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AMS

AMS is a tool to automatically generate AutoML search spaces from users' weak specifications. A weak specification is defined a set of API classes to include in the AutoML search space. AMS then extends this set with complementary classes, functionally-related classes, and relevant hyperparameters and possible values. This configuration can then be paired with existing search techniques to generate ML pipelines. AMS relies on API documentation and corpus of code examples to strengthen the input weak spec.

Artifact

You can download a VM (if you are not already using it) from https://ams-fse.s3.us-east-2.amazonaws.com/ams.ova .

If prompted, the username is ams and the password is ams.

The DOI for the artifact submitted for artifact evaluation was DOI.

This artifact has since been superseded by a version that incorporates changes based on the camera ready. Please use that version of the VM (which you can download from zenodo or through aws as explained below.)

The DOI for the camera-ready version of the artifact is DOI.

$ wget https://ams-fse.s3.us-east-2.amazonaws.com/ams.ova

The should result in a .ova (format version 1.0) that can be imported into virtualbox or vmware. This image was exported and tested with Virtualbox version 5.2.

If you do so, you can skip all steps below relating to building and simply navigate to the ams folder and activate the conda environment

$ cd ~/ams/
$ conda activate ams-env

Docker Container

We have also included a Dockerfile that installs conda and sets up the ams dependencies up for you. You may find that easier (more convenient to use) than your base machine. If so, you can run

docker build . -t ams-container --memory=8g

to build the container. Then you can start it with

docker run -it --memory=8g ams-container

You may want to increase the memory allotted for the docker run command as you see fit (and you may be able to decrease it for the docker build command). You may also find this post useful https://stackoverflow.com/questions/44533319/how-to-assign-more-memory-to-docker-container

After you have started the docker container by executing the run command, you can jump to running scripts/folder_setup.sh (please see the installation section below for more details).

AMS from Source

System Requirements and Notes

AMS should run without issues on Ubuntu 18.04 and Mac OSX (tested on 10.11.6). If you have issues running, we suggest using the pre-packaged VM (or feel free to contribute back fixes that allow AMS to build on your platform).

If you want to install from source, you will need the following basic utilities (installable using apt-get/brew):

  • wget (e.g. apt-get install wget)
  • zip (e.g. apt-get install zip)

If you are not using Ubuntu or Mac OSX, you should also manually install task-spooler (https://vicerveza.homeunix.net/~viric/soft/ts/) and make sure we can call it using tsp (or set a corresponding alias). You will then want to remove the task-spooler install in scripts/setup.sh.

All other software packages needed are either 1) installed by our scripts automatically (which should work without issues for Ubuntu and Mac OSX) or 2) provide a prompt for you to manually install (as in the case of conda). Indeed, the pre-packaged VM was configured using a clean Ubuntu image and running the instructions for installing from source.

Building

AMS should run without issues on Ubuntu and Mac OSX (tested on 10.11.6). If you have issues running, we suggest using the pre-packaged VM.

Installation

First, you should install conda. If you don't have conda already, please install from

https://docs.conda.io/en/latest/miniconda.html

Once you have done so, you can build the conda environment

$ conda env create -f environment.yml

This creates the conda environment ams-env.

All scripts/commands should be executed from the root ams directory and with the ams-env environment active (i.e. run conda activate ams-env when using AMS).

If you would like to modify the location where data/resources etc are saved down, you should edit scripts/folder_setup.sh accordingly. These paths are used/referenced throughout the remainder of the setup. Note that the data folder ($DATA) should point to data/ directory in the root of the project. You can change this, but we do not recommend it.

You should then install some additional supporting resources by running

$ bash scripts/setup.sh

This may take some amount of time as it has to download/build multiple third-party tools.

You can verify that your installation has completed successfully by running

$ python -m core.generate_search_space --help

You should see a help message printed to the console.

Building AMS

To use AMS, AMS first extracts rules for complementary components, indexes the API documents, and extracts hyperparameter/value frequency distributions from the code corpus. To build this, just execute

$ bash scripts/build_ams.sh

This may take some time as AMS traverse the API's module hierarchy and extracts information from the code corpus. You will see messages such as Trying <...> or Failed <...>. These can be safely ignored.

Once you are done with this, you are ready to use AMS and shouldn't need to tweak anything else.

Known Latency Issue

Loading the SciSpacy language model takes approximately 30 seconds.

spacy_nlp = spacy.load("en_core_sci_lg")

This is a known hurdle for language models in Spacy (see explosion/spaCy#2679 for a similar example)

This latency is a cost to starting up AMS on each new weak specification. A simple workaround (that has not yet been implemented), is to run AMS as a server application, with new weak specifications provided as input from a client. We eschew this for the current artifact as it may complicate use of AMS for reviewers.

