/nasaMining

Space Apps NYC project to mine NASA datasets to better find interesting connections between data.

Primary LanguageHTMLMIT LicenseMIT

SpaceTag Automatic Keyword Extraction

NASA SpaceApps 2015

Automatic keyword extraction on data.json schema open data.

This project processes the data.json files released by NASA and other governmental bodies as part of their open data initiatives. The metadata descriptions are processed, and relevant, meaningful keywords are algorithmically extracted. These keywords are added back into each record, providing a richer set of tags to search through and connect datasets, both within and across organizations.

The central focus was on tagging all ~16000 datasets in NASA's data.json, from data.nasa.gov.

An additional 10000 datasets were tagged, from the following agencies and states:

  • Department of Commerce
  • Department of Defense
  • Department of Energy
  • Environmental Protection Agency
  • National Science Foundation
  • State Department
  • USDA
  • Colorado
  • Hawaii
  • Illinois
  • Iowa
  • Maine
  • Maryland
  • Michigan
  • New Jersey
  • New York
  • Oregon
  • Texas
  • Vermont

This codebase also contains a visual interface for searching and exploring the datasets using the extracted keywords, which can be found in the frontEnd/ directory. The front end uses D3/jQuery, and the backend server is written in node.js (an alternate Python implementation using Flask is also included), with the underlying data residing in a MongoDB database.

Keyword Extraction

Keyword extraction is performed by running extract.py on a data.json format dataset. The outline for the keyword extraction algorithm is:

  1. Multi-word keyphrases are calculated through a variant of pointwise mutual information, as implemented by the Phrases class in the Python package Gensim (https://radimrehurek.com/gensim/)
    1. Multiple passes can be performed over the dataset to extract longer n-gram keywords
    2. The statistics collected when training the phrase extraction model can be optionally seeded by an additional dataset, to favorably bias the collocation significance scores towards ngrams found in the seed dataset. This was used when extracting keywords on the non-NASA data. Note that keywords will not be extracted from this seed data; it is solely used in the training phase. An additional advantage to using a seed dataset is that it will tend to improve results when processing a smaller dataset with less text to train the phrase extraction with.
  2. Longer keyphrases are not guaranteed to be syntactically sound, so each keyphrase is then tagged with part-of-speech tags, and parsed to extract noun phrases. Keywords which consist entirely of proper nouns (NNP/NNPS POS tags) are added in their entirety. Keywords which do not contain any noun phrases and are not all proper nouns are discarded.

The options for extract.py are:

usage: extract.py [-h] [-i INPUT] [-s SOURCE] [-o OUTPUT] [-f FIELD]
                  [-m MODEL] [-p PASSES] [-t THRESHOLD] [--seed SEED]

SpaceTag keyword extraction

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        path to a data.json format file
  -s SOURCE, --source SOURCE
                        data source annotation (e.g. data.nasa.gov/data.json
  -o OUTPUT, --output OUTPUT
                        path to output the data with extracted keywords
  -f FIELD, --field FIELD
                        field in each dataset to store the keywords
  -m MODEL, --model MODEL
                        file to save the pickled phrase extraction models
  -p PASSES, --passes PASSES
                        number of phrase extraction passes to make
  -t THRESHOLD, --threshold THRESHOLD
                        phrase extraction significance threshold
  --seed SEED           path to a data.json to seed the phrase extraction
                        statistics with

Example:

To generate keywords for NASA's data.json, which we have saved as data/nasa.json, call extract.py like:

python extract.py --input data/nasa.json --source data.nasa.gov/data.json --output data/nasa_keywords.json --field new_keywords --passes 5 --threshold 10

This will extract keywords and place them in the field "new_keywords", saving the results to data/nasa_keywords.json.

The --passes flag specifies that five keyword extraction passes will be performed, resulting in longer keyphrases. The first pass will produce bigram keyphrases, the second will join the bigrams with collocated unigrams and other bigrams (producing tri- and quad-grams), and so on.

The --threshold flag determines how many keyphrases will be initially extracted. The default is 10, with higher values producing fewer keyphrases.

