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https://github.com/leungll/topk-coding

A method to enumerate top-k cliques.
https://github.com/leungll/topk-coding

clause clique encoding solver-algorithm top-k

Last synced: about 1 month ago
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A method to enumerate top-k cliques.

Host: GitHub
URL: https://github.com/leungll/topk-coding
Owner: leungll
License: apache-2.0
Created: 2020-04-30T09:57:05.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2024-05-12T13:46:35.000Z (7 months ago)
Last Synced: 2024-05-12T14:44:58.413Z (7 months ago)
Topics: clause, clique, encoding, solver-algorithm, top-k
Language: Python
Homepage:
Size: 297 KB
Stars: 0
Watchers: 0
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

# TopK-Coding
![GitHub last commit](https://img.shields.io/github/last-commit/leungll/Topk-Coding?color=9cf&style=flat-square)
![maven](https://img.shields.io/badge/C%2B%2B11-passing-red)
![maven](https://img.shields.io/badge/python2-passing-yellow)
![maven](https://img.shields.io/badge/python3-passing-blue)
![GitHub](https://img.shields.io/github/license/leungll/Topk-Coding?color=orange&style=flat-square)

This project contains the software used in the paper "Fast Enumeration of Large k-Plexes" authored by Alessio Conte, Donatella Firmani, Caterina Mordente, Maurizio Patrignani, and Riccardo Torlone and published at the 23rd SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2017).

# Environment
* Linux
* python2 **( e.g. python2.7 )**：跑 berlowitz 代码
* python3：跑 `kplexes.py`
* c++11
* 枚举kplex部分需要安装 **[snap.py](https://snap.stanford.edu/snappy/)** 库，`snap.py` 库对环境要求很高
* 实验代码已在 `ubtuntu 18.04` 系统执行通过

# Prepare
* 关于python2

- 如果你的 python2 不是 2.7 版本，需要在 `kplexes.py`(代码大概在 108 行，路径：`Topk-Coding/kplexes.py` )的 `call` 函数中修改对应的 `py2` 版本号

```
call("python2.7 %s %s" % (berexe, argstring), shell=True, stdout=DEVNULL)
```
* 安装 **[snap.py](https://snap.stanford.edu/snappy/)** 库
- 可直接命令行安装：`pip install snap-stanford`
- 下载：**https://snap.stanford.edu/snappy/release**
- 执行安装 **( e.g. `ubtuntu 18.04 & py2.7` )**：

```
tar zxvf snap-stanford-5.0.0-5.0-ubuntu18.04.2-x64-py2.7.tar.gz
cd snap-stanford-5.0.0-5.0-ubuntu18.04.2-x64-py2.7
sudo python2.X setup.py install
```

![snap.py-on-linux](https://cdn.jsdelivr.net/gh/leungll/MyImgHosting/img/snap.py-on-linux.jpg)
# Compile & Run

```
cd Topk-Coding
mkdir working_dir
mkdir splex_ans
mkdir input_data
mkdir input_data_c
mkdir ans
g++ -std=c++11 Coding.cpp -o Coding
./Coding XXX.input_file k
```

- 后台运行
```
./Coding XXX.input_file k &
python3 kplexes.py --k=XXX --m=0 --fileName=XXX.input_file > ans/XXX.txt &
```

- 查看进程：
```
ps -ef | grep Coding
ps -ef | grep kplexes.py
```

# Common Commands
* 查看版本当前**操作系统内核**信息：`uname -a`
* 查看当前**操作系统版本**信息：`cat /proc/version`
* 查看版本当前**操作系统发行版**信息：`cat /etc/issue`
* 查看 cpu 信息：`cat /proc/cpuinfo`
* 查看 python 具体版本：`python --version`
* 查看 python 具体安装路径：`which python`
* 查看 pip 具体版本： `pip --version`
* 查看 pip 具体安装路径：`which pip`
* tar.gz 解压：`tar zxvf XXX.tar.gz`
* zip 解压：`unzip XXX.zip`
* vim 编辑：

```
vim /usr/bin/yum
i
ESC
:wq / :q!
```
* 查看系统 python 版本：`ll /usr/bin/python*`
* 备份 python 原版本：`mv /usr/bin/python /usr/bin/python.bak`
* 建立 python 软链接：`ln -s /usr/local/python27/bin/python2.7 /usr/bin/python`
* 恢复原来的 python 指向：`cp /usr/bin/python.bak /usr/bin/python`
* pip 国内镜像源：
- 清华：`pip install 包名 -i https://pypi.tuna.tsinghua.edu.cn/simple `
- 阿里云：`pip install 包名 -i http://mirrors.aliyun.com/pypi/simple/`
- 豆瓣源（ python 指定 pip ）：`python -m pip install 包名 -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com`

# Pay Attention
* `Coding.cpp` 中的 `ss_python_cmd` 文件后缀名(1115行)要与 `kplexes.py` 中的 `extension` (33行)匹配
* 执行命令前需要创建 `5` 个文件夹，否则会报错

- mkdir working_dir
- mkdir splex_ans
- mkdir input_data
- mkdir input_data_c
- mkdir ans

# Update kplexes.py
* 修改命令行参数（ `argparse` & `parser` ）
* 注释

- 169行：`print("%s remove %d edges" % (datetime.today().strftime('%Y-%m-%d %H:%M:%S'), len(cond)))`
- 246行：

```
print("%s started %d threads (batch_size=%d, procnum=%d)" % (datetime.today().strftime('%Y-%m-%d %H:%M:%S'), i+1, batch_size, procnum), file = sys.stderr)
```
- 250行：`print("%s ended thread %d" % (datetime.today().strftime('%Y-%m-%d %H:%M:%S'), i), file = sys.stderr)`
- 293行：`print(sorted_files)`
* `k` 从命令行接收：
- 27行：`k_cmd = args.k`
- 304行：`for k in [k_cmd]`
* 注释 `m` 的运算规则，从命令行接收：
- 318行：`m = max(k**2, math.ceil(fatt))`
- 401行：`m = max(k**2, math.ceil(fatt))`
- 28行：`m = args.m`
* 增加文件比较
- 29行：`fileNameStr = args.fileName`
- 297行：`if filename == fileNameStr`
* 修改 `print` 规则
* 注释 413 行：`print(P, file=sys.stderr)`
* 增加代码 414 行：print(P)

# References
* http://patrignani.dia.uniroma3.it/large-k-plexes
* https://github.com/ddfir/kplexes-meta
* https://snap.stanford.edu/snappy
* https://github.com/joey001/splex-big