# john-hewitt/structural-probes

Codebase for testing whether hidden states of neural networks encode discrete structures.
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# structural-probes

Codebase for testing whether hidden states of neural networks encode discrete structures.

Based on the paper A Structural Probe for Finding Syntax in Word Representations.

See the blog post on structural probes for a brief introduction.

## Installing & Getting Started

1. Clone the repository.

 git clone https://github.com/john-hewitt/structural-probes/
cd structural-probes

2. [Optional] Construct a virtual environment for this project. Only python3 is supported.

 conda create --name sp-env
conda activate sp-env

3. Install the required packages. This mainly means pytorch, scipy, numpy, seaborn, etc. Look at pytorch.org for the PyTorch installation that suits you and install it; it won't be installed via requirements.txt. Everything in the repository will use a GPU if available, but if none is available, it will detect so and just use the CPU, so use the pytorch install of your choice.

 conda install --file requirements.txt
pip install pytorch-pretrained-bert

4. Download some pre-packaged data from the English Universal Dependencies (EWT) dataset and pretrained probes to get your feet wet.

 bash ./download_example.sh


This will make the directory example/data, and in it will be 9 files, 3 for each of train,dev,test.

• en_ewt-ud-{train,dev,test}.conllu: the parsed language data
• en_ewt-ud-{train,dev,test}.txt: whitespace-tokenized, sentence-per-line language data.
• en_ewt-ud-{train,dev,test}.elmo-layers.hdf5: the ELMo hidden states for each sentence of the language data, constructed by running elmo on the .txt files.
5. Test a pre-trained structural probe on BERTlarge with our demo script!

 printf "The chef that went to the stores was out of food" | python structural-probes/run_demo.py example/demo-bert.yaml


The script will make a new directory under example/results/ and store some neat visualizations there. It will use pre-trained probe parameters stored at example/data, downloaded with download_example.sh. Try out some other sentences too!

6. Run an experiment using an example experiment configuration, and take a look at the resultant reporting!

 python structural-probes/run_experiment.py example/config/prd_en_ewt-ud-sample.yaml


The path to a new directory containing the results of the experiment will be in the first few lines of the logging output of the script. Once you go there, you can see dev-pred*.png: some distance matrices printed by the script, as well as files containing the quantitative reporting results, like dev.uuas, the unlabeled undirected attachment score. These will all be very low, since the probe was trained on very little data!

## Run a pretrained structural probe on BERT-large quickly on the command line.

It's easy to get predictions on a sentence (or file of sentences) using our demo script and the pre-trained structural probes we release. We use pytorch-pretrained-bert to get BERT subword embeddings for each sentence; it should be installed during setup of the repository.

Make sure you've run download_example.sh; this will download two probe parameter files to example/data/. Also make sure you've installed all dependencies. One is a distance probe on the 16th hidden layer of BERT large, and the other is a depth probe on the same layer. The configuration file example/demo-bert.yaml has the right paths already plugged in; just pipe text into the demo file, as follows:

 printf "The chef that went to the stores was out of food" | python structural-probes/run_demo.py example/demo-bert.yaml


If you want to run multiple sentences at once, you can either do so via printf:

 printf "The chef that went to the stores was out of food\nThe chef that went to the stores and talked to the parents was out of food" | python structural-probes/run_demo.py example/demo-bert.yaml


Or piping/redirecting a file to stdin:

 cat my_set.txt | python structural-probes/run_demo.py example/demo-bert.yaml


The script will print out a directory to which it has written visualizations of both parse depths and parse distances as predicted by a distance probe and a depth probe. You'll also see demo.tikz, which is a bit of LaTeX for the tikz-dependency package. With tikz-dependency in the same directory as your LaTeX file, you can plop this bit of LaTeX in a figure environment and see the minimum spanning tree it constructs. It'd look a bit like this:

\documentclass{article}
\usepackage{tikz-dependency}
\usepackage{tikz}

\pgfkeys{%
/depgraph/reserved/edge style/.style = {%
white, -, >=stealth, % arrow properties
black, solid, line cap=round, % line properties
rounded corners=2, % make corners round
},%
}
\begin{document}
\begin{figure}
\centering
\small
\begin{dependency}[hide label, edge unit distance=.5ex]
\begin{deptext}[column sep=0.05cm]
The\& chef\& who\& ran\& to\& the\& stores\& is\& out\& of\& food \\
\end{deptext}
\depedge[edge style={red}, edge below]{8}{9}{.}
\depedge[edge style={red}, edge below]{5}{7}{.}
\depedge[edge style={red}, edge below]{4}{5}{.}
\depedge[edge style={red}, edge below]{1}{2}{.}
\depedge[edge style={red}, edge below]{6}{7}{.}
\depedge[edge style={red}, edge below]{9}{10}{.}
\depedge[edge style={red}, edge below]{10}{11}{.}
\depedge[edge style={red}, edge below]{3}{4}{.}
\depedge[edge style={red}, edge below]{2}{4}{.}
\depedge[edge style={red}, edge below]{2}{8}{.}
\end{dependency}
\end{figure}
\end{document}


Which results in a PDF with the following:

Note that your text should be whitespace-tokenized! If you want to evaluate on a test set with gold parses, or if you want to train your own structural probes, read on.

