In this tutorial, we will walk through the process of using Snorkel to generate labels for an unlabelled dataset. We will provide you examples of basic Snorkel components by guiding you through a real clinical application of Snorkel. Specifically, we will use Snorkel to try to boost our results in predicting Multiple Sclerosis (MS) severity scores. Enjoy!
Check out our other work focused on NLP for MS severity classification here.
What is Snorkel?
Snorkel is a system that facilitates the process of building and managing training datasets without manual labelling. The first component of a Snorkel pipeline includes labelling functions, which are designed to be weak heuristic functions that predict a label given unlabelled data. The labelling functions that we developed for MS severity score labelling were the following:
- Multiple key-word searches (using regular expressions) within the text. For example, in finding a severity score we searched for the phrase in numeric format and in roman numeral format.
- Common baselines such as logistic regression, linear discriminant analysis, and support vector machines which were trained using term frequency-inverse document frequency (or tf-idf for short) features.
- Word2Vec Convolutional Neural Network (CNN).
- Our MS-BERT classifier described in this blog post.
The second component of the Snorkel pipeline is a generative model that outputs a single confidence weighted training label per data point given predictions from all the labelling functions. It does this by learning to estimate the accuracy and correlations of the labelling functions based on their agreements and disagreements.
To reiterate, in this article we demonstrate label generation for MS severity scores. A common measurement of MS severity is EDSS or the Expanded Disability Status Scale. This is a scale that increases from 0 to 10 depending on the severity of MS symptoms. We will refer to EDSS in general as the MS severity score but for our keen readers we thought we would provide this information. This score is further described here.
Step 0: Acquire a Dataset
In our task, we worked with a dataset compiled by a leading MS research hospital, containing over 70,000 MS consult notes for about 5000 patients. Of the 70,000 notes only 16,000 are manually labeled by an expert for MS severity. This means that their are approximately 54,000 unlabelled notes. As you may or not be aware, having a larger dataset to train models generally lead to better model performance. Hence, we used Snorkel to generate what we call ‘silver’ labels for our 54,000 unlabelled notes. The 16,000 ‘gold’ labelled notes were used to train our classifiers before creating their respective labelling function.
Step 1: Installing Snorkel
To install Snorkel to your project, you can run the following:
Step 2: Adding the Labelling Functions
Labelling functions allow you to define weak heuristics and rules that predict a label given unlabelled data. These heuristics can be derived from expert knowledge or other labelling models. In the case of MS severity score prediction, our labelling functions included: key-word search functions derived from clinicians, baseline models trained to predict MS severity scores (tf-idf, word2vec cnn, etc.), and our MS-BERT classifier.
As you will see below, you mark labelling functions by adding “@labeling_function()” above the function. For each labelling function, a single row of a dataframe containing unlabelled data (i.e. one observation/sample) is passed in. Each labelling function applies heuristics or models to obtain a prediction for each row. If the prediction is not found, the function abstains (i.e. returns -1).
When all labelling functions have been defined, you can make use of the “PandasLFApplier” to obtain a matrix of predictions given all labelling functions.
Labelling Function Example #1: Key-Word Search
Below shows an example of a key-word search (using regular expressions) used to extract MS severity scores recorded in decimal form. The regular expression functions are applied to attempt to search for the MS severity score recorded in decimal form. If found, the function returns the score in the appropriate output format. Else, the function abstains (i.e. returns -1) to indicate that the score is not found.
Labelling Function Example #2: Trained Classifier
Above we see an example using a key-word search. To integrate a trained classifier, you must perform one extra step. That is, you must train and export your model before creating your labelling function. Here is an example of how we trained a logistic regression that was built on top of tf-idf features.
With the model trained, implementing a labelling function is as simple as this:
Step 3(a): Using Snorkel’s Majority Vote
Some would say the simpliest function Snorkel uses to generate a label is ‘Majority Vote’. Majority Vote, as the name implies, makes a prediction based on the most voted for class.
Step 3(b): Using Snorkel’s Label Model
To take advantage of Snorkel’s full functionality, we used the ‘Label Model’ to generate a single confidence-weighted label given a matrix of predictions obtained from all the labelling functions (i.e. L_unlabelled). The Label Model predicts by learning to estimate the accuracy and correlations of the labelling functions based on their agreements and disagreements.
