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README.md

What is FASTREAD?

FASTREAD is a tool to support primary study selection in systematic literature review.

Latest Versions:

Cite as:

@misc{zhe_yu_2017_837861,
  author       = {Zhe Yu and
                  Tim Menzies},
  title        = {fastread/src: Core Algorithm Update},
  month        = aug,
  year         = 2017,
  doi          = {10.5281/zenodo.837861},
  url          = {https://doi.org/10.5281/zenodo.837861}
}

Setting up FASTREAD

  1. Setting up Python:
  • We use anaconda by continuum.io (see Why?)
    • We won't need the entire distribution. Download a Python 2.7 version & install a minimal version of anaconda.
  • Make sure you select add to PATH during install.
  • Next, run setup.bat. This will install all the dependencies needed to run the tool.
  • If the above does not work well. Remember you only need a Python 2.7 and three packages listed in requirements.txt installed. So pip install -r requirements.txt will work.
  1. Running script:
  • Navigate to src and run index.py.
  • If all is well, you'll be greeted by this:
  1. The Interface:

Use FASTREAD

  1. Get data ready:
  • Put your candidate list (a csv file) in workspace > data.
  • The candidate list can be as the same format as the example file workspace > data > Hall.csv or a csv file exported from IEEExplore.
  1. Load the data:
  • Click Target: Choose File button to select your csv file in workspace > data. Wait a few seconds for the first time. Once the data is successfully loaded, you will see the following:
  1. Begin reviewing studies:
  • Choose from Relevant, Irrelevant, or Undetermined for each study and hit Submit.
  • Hit Next when you want a to review more.
  • Statistics are displayed as Documents Coded: x/y (z), where x is the number of relevant studies retrieved, y is the number of studies reviewed, and z is the total number of candidate studies.
  • When x is greater than or equal to 1, an SVM model will be trained after hitting Next. From now on, different query strategies can be chosen.
  • It is suggested to keep using Uncertain until the highest probability score for Certain is greater than 0.9 or no Relevant studies can be found throught Uncertain (switch to Certain at that point of time).
  • keep reviewing studies until you think most relevant ones have been retrieved. (If Estimation is enabled, stop when x is close to or greater than 0.95 of the estimated number of Relevant studies.)

3.5. Auto review:

  • If your data contains true label, like Hall.csv does, another button called Auto Review will be enabled. By clicking it, it automatically labels all your current studies (depending on the selection Certain or Uncertain).
  1. Plot the curve:
  • Click Plot button will plot a Relevant studies retrieved vs. Studies reviewed curve.
  • Check Auto Plot so that every time you hit next, a curve will be automatically generated.
  • You can also find the figure in src > static > image.
  1. Export csv:
  • Click Export button will generate a csv file with your coding in workspace > coded.
  1. Restart:
  • Click Restart button will give you a fresh start and loose all your previous effort on the current data.
  1. Remember to click Next button:
  • User data will be saved when and only when you hit Next button, so please don't forget to hit it before you want to stop reviewing.

Better ways to start the review:

 

  • Start with keyword search (New feature in v1.4.0)

A simple search with two or three keywords can help find Relevant studies fast before any training starts. After finding the first Relevant study, Uncertain sampling can begin.

  • Re-Use FASTREAD

Exported primary study selection results (e.g. workspace > coded > Hall.csv ) can be re-applied to bootstrap new selections (e.g. workspace > data > Wahono.csv ).

  1. Get data ready:
  • Make sure previously exported data is in workspace > coded.
  • Or create csv file with the same format as workspace > coded > Hall.csv and put it in workspace > coded.
  • Put your candidate list (a csv file) for the new selection in workspace > data.
  1. Load the data for current selection:
  • Click target: Choose File button to select your csv file in workspace > data. Wait a few seconds for the first time. Once the data is successfully loaded, you will see the following:
  1. Load old data:
  • Click import: Choose File button to select your csv file in workspace > coded. Wait a few seconds for the first time. Once the data is successfully loaded, you will see the following:
  1. Begin reviewing studies:
  • Select Certain instead of Uncertain
  • choose from Relevant, Irrelevant, or Undetermined for each study and hit Submit.
  • hit Next when you want a to review more.
  • statistics are displayed as Documents Coded: x/y (z), where x is the number of relevant studies retrieved, y is the number of studies reviewed, and z is the total number of candidate studies.
  • keep reviewing studies until you think most relevant ones have been retrieved. (If Estimation is enabled, stop when x is close to or greater than 0.95 of the estimated number of Relevant studies.)

Better ways to start the review:

Now we allow users to recheck their previously labeled results and change their decisions. Therefore human errors/concept drift can be handled. Model learned so far is also used to suggest which labels are most suspicious. Two options added:

  • Labeled Pos: recheck the studies previously labeled as Relevant. Sorted by the level of disagreement between current model prediction and human label.
  • Labeled Neg: recheck the studies previously labeled as Irrelevant. Sorted by the level of disagreement between current model prediction and human label. It is recommended to recheck the top 10 suspicious labels every 50 studies reviewed.

Version Logs

Dec 5, 2016. v1.0.0 The very first, basic version is released.

May 14, 2017. v1.1.0 Features of UPDATE/REUSE are edited to allow FASTREAD import previously exported data to bootstrap a new review.

Jun 29, 2017. v1.2.0 Estimate the number of Relevant studies in the pool. Enabling Estimation will slow down the training, but provide the following benefits:

  • number of Relevant studies will be estimated, thus helps to decide when to stop;
  • probability scores will be more accurate.

Aug 01, 2017. v1.3.0 Core algorithm updated to utilize both Weighting and aggressive undersampling.

Aug 28, 2017. v1.4.0 Integrated as FAST2.

Nov 15, 2017. v1.5.0 Allow user to change their decision on previous labels. Machine suggestions used to efficiently handle human errors or concept drift.