method seminar

Method SeminarTutorial : Using Stanford Topic Modeling Toolbox

Lili Lin

Contents Introduction Getting Started

Prerequisites Installation

Toolbox Running Latent Dirichlet Allocation Model (LDA

Model) Labeled LDA Model

Contents Introduction Getting Started

Prerequisites Installation

Toolbox Running Latent Dirichlet Allocation Model (LDA

Model) Labeled LDA Model

Introductionhttp

://nlp.stanford.edu/software/tmt/tmt-0.4/

The Stanford Topic Modeling Toolbox was written at the Stanford NLP group by: Daniel Ramage and Evan Rosen, first released in September 2009

Topic models (e.g. LDA, Labeled LDA) training and inference to create summaries of the text

Introduction - LDA ModelLDA model is a unsupervised topic modelUser need to define some important

parameters, such as number of topicsIt is hard to choose the number of topics Even with some top terms for each topic,

it is still difficult to interpret the content of the extracted topics

Introduction – Labeled LDA ModelLabeled LDA is a supervised topic model

for credit attribution in multi-labeled corpora.

If one of the columns in your input text file contains labels or tags that apply to the document, you can use Labeled LDA to discover which parts of each document go with each label, and to learn accurate models of the words best associated with each label globally

Contents Introduction Getting Started

Prerequisites Installation Simple Testing

Toolbox Running LDA Model Labeled LDA Model

Prerequisites A text editor (e.g. TextWrangler) for

creating TMT processing scripts.TMT scripts are written in Scala, but

no knowledge of Scala is required to get started.

An installation of Java 6SE or greater: http://java.com/en/download/index.jsp.

Windows, Mac, and Linux are supported.

InstallationDownload the TMT executable

(tmt-0.4.0.jar) from http://nlp.stanford.edu/software/tmt/tmt-0.4/

Double-click the jar file to open toolbox or run the toolbox with the command line : java -jar tmt-0.4.0.jar

You should see a simple GUI

Simple TestingExample data and scripts for

simple testing◦Download the example data file:

pubmed-oa-subset.csv◦Download the first testing script:

example-0-test.scalaNote: the data file and the script

should be put into the same folder

Simple Testing - GUILoad script: File Open script

Simple Testing - GUIEdit script: val pubmed = CSVFile("pubmed-oa-subset.csv”)

Simple Testing - GUIRun the script: click the button

‘Run’

Simple Testing - Command Line

Contents Introduction Getting Started

Prerequisites Installation

Toolbox Running Latent Dirichlet Allocation Model (LDA

Model) Labeled LDA Model

LDA Model – Data Preparation173, 777 Astronomy papers were

collected from the Web of Science (WOS) covering the period from 1992 to 2012

In the file ‘astro_wos_lda.csv’, every record includes paper ID (the first column), title (the second column) and published year (the third column)

LDA Training – Script LoadingFile Open script Navigate to

example-2-lda-learn.scala Open

LDA Training – Data LoadingEdit Script : ‘val source = CSVFile("astro_wos_lda.csv”)’ ‘Column(2) ~>’ Note: if your text cover 2 columns or more than 2

columns, such as the third and forth columns, you can use ‘Columns(3,4) ~> Join(" ") ~>’ to replace ’Column(2) ~>’

LDA Training – Parameter SelectionEdit Script : val params = LDAModelParams(numTopics = 30, dataset = dataset, topicSmoothing = 0.01, termSmoothing = 0.01)

LDA Training – Model TrainingRun : Out of Memory due to the

big data

LDA Training – Model TrainingChange the size of Memory Run

LDA Training – Output Generation lda-b2aa1797-30-751edefe

◦ description.txt : A description of the model saved in this folder

◦ document-topic-distributions.csv : A csv file containing the per-document topic distribution for each document in the training dataset