As a second example, to extract keywords from the Department of Defense data.json file (data/defense.json here), and also seed the phrase extraction with the descriptions from data/nasa.json, call extract.py like:

python extract.py --input data/defense.json --source defense.gov/data.json --output data/defense_keywords.json --seed data/nasa.json --field new_keywords --passes 5 --threshold 10

Related Datasets (Word Embedding Method)

keyword_similarity_vec.py

Run keyword_similarity_vec.py to generate the keyword vectors

  • This depends on the word embedding vectors provided by the Spacy library (http://honnibal.github.io/spaCy/)
  • Vectors for multi-word keyphrases are produced by adding together the vectors of each individual word. The motivation for this is that the word embedding vectors exhibit the same semantically meaningful algebraic properties as other word2vec embeddings. E.g. when considering the keywords "earth science" and "geology", the cosine similarity between Vearth + Vscience and Vgeology is much closer than between either Vearth or Vscience individually

project_similarity_vec_centroid.py

Run project_similarity_vec_centroid.py after keyword_similarity_vec.py to calculate the 25 most similar datasets for each dataset based on the cosine similarity between mean keyword vectors.

  • Each dataset contains some number of keywords, N, each with their own vector representation of dimension D; in order to simplify the distance calculation between one dataset with a keyword matrix K1 of dimension N1 x D, and a second with K2 of dimension N2 x D, we take the mean value across keywords for each dimension in D, producing 1 x D centroid vectors C1 and C2. Project similarities are then calculated by taking the cosine distance between each centroid vector.
  • The related datasets will be inserted into a mongo collection

Related Datasets (Synsets Method)

Generating project similiarty scores is a two step process, and there are two scripts that must be run:

keyword_similarity.py:

This generates a similarty score for every pair of words among all keywords. So the keywords 'earth science', 'atmosphere', and 'air quality' would product a five words [earth, science, atmosphere, air, quality] and 10 pairs. Words are not pair with themselves, are case insensitive, and are unordered.

For each pair of words a core between 0 and 1 is set, 0 being not at all related and 1 being identical. Each element in the synset of the first word is compared to each in the synset of the second word. The highest scoring pair is kept as the score for that pair of words. If either word is not in WordNet, the score is 0, unless they happen to be identical, in which case it is 1.

Synset are groups of cognitively related words and are available as a free resource as part of WordNet. More info is available at https://wordnet.princeton.edu/

The similarty function path_similarity() is used, which measures "shortest path that connects the senses in the is-a (hypernym/hypnoym) taxonomy". There are several other similarty function available, but there was not enough time to test them all. See section 5 on http://www.nltk.org/howto/wordnet.html for details.

This step is kept separate from the project level scores because it can take a very long time to run, and because it may not be necesary to rerun when new projects are added if those new project only contain preexisting keywords

To run:

Execute the script. The following values are hard coded:

	input:	data/nasa_kw.json
	output:	data/keyword_synset_scores.json

project_similarity.py:

This generates a similarty score for every pair of projects based on their keywords. Each individual word from the keywords of one project are compared to the words from the keywords in a second project. Scores for each pair of words are looked up from keyword data produced by the keyword similarty script. Those scores are simply summed together. The result is the similarty score between the two projects

Example:

Using the 2 projects in example.json

Project 1 contains the keywords "EARTH SCIENCE", "HYDROSPHERE", "SURFACE WATER" and project 2 contains "EARTH SCIENCE", "ATMOSPHERE", "AIR QUALITY", "ATMOSPHERIC CHEMISTRY"

Produces the list of words (note the 'u' in a python generated flag denoting Unicode)

[u'earth', u'science', u'hydrosphere', u'surface', u'water', u'atmosphere', u'air', u'quality', u'atmospheric', u'chemistry']

The keyword script generates 45 scored pairs from these words:

	[{"score": 0.1111111111111111, "keyword": ["earth", "science"]},
	 {"score": 0.2, "keyword": ["earth", "hydrosphere"]},
	 {"score": 0.25, "keyword": ["earth", "surface"]},
	 {"score": 0.3333333333333333, "keyword": ["earth", "water"]},
	 {"score": 0.25, "keyword": ["earth", "atmosphere"]},
	 {"score": 0.3333333333333333, "keyword": ["earth", "air"]},
	 {"score": 0.25, "keyword": ["earth", "quality"]},
	 {"score": 0.25, "keyword": ["earth", "atmospheric"]},
	 {"score": 0.25, "keyword": ["earth", "chemistry"]},
	 {"score": 0.08333333333333333, "keyword": ["science", "hydrosphere"]},
	 {"score": 0.2, "keyword": ["science", "surface"]},
	 {"score": 0.1111111111111111, "keyword": ["science", "water"]},
	 {"score": 0.125, "keyword": ["science", "atmosphere"]},
	 {"score": 0.125, "keyword": ["science", "air"]},
	 {"score": 0.14285714285714285, "keyword": ["science", "quality"]},
	 {"score": 0.0, "keyword": ["science", "atmospheric"]},
	 {"score": 0.3333333333333333, "keyword": ["science", "chemistry"]},
	 {"score": 0.3333333333333333, "keyword": ["hydrosphere", "surface"]},
	 {"score": 0.125, "keyword": ["hydrosphere", "water"]},
	 {"score": 0.25, "keyword": ["hydrosphere", "atmosphere"]},
	 {"score": 0.25, "keyword": ["hydrosphere", "air"]},
	 {"score": 0.1, "keyword": ["hydrosphere", "quality"]},
	 {"score": 0.0, "keyword": ["hydrosphere", "atmospheric"]},
	 {"score": 0.1111111111111111, "keyword": ["hydrosphere", "chemistry"]},
	 {"score": 0.25, "keyword": ["surface", "water"]},
	 {"score": 0.25, "keyword": ["surface", "atmosphere"]},
	 {"score": 0.25, "keyword": ["surface", "air"]},
	 {"score": 0.25, "keyword": ["surface", "quality"]},
	 {"score": 0.25, "keyword": ["surface", "atmospheric"]},
	 {"score": 0.125, "keyword": ["surface", "chemistry"]},
	 {"score": 0.2, "keyword": ["water", "atmosphere"]},
	 {"score": 0.3333333333333333, "keyword": ["water", "air"]},
	 {"score": 0.2, "keyword": ["water", "quality"]},
	 {"score": 0.2, "keyword": ["water", "atmospheric"]},
	 {"score": 0.25, "keyword": ["water", "chemistry"]},
	 {"score": 1.0, "keyword": ["atmosphere", "air"]},
	 {"score": 0.5, "keyword": ["atmosphere", "quality"]},
	 {"score": 0.0, "keyword": ["atmosphere", "atmospheric"]},
	 {"score": 0.16666666666666666, "keyword": ["atmosphere", "chemistry"]},
	 {"score": 0.5, "keyword": ["air", "quality"]},
	 {"score": 0.3333333333333333, "keyword": ["air", "atmospheric"]},
	 {"score": 0.25, "keyword": ["air", "chemistry"]},
	 {"score": 0.0, "keyword": ["quality", "atmospheric"]},
	 {"score": 0.16666666666666666, "keyword": ["quality", "chemistry"]},
	 {"score": 0.0, "keyword": ["atmospheric", "chemistry"]}]

Note that 'air' and 'atmosphere' have a score of 1.0. This is because 'air' is in the synset for 'atmosphere' and vice versa

air:

[Synset('air.n.01'), Synset('air.n.02'), Synset('air.n.03'), Synset('breeze.n.01'), Synset('atmosphere.n.03'), 
 Synset('air.n.06'), Synset('tune.n.01'), Synset('air.n.08'), Synset('air_travel.n.01'), Synset('air_out.v.01'), 
 Synset('air.v.02'), Synset('air.v.03'), Synset('publicize.v.01'), Synset('air.v.05'), Synset('vent.v.02')]

atmosphere:

[Synset('atmosphere.n.01'), Synset('standard_atmosphere.n.01'), Synset('atmosphere.n.03'), 
 Synset('atmosphere.n.04'), Synset('atmosphere.n.05'), Synset('air.n.03')]

A similarty matrix is created, measuring the distance between each word in synset 1 with each word in synset 2. The highest score is kept. In this case, that is 1.0

The score the similarity of the 2 projects, they keywords of each are again broken into single word entities:

[u'earth', u'science', u'hydrosphere', u'surface', u'water']
[u'earth', u'science', u'atmosphere', u'air', u'quality', u'atmospheric', u'chemistry']

Each combination of words, using one from each set, is looked up in the similarity table. The following matches are found, and contribute to the final sum score (all other pairs scored 0):

(u'earth', u'earth', 1.0)
(u'earth', u'science', 0.1111111111111111)
(u'earth', u'quality', 0.25)
(u'science', u'science', 1.0)
(u'hydrosphere', u'science', 0.08333333333333333)
(u'hydrosphere', u'quality', 0.1)

The final similarity score between these two projects is then 2.5444444444444447