Step 4: Evaluation Tools
LF Analysis — Coverage, Overlaps, Conflicts
To better understand how your labelling functions are functioning, you can make use of Snorkel’s LFAnalysis. The LF analysis reports the polarity, coverage, overlap, and conflicts of each labelling function.
The definition of these terms are as follows and you can refer to the Snorkel documentation for more information:
- Polarity: Infer the polarities of each LF based on evidence in a label matrix.
- Coverage: Computes the fraction of data points with at least one label.
- Overlap: Computes the fraction of data points with at least two (non-abstain) labels.
- Conflicts: Computes the fraction of data points each labelling function disagrees with at least one other labelling function.
Snorkel provides some more evaluation tools to help you understand the quality of your labelling functions. In particular, ‘get_label_buckets’ is a handy way to combine labels and make comparisons. For more information, read the Snorkel documentation.
The following code allows you to compare the true labels (y_gold) and predicted labels (y_preds) to view data points that were correctly or incorrectly labelled by Snorkel. This will allow you to pin-point which data points are difficult to correctly label, so that you can fine-tune your labelling functions to cover these edge cases.
Alternatively, you can use ‘get_label_buckets’ to make comparisons between labelling functions.
Step 5: Deployment
Choosing the Best Labelling Model to Label Unlabelled Data
Following the procedure outlined above, we developed various labelling functions based on key-word searches, baseline models, and our MS-BERT classifier. We experimented with various ensembles of labelling functions and used Snorkel’s Label Model to obtain predictions for a held-out labelled dataset. This allowed us to determine which ensemble of labelling functions would be best to label our unlabelled dataset.
As shown in the table below, we observed that the MS-BERT classifier (MSBC) alone outperformed all ensembles that contain itself by at least 0.02 on Macro-F1. The addition of weaker heuristics and classifiers consistently decreased the ensemble’s performance. Furthermore, we observed that the amount of conflict for the MS-BERT classifier increased as weaker classifiers and heuristics were added to the ensemble.
To understand our findings, we have to remind ourselves that Snorkel’s label model learns to predict the accuracy and correlations of the labelling functions based on agreements and disagreements amongst each other. Therefore in the presence of a strong labelling function, such as our MS-BERT classifier, the addition of weaker labelling functions introduces more disagreements with the strong labelling functions and therefore decreases performance. From these findings, we learned that Snorkel may be more suited for situations where you only have weak heuristics and rules. However, if you already have a strong labelling function, developing a Snorkel ensemble with weaker heuristics may compromise performance.
Therefore, the MS-BERT classifier alone was chosen to label our unlabelled dataset.
Semi-Supervised Labelling Results
The MS-BERT classifier was used to obtain ‘silver’ labels for our unlabelled dataset. These ‘silver’ labels were combined with our ‘gold’ labels to obtain a silver+gold dataset. To infer the quality of the silver labels, new MS-BERT classifiers were developed: 1) MS-BERT+ (trained on silver+gold labelled data); and 2) MS-BERT-silver (trained on silver labelled data). These classifiers were evaluated on a held-out test dataset that was previously used to evaluate our original MS-BERT classifier (trained on gold labelled data). MS-BERT+ achieved a Macro-F1 of 0.86238 and a Micro-F1 of 0.92569, and MS-BERT-silver achieved a Macro-F1 of 0.82922 and a Micro-F1 of 0.91442. Although their performance was slightly lower that our original MS-BERT classifier (Macro-F1 of 0.88296, Micro-F1 of 0.94177), they still outperformed the previous best baseline models for MS severity prediction. The strong results of MS-BERT-silver helps show the effectiveness of using our MS-BERT classifier as a labelling function. It demonstrates potential to reduce tedious hours required by a professional to read through a patient’s consult note and manually generate MS severity scores.
Thanks for reading everyone! If you have any questions please do not hesitate to contact us at nlp4health (at gmail dot) com. 🙂
We would like to thank the researchers and staff at the Data Science and Advanced Analytics (DSAA) department, St. Michael’s Hospital, for providing consistent support and guidance throughout this project. We would also like to thank Dr. Marzyeh Ghassemi, and Taylor Killan for providing us the opportunity to work on this exciting project. Lastly, we would like to thank Dr. Tony Antoniou and Dr. Jiwon Oh from the MS clinic at St. Michael’s Hospital for their support on the neurological examination notes.
Originally published at https://nlp4h.com.
Bio: The authors are a group of graduate students at University of Toronto working on NLP for healthcare.
Original. Reposted with permission.