given as a `numpy.array`.
- `algorithm`: The selected algorithm given as a `bp.Algorithm` object.
- `bp.save_bi_clusters_as_xml(filename, bi_clusters, obj_val, is_optimal, instance = "")`: Use this function to save the obtained solution as an XML file.
- `filename`: The name of the XML file.
- `bi_clusters`: The bi-clusters returned by `bp.compute_bi_clusters`.
- `obj_val`: The objective value of the bi-clusters returned by `bp.compute_bi_clusters`.
- `is_optimal`: A flag returned by `bp.compute_bi_clusters` that indicates whether the computed bi-clusters are guaranteed to be optimal.
- `instance`: A string that contains information about the problem instance.
### Example
```
import numpy as np
import biclustpy as bp
algorithm = bp.Algorithm
algorithm.algorith_name = "ILP"
algorithm.ilp_time_limit = 100
algorithm.ilp_tune = True
n = 30
m = 40
t = .95
weights = np.random.rand(n, m) - (t * np.ones((n, m)))
bi_clusters, obj_val, is_optimal = bp.compute_bi_clusters(weights, algorithm)
filename = "bi_clusters.xml"
instance = "random instance with 30 rows and 40 columns"
bp.save_bi_clusters_as_xml(filename, bi_clusters, obj_val, is_optimal, instance)
```
## Command Line Usage
Upon installation, you can run `biclustpy` from the command line. Usage:
```
biclustpy [-h]
(--load input-file | --random num-rows num-cols threshold seed)
[--save output-file] [--alg {ILP,CH}]
[--ilp_options time-limit tune]
```
More more information, execute `biclustpy -h`.
## License
You may use and distribute __biclustpy__ under the terms of the [GNU Lesser General Public License](https://www.gnu.org/licenses/lgpl-3.0.html).
نیازمندی
| مقدار | نام |
|---|---|
| - | numpy |
| - | argparse |
| - | networkx |
| - | progress |
| - | gurobipy |
نحوه نصب
نصب پکیج whl biclustpy-0.2:
pip install biclustpy-0.2.whl
نصب پکیج tar.gz biclustpy-0.2:
pip install biclustpy-0.2.tar.gz