## The experiment config file

Experiments run with this repository are specified via yaml files that completely describe the experiment (except the random seed.) In this section, we go over each top-level key of the experiment config.

### Dataset:

• observation_fieldnames: the fields (columns) of the conll-formatted corpus files to be used. Must be in the same order as the columns of the corpus. Each field will be accessable as an attribute of each Observation class (e.g., observation.sentence contains the sequence of tokens comprising the sentence.)
• corpus: The location of the train, dev, and test conll-formatted corpora files. Each of train_path, dev_path, test_path will be taken as relative to the root field.
• embeddings: The location of the train, dev, and test pre-computed embedding files (ignored if not applicable. Each of train_path, dev_path, test_path will be taken as relative to the root field. - type is ignored.
• batch_size: The number of observations to put into each batch for training the probe. 20 or so should be great.
dataset:
observation_fieldnames:
- index
- sentence
- lemma_sentence
- upos_sentence
- xpos_sentence
- morph
- governance_relations
- secondary_relations
- extra_info
- embeddings
corpus:
root: example/data/en_ewt-ud-sample/
train_path: en_ewt-ud-train.conllu
dev_path: en_ewt-ud-dev.conllu
test_path: en_ewt-ud-test.conllu
embeddings:
type: token #{token,subword}
root: example/data/en_ewt-ud-sample/
train_path: en_ewt-ud-train.elmo-layers.hdf5
dev_path: en_ewt-ud-dev.elmo-layers.hdf5
test_path: en_ewt-ud-test.elmo-layers.hdf5
batch_size: 40


### Model

• hidden_dim: The dimensionality of the representations to be probed. The probe parameters constructed will be of shape (hidden_dim, maximum_rank)
• embedding_dim: ignored
• model_type: One of ELMo-disk, BERT-disk, ELMo-decay, ELMo-random-projection as of now. Used to help determine which Dataset class should be constructed, as well as which model will construct the representations for the probe. The Decay0 and Proj0 baselines in the paper are from ELMo-decay and ELMo-random-projection, respectively. In the future, will be used to specify other PyTorch models.
• use_disk: Set to True to assume that pre-computed embeddings should be stored with each Observation; Set to False to use the words in some downstream model (this is not supported yet...)
• model_layer: The index of the hidden layer to be used by the probe. For example, ELMo models can use layers 0,1,2; BERT-base models have layers 0 through 11; BERT-large 0 through 23.
• tokenizer: If a model will be used to construct representations on the fly (as opposed to using embeddings saved to disk) then a tokenizer will be needed. The type string will specify the kind of tokenizer used. The vocab_path is the absolute path to a vocabulary file to be used by the tokenizer.
model:
hidden_dim: 1024 # ELMo hidden dim
#embedding_dim: 1024 # ELMo word embedding dim
model_type: ELMo-disk # BERT-disk, ELMo-disk,
tokenizer:
type: word
vocab_path: example/vocab.vocab
use_disk: True
model_layer: 2 # BERT-base: {1,...,12}; ELMo: {1,2,3}


### Probe, probe-training

• task_signature: Specifies the function signature of the task. Currently, can be either word, for parse depth (or perhaps labeling) tasks; or word_pair for parse distance tasks.
• task_name: A unique name for each task supported by the repository. Right now, this includes parse-depth and parse-distance.
• maximum_rank: Specifies the dimensionality of the space to be projected into, if psd_parameters=True. The projection matrix is of shape (hidden_dim, maximum_rank). The rank of the subspace is upper-bounded by this value. If psd_parameters=False, then this is ignored.
• psd_parameters: though not reported in the paper, the parse_distance and parse_depth tasks can be accomplished with a non-PSD matrix inside the quadratic form. All experiments for the paper were run with psd_parameters=True, but setting psd_parameters=False will simply construct a square parameter matrix. See the docstring of probe.TwoWordNonPSDProbe and probe.OneWordNonPSDProbe for more info.
• diagonal: Ignored.
• prams_path: The path, relative to args['reporting']['root'], to which to save the probe parameters.
• epochs: The maximum number of epochs to which to train the probe. (Regardless, early stopping is performed on the development loss.)
• loss: A string to specify the loss class. Right now, only L1 is available. The class within loss.py will be specified by a combination of this and the task name, since for example distances and depths have different special requirements for their loss functions.
probe:
maximum_rank: 32
psd_parameters: True
diagonal: False
params_path: predictor.params
probe_training:
epochs: 30
loss: L1


