from snorkel.parser import CorpusParser
cp = CorpusParser(doc_parser, sent_parser)
%time corpus = cp.parse_corpus(session, 'News Training')
---------------------------------------------------------------------------
ConnectionError                           Traceback (most recent call last)
<ipython-input-5-277d2c9f9bed> in <module>()
      2 
      3 cp = CorpusParser(doc_parser, sent_parser)
----> 4 get_ipython().magic(u"time corpus = cp.parse_corpus(session, 'News Training')")

/usr/local/lib/python2.7/dist-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
   2156         magic_name, _, magic_arg_s = arg_s.partition(' ')
   2157         magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2158         return self.run_line_magic(magic_name, magic_arg_s)
   2159 
   2160     #-------------------------------------------------------------------------

/usr/local/lib/python2.7/dist-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line)
   2077                 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
   2078             with self.builtin_trap:
-> 2079                 result = fn(*args,**kwargs)
   2080             return result
   2081 

<decorator-gen-59> in time(self, line, cell, local_ns)

/usr/local/lib/python2.7/dist-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/usr/local/lib/python2.7/dist-packages/IPython/core/magics/execution.pyc in time(self, line, cell, local_ns)
   1178         else:
   1179             st = clock2()
-> 1180             exec(code, glob, local_ns)
   1181             end = clock2()
   1182             out = None

<timed exec> in <module>()

/home/yejunbin/Github/snorkel/snorkel/parser.pyc in parse_corpus(self, session, name)
     38                     break
     39             corpus.append(doc)
---> 40             for _ in self.sent_parser.parse(doc, text):
     41                 pass
     42         if self.max_docs is not None:

/home/yejunbin/Github/snorkel/snorkel/parser.pyc in parse(self, doc, text)
    274     def parse(self, doc, text):
    275         """Parse a raw document as a string into a list of sentences"""
--> 276         for parts in self.corenlp_handler.parse(doc, text):
    277             yield Sentence(**parts)

/home/yejunbin/Github/snorkel/snorkel/parser.pyc in parse(self, document, text)
    211         if isinstance(text, unicode):
    212             text = text.encode('utf-8', 'error')
--> 213         resp = self.requests_session.post(self.endpoint, data=text, allow_redirects=True)
    214         text = text.decode('utf-8')
    215         content = resp.content.strip()

/usr/local/lib/python2.7/dist-packages/requests/sessions.pyc in post(self, url, data, json, **kwargs)
    520         """
    521 
--> 522         return self.request('POST', url, data=data, json=json, **kwargs)
    523 
    524     def put(self, url, data=None, **kwargs):

/usr/local/lib/python2.7/dist-packages/requests/sessions.pyc in request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
    473         }
    474         send_kwargs.update(settings)
--> 475         resp = self.send(prep, **send_kwargs)
    476 
    477         return resp

/usr/local/lib/python2.7/dist-packages/requests/sessions.pyc in send(self, request, **kwargs)
    594 
    595         # Send the request
--> 596         r = adapter.send(request, **kwargs)
    597 
    598         # Total elapsed time of the request (approximately)

/usr/local/lib/python2.7/dist-packages/requests/adapters.pyc in send(self, request, stream, timeout, verify, cert, proxies)
    485                 raise ProxyError(e, request=request)
    486 
--> 487             raise ConnectionError(e, request=request)
    488 
    489         except ClosedPoolError as e:

ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=12345): Max retries exceeded with url: /?properties=%7B%22annotators%22:%20%22tokenize,ssplit,pos,lemma,depparse,ner%22,%20%22outputFormat%22:%20%22json%22%7D (Caused by ProtocolError('Connection aborted.', BadStatusLine("''",)))

Hi,

I have two questions about the ways of using the snorkel:

1. I am trying to train a Stanford Core-NLP NER model for picking all the software names and vendor names from the comments and descriptions of a software ( raw text). For this I tried to do some manual labeling which is very time consuming but I can clearly see the improvement in accuracy when keep increasing the training data. In this case I am trying to use Snorkel to produce some training data for me but it seems like(in Tutorials) it is already using Core-NLP NER models and generating training data for abstracting relation between two entities. Is their a way to use snorkel for creating train data for abstracting entities rather than their relation?

2. I have also used DeepDive to abstract relations between entities, when I skim through the tutorials I am not able to find much difference between DeepDive and Snorkel. Is Snorkel is the python version of DeepDive ?

Hello all,

I am trying to execute the gene tagging example and I am stuck on step 1: Obtain and parse input data. I am trying to import functions from the snorkel.parser module but keep getting an error as follows:

from snorkel.parser import HTMLDocParser causes the following error: ImportError Traceback (most recent call last) in () ----> 1 from snorkel.parser import HTMLDocParser

ImportError: No module named 'snorkel'

Description of proposed changes

Just add the new parameter of wapper to support spacy v3.

Related issue(s)

#1701 Fixes # (issue) Preliminary spacy v3 support.

Need help on these? Just ask! Hallo, I just reviewed the wrapper of spacy v3, and add the parameter exclude, write the docs for changed parameters exclude, disable. I am not sure what other functions snorkel used from spacy, please help me to confirm other needed changes. Thanks.