Using AMS

If you would like to use AMS to generate search spaces for your weak specs, you can use the script scripts/use_ams.sh.

For example,

$ (bash scripts/use_ams.sh sklearn.linear_model.LogisticRegression sklearn.preprocessing.MinMaxScaler) > config.json

produces a strengthened search space for this weak specification.

$ cat config.json | jq # note we don't install jq
{
  "sklearn.linear_model.SGDClassifier": {
    "loss": [
      "log",
      "hinge"
    ],
    "penalty": [
      "l2",
      "elasticnet",
      "l1"
    ],
    "alpha": [
      1e-05,
      0.0001
    ]
  },
  "sklearn.linear_model.LogisticRegression": {
    "C": [
      100000,
      7,
      100,
      1
    ],
    "penalty": [
      "l1",
      "l2"
    ],
    "class_weight": [
      "auto",
      "balanced",
      null
    ]
  },
  "sklearn.linear_model.RidgeClassifier": {
    "solver": [
      "sag",
      "auto"
    ],
    "tol": [
      0.01,
      0.001
    ]
  },
  "sklearn.preprocessing.StandardScaler": {
    "copy": [
      true,
      false
    ],
    "with_mean": [
      true,
      false
    ],
    "with_std": [
      true
    ]
  },
  "sklearn.linear_model.Log": {},
  "sklearn.preprocessing.MinMaxScaler": {
    "copy": [
      true
    ]
  },
  "sklearn.preprocessing.RobustScaler": {},
  "sklearn.preprocessing.MaxAbsScaler": {},
  "sklearn.preprocessing.Binarizer": {}
}

The script hardcodes various AMS choices, which you can modify as desired. In particular, the script sets:

NUM_COMPONENTS=4
NUM_ASSOC_RULES=1
ALPHA_ASSOC_RULES=0.5
NUM_PARAMS=3
NUM_PARAM_VALUES=3

NUM_COMPONENTS refers to the number of functionally related components to add (at most) per component in the weak spec. NUM_ASSOC_RULES refers to the number of complementary components to add (at most) per component in the weak spec. ALPHA_ASSOC_RULES combines a rule's normalized-PMI and support fraction to obtain a single score for an association rule, we used 0.5 in our evaluations but you can modify if you'd like. Please see the paper for details. NUM_PARAMS is the (max) count of hyperparameters to include in the search space for each component in the extended specification, and NUM_PARAM_VALUES is the (max) number of possible values (in addition to the default value) for each hyperparameter in the extended search space.

Using an AMS generated search space

AMS produces a search space in JSON format. This configuration can be read in and used directly with TPOT, or with the random search procedure used for AMS evaluation.

For example, we first generate the search space from the prior example and dump it into a text file

$ (bash scripts/use_ams.sh sklearn.linear_model.LogisticRegression sklearn.preprocessing.MinMaxScaler) > config.json

We then launch the python interpreter, read in the configuration, and show how it can be used on a generated dataset

$ python
import json
import tpot
import sklearn.datasets
from core.search import RandomSearch

X, y = sklearn.datasets.make_classification(100, 10)
config = json.load(open("config.json", "r"))

# GP-based search
clf_tpot = tpot.TPOTClassifier(max_time_mins=1, config_dict=config, verbosity=3)

# Random search
clf_rand = RandomSearch(max_time_mins=1, max_depth=3, config_dict=config)


clf_tpot.fit(X, y)
clf_rand.fit(X, y)

Reproducing FSE evaluation

You can reproduce FSE experiments and figures by using scripts in scripts/fse/. As others, these should be run from the root AMS directory. Given that some of the experiments explained below take on the order of days to run on a well-provisioned machine, we provide a download of our experimental results. (If you are using the artifact VM, these results have already been loaded and you can skip the following step).

Datasets

Note that we have included all necessary datasets directly in the repository (and artifact), as the library that packages these datasets has implemented breaking changes with no backwards compatibility.

Downloading Results

If you want to download the results, you can run

$ bash scripts/fse/download_results.sh

This will download results from an AWS S3 bucket and will place results in $RESULTS, $ANALYSIS_DIR, and $DATA. In particular,

${RESULTS} will now contain folders of the form q[0-9]+, one for each of the 15 weak specifications in our experiments. In it, you will find the weak specification (simple_config.json), the specification with expert-defined hyperparameters (simple_config_with_params_dict.json), and the AMS-generated search space (gen_config.json).

The folder random contains results (again organized by weak specification experiment) when using random search, while tpot contains results when using genetic programming (the TPOT tool).

rule-mining/ has experimental results for the complementary component experiments.

${DATA}/corpus-size* contains objects derived by AMS from a subsample of the corpus.