◦ 00000-01000 : Snapshots of the model during training

LDA Training – Output Generation /params.txt : Model parameters used during training /tokenizer.txt : Tokenizer used to tokenize text for use with

this model /summary.txt : Human readable summary of the topic

model, with top-20 terms per topic and how many words instances of each have occurred

/log-probability estimate.txt : Estimate of the log probability of the dataset at this iteration

/term-index.txt : Mapping from terms in the corpus to ID numbers

/description.txt : A description of the model saved in this iteration

/topic-termdistributions.csv.gz : For each topic, the probability of each term in that topic

LDA Training – Command LineJava –Xmx4G –jar tmt-0.4.0.jar

example-2-lda-learn.scala

LDA Inference – Script Loading File Open script Navigate to

example-3-lda-infer Open

LDA Inference – Trained Model Loading Edit Script: val modelPath = file("lda-b2aa1797-30-751edefe”)

LDA Inference – Data Loading Edit Script: ‘val source = CSVFile("astro_wos_lda.csv”)’ ‘Column(2) ~>’ Note: Here we just use the same dataset as the

inference data, but actually it should be some new dataset

LDA Inference – Model InferenceChange the size of Memory Run

LDA Inference – Output GenerationNavigate to the folder ’lda-b2aa1797-30-

751edefe’◦ astro_wos_lda-document-topic-distributuions.csv :

A csv file containing the per-document topic distribution for each document in the inference dataset

◦ astro_wos_lda-top-terms.csv: A csv file containing the top terms in the inference dataset for each topic

◦ astro_wos_lda-usage.csv

LDA Inference – Command LineJava –Xmx4G –jar tmt-0.4.0.jar

example-3-lda-infer.scala

LLDA Model – Data Preparation4,770 metformin papers were collected from

pubMed covering the period from 1997 to 2011Training data : metformin_train_data_llda.csv

(2798 papers), every record includes paper ID (the first column), bio-term list (the second column), title (the third column) and abstract (the forth column), the number of bio-terms in very record is at least 3

Inference data: metformin_infer_data_llda.csv (4770 papers), every record includes paper ID (the first column), title (the second column) and abstract (the third column)

LLDA Training – Script LoadingFile Open script Navigate to

example-6-llda-learn.scala Open

LLDA Training – Data LoadingEdit Script : ‘val source = CSVFile("metformin_train_data_llda.csv")’ ‘Columns(3,4) ~> Join(" ") ~>’ ’Column(2) ~>’

LLDA Training – Model TrainingRun

LLDA Training – Output Generation llda-cvb0-bd54e9b6-176-1213c7f4-222a08a4

◦ description.txt : A description of the model saved in this folder

◦ document-topic-distributions.csv : A csv file containing the per-document topic distribution for each document in the training dataset

◦ 00000-01000 : Snapshots of the model during training

LLDA Training – Output Generation /params.txt : Model parameters used during training /tokenizer.txt : Tokenizer used to tokenize text for use

with this model /summary.txt : Human readable summary of the topic

model, with top-20 terms per topic and how many words instances of each have occurred

/term-index.txt : Mapping from terms in the corpus to ID numbers

/description.txt : A description of the model saved in this iteration

/label-index.txt : Topics extracted after LLDA training /topic-termdistributions.csv.gz : For each topic, the

probability of each term in that topic

LLDA Training – Command LineJava –Xmx4G –jar tmt-0.4.0.jar

example-6-llda-learn.scala

LLDA Inference – Jar ScriptThe TMT toolbox doesn’t provide

script for LLDA inferenceA java script, packaged into ‘llda-

infer.jar’, was generated in order to conduct LLDA inference

LLDA Inference – Command Linejava -jar llda-infer.jar

metformin_infer_data_llda.csv llda-cvb0-bd54e9b6-176-1213c7f4-222a08a4 metformin_infer_result.csv

A file named metformin_infer_result.csv will be generated after LLDA Inference

LLDA Inference – Output Generation

Thanks….. Any Question?