Discovery via Eigenbasis Modeling of Uninteresting Data
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README.md

DEMUD: Discovery via Eigenbasis Modeling of Uninteresting Data

Contact author: Kiri Wagstaff, kiri.wagstaff@jpl.nasa.gov

Contributors: James Bedell, Jake Lee

DEMUD is a data analysis algorithm that incrementally selects the most interesting or novel item from a data set. In addition, it provides explanations for why each item is chosen. Its incremental approach minimizes redundancy in selected items; unlike many anomaly detection systems, it will highlight a particular anomaly only the first time it is encountered.

Under the hood, DEMUD uses an SVD-based model of the items it selects and incrementally (1) selects the item that is least well represented by the current model (i.e., contains the most unexpected information) and (2) updates its SVD model to "learn" about that item and avoid selecting similar items in the future.

Installation

You should be able to install demud by simply doing

$ python setup.py install

That will make the demud console script available system-wide.

If this doesn't work, use

$ python demud.py [options]

in all of the examples below.

To get started

  1. DEMUD has an extensive help message. Start by running (from src/)

    $ demud -h

  2. Create an empty demud.config file by running

    $ demud --make-config

  3. DEMUD supports a variety of different input data types. See the "Datatype Options:" section of the help message and select the appropriate option for your data.

    Please do not check your demud.config file back in to this repository. It is a local configuration file for your system.

    Example 1: Images.

    To run DEMUD on a collection of images using the pixel representation, specify the directory containing the images on the imagedatafolder line in demud.config. Then run

    $ demud -I

    The results will appear in the results/ directory under your current directory. You will also find a log file (demud.log) and a list of the selections (selections.csv).

    Example 2: UCI data sets (included test cases).

    Several UCI data sets are already supported, and the glass and ecoli data sets are provided in the data/ directory. You can try them out by specifying the appropriate pathname for the data file of your choice in demud.config (see the ucidatafile variable), then running:

    $ demud -g

    $ demud -e

    Note: UCI data sets were obtained from

    Lichman, M. (2013). UCI Machine Learning Repository http://archive.ics.uci.edu/ml. Irvine, CA: University of California, School of Information and Computer Science.

  4. Other data types.

    If your data type is not yet supported, consider adding it by (1) adding a new command-line option (2) adding parsing support for this option in demud.py (3) adding a new file called dataset_yourtype.py that inherits from the Dataset class and implements __init__(), readin(), and plot_item(). See existing classes for examples.

Other relevant options

There are many other options you can specify for DEMUD, which are detailed in the help message. Here are some of the most commonly used:

Model options:

  • --k=K: Number of principal components for SVD model; default is specific to data set (demud.py)
  • --variance=K_VAR: Optimize --k to capture this much data variance Range: [0.0 1.0]
  • --increm: Use an incremental SVD update; usually faster.

Selection and output options:

  • --n=N, --iters=N: Number of iterations of SVD and selection; default 10
  • --all: Iterate through all data items
  • --init-item=IITEM: Index of initialization item (default: 0; -1 or svd for full-data SVD; r for random)

By default, DEMUD starts by selecting the first item in the data set. You may get more interesting results by using an initial SVD to select the "most anomalous" item from the data set as a starting point, e.g.:

$ demud -g --init-item=-1

By default, DEMUD recomputes a full SVD (of the previously selected items) at each iteration. If you will be selecting a lot of items, you may get faster results using an incremental SVD. See:

$ demud --svdmethods

By default, DEMUD sets any missing values to 0. You can try different methods; see:

$ demud --missingdatamethods

By default, DEMUD treats all features equally. You can specify different feature weighting methods; see:

$ demud --featureweightmethods

Additional scripts

scripts/ provides additional scripts for preprocessing data for use with DEMUD. Usage instructions are included within each subdirectory.

This includes an image feature extraction script used for experiments presented at WHI 2018.

References

  1. "Guiding Scientific Discovery with Explanations using DEMUD." Kiri L. Wagstaff, Nina L. Lanza, David R. Thompson, Thomas G. Dietterich, and Martha S. Gilmore. Proceedings of the Twenty-Seventh Conference on Artificial Intelligence (AAAI-13), 2013. http://wkiri.com/research/papers/wagstaff-demud-13.pdf

    This paper describes the non-interactive DEMUD algorithm; it identifies diverse items within a larger data set for your review. The paper reports on results from CRISM and (laboratory) ChemCam data analysis.

  2. "Unusual ChemCam Targets Discovered Automatically in Curiosity's First Ninety Sols in Gale Crater, Mars." Kiri L. Wagstaff, Nina L. Lanza, and Roger C. Wiens. 45th Lunar and Planetary Science Conference, March 2014. http://www.hou.usra.edu/meetings/lpsc2014/pdf/1575.pdf

    This abstract reports on DEMUD results when applied to Mars data collected by ChemCam.

  3. DEMUD was created as part of the IMBUE project. You can read more about IMBUE and access relevant publications and data sets at the IMBUE website:
    http://imbue.jpl.nasa.gov/