Tables and Figures

The folder $ANALYSIS_DIR (analysis_output in the VM) holds figures/tables produced in analysis and used in the paper. In particular,

  • Table 2: rules/roles.tex
  • Figure 3: rules/precision.pdf
  • Figure 4: relevance/plot.pdf
  • Figure 5:
    • (a) hyperparams/num_params_tuned.pdf
    • (b) hyperparams/distance_params_tuned.pdf
    • (c) hyperparams/num_param_values.pdf
  • Figure 6: hyperparams/perf.pdf
  • Figure 7: performance/combined_wins.pdf
  • Figure 8: tpot-sys-ops/combined.pdf (includes extended examples)
  • Figure 9:
    • (a) corpus-size/hyperparameters.pdf
    • (b) corpus-size/hyperparameter_values.pdf
    • (c) corpus-size/num_mined_rules.pdf
    • (d) corpus-size/jaccard_mined_rules.pdf

(Tip: To open PDFs from the terminal in the Ubuntu VM, you can use xdg-open file.pdf)

Scripts

bash scripts/fse/reproduce_complementary_experiments.sh reproduces experimental results relating to extraction of complementary components to add to weak specifications. These experiments should take on the order of a couple of hours to run.

bash scripts/fse/reproduce_functional_related_experiments.sh generates the data used for manual annotation of functionally related components. We have already included our manually annotated results as part of the artifact, so running this script will prompt you to confirm before overwriting those with (unannotated) data.

bash scripts/fse/reproduce_performance_experiments.sh generates search space configurations and evaluates them against our comparison baselines (weak spec, weak spec + search, and expert + search). Running these experiments from scratch takes on the order of 1-2 days on a machine with 30 cores. Given this computational burden, we have also included our results in the artifact.

bash scripts/fse/reproduce_corpus_size.sh generates subsampled versions of our code corpus, and rebuilds portions of AMS that rely on code examples (i.e. hyperparameter mining and complementary component mining). Running these experiments from scratch takes on the order of 2 hours on a machine with 30 cores. Given this computational burden, we have also included our results in the artifact. Note that in contrast to other scripts, this is "creating new data" and as such the outputs are stored in ${DATA}, following the naming convention corpus-size-${corpus_size}-iter-${corpus_iter}/ where ${corpus-size} is the downsampling ratio (e.g. 0.1) and ${corpus-iter} is the iteration index (e.g. 1) as we repeat the downsampling 5 times per ratio.

bash scripts/fse/reproduce_analysis.sh generates figures from the outputs of the prior 3 scripts and also runs some additional (~ 1 hour execution) experiments to characterize the hyperparameters found in our code corpus.

The figures/tables are generated and saved to $ANALYSIS_DIR (set to analysis_output/, if not modified in folder_setup.sh). Please see the prior section for details on figure/table mappings.

Codebase Overview

We provide a short overview of the AMS codebase:

  • core/ contains the main tool logic:

    • extract_sklearn_api.py: traverse sklearn modules to find classes to import and represent with embeddings (also has stuff on default parameters)
    • nlp.py: helper functions to parse/embed natural language
    • code_to_api.py: takes a code specification and maps it to possibly related API components using pre-trained embeddings
    • extract_kaggle_scripts.py: filter down meta-kaggle to find useful scripts (i.e. those that import target scikit-learn library)
    • extract_parameters.py: (light) parse of python scripts from kaggle to extract calls to APIs and their parameters
    • summarize_parameters.py: tally up frequent parameter names/values by API component
    • generate_search_space.py: given weak spec (code/nl) generate search space dictionary
    • search.py: various search strategies and helpers
  • experiments/ contains all code to run experiments:

    • generate_experiment.py: generate experiment configurations based on some predefined components of interest
    • simple_pipeline.py: compile weak spec directly into a sklearn pipeline for benchmarking
    • run_experiment.py: driver to run different search strategies/configurations
    • build_corpus_size_experiment.py: driver to run corpus size experiments, downsamples corpus and rebuilds portions of AMS that use that data
  • analysis/: contains code to run analysis on experiment outputs and conduct additional characterization of our data.

    • annotation_rules_component_relevance.md: details our annotation guidelines for manually assessing functionally related components
    • association_rules_analysis.py: evaluates the rules used to extend specifications with complementary components
    • combined_wins_plot.py: is a utility to combine win counts into a single plot
    • distribution_hyperparameters.py: characterizes hyperparameters found in our code corpus
    • frequency_operators.py: compute distribution of components in pipelines
    • performance_analysis.py: compute table/plots of wins from performance experiments data
    • pipeline_to_tree.py: convert pipeline from API into a tree (easier to analyze) utility
    • relevance_markings.py: create plot of functionally related components' manual annotation results
    • corpus_size_analysis.py: create plots for impact of corpus size
    • utils.py: misc utils

Contact

Feel free to email Jose Cambronero (jcamsan@mit.edu) with questions.