### Reporting

• root: The path to the directory in which a new subdirectory should be constructed for the results of this experiment.
• observation_paths: The paths, relative to root, to which to write the observations formatted for quick reporting later on.
• prediction_paths: The paths, relative to root, to which to write the predictions of the model.
• reporting_methods: A list of strings specifying the methods to use to report and visualize results from the experiment. For parse-distance, the valid methods are spearmanr, uuas, write_predictions, and image_examples. When reporting uuas, some tikz-dependency examples are written to disk as well. For parse-depth, the valid methods are spearmanr, root_acc, write_predictions, and image_examples. Note that image_examples will be ignored for the test set.
reporting:
root: example/results
observation_paths:
train_path: train.observations
dev_path: dev.observations
test_path: test.observations
prediction_paths:
train_path: train.predictions
dev_path: dev.predictions
test_path: test.predictions
reporting_methods:
- spearmanr
#- image_examples
- uuas


## Reporting + visualization

It can be time-consuming to make nice visualizations and make sense of the results from a probing experiment, so this repository does a bit of work for you. This section goes over each of the reporting methods available (under args['reporting']['reporting_methods'] in the experiment config), and exmaples of results.

• spearmanr: This reporting method calculates the spearman correlation between predicted (distances/depths) and true (distances/depths) as defined by gold parse trees. See the paper or reporting.py docstrings for specifics. With this option enabled, you'll see dev.spearmanr, a TSV with an average Spearman correlation for each sentence length represented in the dev set, as well as dev.spearmanr-5-50-mean, which averages the sentence-average values for all sentence lengths between 5 and 50 (inclusive.)
• image_examples: This reporting method prints out true and predicted distance matrices as pngs for the first 20 examples in the split. These will be labeled dev-pred0.png, dev-gold0.png, etc. They'll look something like this:

• uuas: This reporting method (only used by parse-distance tasks) will print the unlabeled undirected attachment score to dev.uuas, and write the first 20 development examples' minimum spanning trees (for both gold and predicted distance matrices) in a tikz-dependency LaTeX code format, to dev.tikz. Each sentence can be copy-pasted into a LaTeX doc for visualization. Then they'l look something like this:

• root_acc: This reporting method (only used by parse-depth tasks) will print to dev.root_acc the percentage of sentences where the least-deep word in the gold tree (the root) is also the least-deep according to the predicted depths.

## Replicating PTB Results for the NAACL'19 Paper

As usual with the PTB, a bit of work has to be done in prepping data (and you have to have the unadulterated PTB data already, not the mangled language modeling benchmark version.)

To replicate our results on the PTB, you'll have to prep some data files. The prep scripts will need to be modified to use paths on your system, but the process is as follows:

1. Have Stanford CoreNLP installed / on your java classpath, and have allennlp installed.
2. Convert the PTB constituency trees to Stanford Dependencies in conllx format, using the script scripts/convert_splits_to_depparse.sh. This will write a single conllx file for each of train/dev/test. (This uses CoreNLP.)
3. Convert the conllx files to sentence-per-line whitespace-tokenized files, using scripts/convert_conll_to_raw.py.
4. Use scripts/convert_raw_to_bert.py and scripts/convert_raw_to_elmo.sh to take the sentencep-er-line whitespace-tokenized files and write BERT and ELMo vectors to disk in hdf5 format.
5. Replace the data paths (and choose a results path) in the yaml configs in example/config/naacl19/*/* with the paths that point to your conllx and .hdf5 files as constructed in the above steps. These 118 experiment files specify the configuration of all the experiments that end up in the paper.

## Experiments on new datasets or models

In the future I hope to streamline support for plugging in arbitrary PyTorch models in model.py, but because of subword models, tokenization, batching etc. this is beyond my current scope.

Right now, the official way to run experiments on new datasets and representation learners is:

1. Have a conllx file for the train, dev, and test splits of your dataset.
2. Write contextual word representations to disk for each of the train, dev, and test split in hdf5 format, where the index of the sentence in the conllx file is the key to the hdf5 dataset object. That is, your dataset file should look a bit like {'0': <np.ndarray(size=(1,SEQLEN1,FEATURE_COUNT))>, '1':<np.ndarray(size=(1,SEQLEN1,FEATURE_COUNT))>...}, etc. Note here that SEQLEN for each sentence must be the number of tokens in the sentence as specified by the conllx file.
3. Edit a config file from example/config to match the paths to your data, as well as the hidden dimension and labels for the columns in the conllx file. Look at the experiment config section of this README for more information therein. One potential gotcha is that you must have an xpos_sentence field in your conllx (as labeled by your yaml config) since this will be used at evaluation time.

## Citation

If you use this repository, please cite:

  @InProceedings{hewitt2019structural,
author =      "Hewitt, John and Manning, Christopher D.",
title =       "A Structural Probe for Finding Syntax in Word Representations",
booktitle =   "North American Chapter of the Association for Computational Linguistics: Human Language Technologies",
year =        "2019",
publisher =   "Association for Computational Linguistics",
location =    "Minneapolis, USA",
}

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