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Hierarchical Document Topic Model

Install

  1. Clone this repo

     git clone https://github.com/nddsg/HDTM.git

  2. Configure GraphLab project

     cd HDTM/src/graphlab/
 ./configure

  3. Compile HDTM

     cd ./release/apps
 make -j2

Execution

HDTM arguments

	--vertices	The file contains article vertices
	--edges	The file contains article edges
	--root	Id of root article
	--gamma	Gamma for RWR calculation, default 0.25
	--alpha	Alpha, default 10
	--eta	Eta, default 0.1
	--iter	Iter, default 5
	--burn	Burn-in, default 100
	--sample	Sample interval, default 10
	--token	Number of tokens, run wc -l on dictionary file
	--prefix	Prefix of binary graph files
	--load	Load graph from binary files

Example:

	./hdtm --vertices /data/bshi/wikipedia/vertices.txt --edges /data/bshi/wikipedia/edges.txt \
	       --root 26700 --token 6064216 --iter 400 --burn 100 --sample 50 \
				 --prefix /data/bshi/wikipedia/graphlab/result/

HDTM requires:

  • a vertices file with a vertex id, a tab and a list of words id space separated

    4	3 4 5 6 7
5	3 4 5 7 8
6	8 10 12 14
....

  • edges file with vertex id, tab and vertex id

4	5
4	6
  ```

Actually, the algorithm requires that the words of the articles should be converted as int and that
the values 0 and 1 have not to be used since are utilized for `empty_key` and `deleted_key`.


When `hdtm` is finished, you will get a set of results that looks like this

  	bshi@dsg1:/data/bshi/wikipedia/graphlab/result$ ls
  	0_0_0.bin    140_0_0.bin  190_0_0.bin  240_0_0.bin  290_0_0.bin  340_0_0.bin  390_-1.89962e+14_0.bin
  	100_0_0.bin  150_0_0.bin  200_0_0.bin  250_0_0.bin  300_0_0.bin  350_0_0.bin
  	110_0_0.bin  160_0_0.bin  210_0_0.bin  260_0_0.bin  310_0_0.bin  360_0_0.bin
  	120_0_0.bin  170_0_0.bin  220_0_0.bin  270_0_0.bin  320_0_0.bin  370_0_0.bin
  	130_0_0.bin  180_0_0.bin  230_0_0.bin  280_0_0.bin  330_0_0.bin  380_0_0.bin

The first number in file names is the iteration number.

### Convert `HDTM` binary graph to text file

  	./hdtm_ana BINARY_FILE.bin ORIGINAL_GRAPH_OUT HIERARCHY_OUT NODE_CHANGES_OUT

* `ORIGINAL_GRAPH_OUT` is a baseline tree generated from input graph. Namely if in the original input graph a node has more than one in-coming edges, it will randomly pick one and discards the rest to construct a tree. The output file format is `src \t dst`.
* `HIERARCHY_OUT` is the result hierarchy. This is also a tree but the parent are selected based on HDTM's result. The output format is `src \t height \t dst`.
* `NODE_CHANGES_OUT` is the change log of every node in original graph. The output format is `node_id \t (#current_parent_been_chosen / #iterations) \t #in-coming_edges(parent candidates)`

## Data analysis

All scripts used in this project is under `scripts` folder. You can use `data_preprocess.py` to reproduce the result.

Graph generation is done in `R`, and you can find the code under `analysis` folder. You can find R package `rdsg` at http://github.com/bxshi/rdsg.