• [*] I have read the CONTRIBUTING document.
• [*] I have updated the documentation accordingly.
• [*] I have added tests to cover my changes.
• [ ] I have run tox -e complex and/or tox -e spark if appropriate.
• [ ] All new and existing tests passed.

Hi, I am using snorkel for a search result quality prediction project. I have quite a few cases where the predictions do not quite make sense to me. There are false negative results where the predictions are 0 (negative), but if you look at the labels assigned by each labeling functions, they are either 1(positive) or -1(abstain). There are nearly no 0(negative) at all. Could anyone help clarify this for me please? Thanks, Peng

Issue description

I am using snorkel for creating binary text classification training examples with 9 labeling functions. However, I find that for some data that are trained with the label model, they receive a probabilistic label of equal probabilities (i.e. [0.5 0.5]), despite that they only receive label of one class from the labeling functions (e.g. [-1 0 -1 -1 0 -1 -1 -1 -1], so only class 0 or ABSTAIN), why is that?

Besides, I find that setting verbose = True when defining the LabelModel does not print the logging information.

Lastly, if producing the label [0.5 0.5] is a normal behavior, then when filtering out unlabeled data points, they should be removed as well, because they do not contribute to the training (of a classifier), and if the classifier that does not support probablistic labels (e.g. FastText), using argmax will always lead to class 0 (which is undesired).

Code example/repro steps

Below I show my code of defining LabelModel:

print('==================================================')
print('Training label model...')
label_model = LabelModel(cardinality=2, verbose=True)
label_model.fit(L_train=L_train, n_epochs=10000, lr=0.001, log_freq=100, seed=1)
print('Done!')

Below I show some of the logs I print:

Check results for data in the training set:  a_text_in_the_training_set_but_I_removed_here
        * Output of L_train for this data point is: [-1  0 -1 -1  0 -1 -1 -1 -1]
        * Output of probs_train for this data point is: [0.5 0.5]
        * Output of probs_train_filtered for this data point is: [0.5 0.5]
        * Output of preds_train_filtered for this data point is: 0

Expected behavior

I expect that if a datapoint receives label of only a single class, then it should not get equal probabilities of both classes when the label model is trained.

System info

• How you installed Snorkel (conda, pip, source): pip
• Build command you used (if compiling from source):
• OS: Windows
• Python version: 3.7
• Snorkel version: 0.9
• Versions of any other relevant libraries:

I am working on a binary classifier/detector involving Images. True if a particular object in present in the image and false if it doesnt. Is there an example to make snorkel work on Image data? Thanks.

I have a very large sampling of tabular data including mainly numerical fields where each line is an example I would like to try and label. Looking through the documentation and examples, I don't see a way to use the tool in this manner or at least easily get the data into a usable format. Does anyone know if this can or has been done? Any thoughts? The "concept" seems similar, but your sought after audience was text based labeling. Just wondering if it could be adapted. Thanks! Also, great work. Heard about the package on O'Reilly Data Show.

Thank you for the very interesting work!

I was wondering if Snorkel is planning to extend its features to multilabel classifications? e.g., Semantic Role Labelling task.

Thanks a lot

I would like to bring snorkel to the conda users community and it would be great to learn if there will be a release file anytime soon for the latest/stable master repo. The gunzipped tarball of the most recent version (i.e., 0.7-beta) is 150 commits behind and a year older.

any thoughts?

• Temporary redesign and restructure for Workshop
• Highlight Snorkel captures Augment, Slice, and Label
• Old links to Blogs, Papers, and Use Cases maintained
• Overview Image for SFs

Issue description

On anaconda, snorkel requires numpy=1.19.5, on Apple m chip, NumPy in such version can not work. I am testing if snorkel works with apple metal GPU acceleration.

Code example/repro steps

import numpy
Traceback (most recent call last):
  File "/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/__init__.py", line 22, in <module>
    from . import multiarray
  File "/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/multiarray.py", line 12, in <module>
    from . import overrides
  File "/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/overrides.py", line 7, in <module>
    from numpy.core._multiarray_umath import (
ImportError: dlopen(/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so, 0x0002): Library not loaded: '@rpath/libcblas.3.dylib'
  Referenced from: '/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so'
  Reason: tried: '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/../../../../libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/../../../../libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/bin/../lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/bin/../lib/libcblas.3.dylib' (no such file), '/usr/local/lib/libcblas.3.dylib' (no such file), '/usr/lib/libcblas.3.dylib' (no such file)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/__init__.py", line 140, in <module>
    from . import core
  File "/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/__init__.py", line 48, in <module>
    raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.9 from "/Users/jhj/anaconda3/envs/snorkel/bin/python"
  * The NumPy version is: "1.19.5"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so, 0x0002): Library not loaded: '@rpath/libcblas.3.dylib'
  Referenced from: '/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so'
  Reason: tried: '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/../../../../libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/lib/python3.9/site-packages/numpy/core/../../../../libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/bin/../lib/libcblas.3.dylib' (no such file), '/Users/jhj/anaconda3/envs/snorkel/bin/../lib/libcblas.3.dylib' (no such file), '/usr/local/lib/libcblas.3.dylib' (no such file), '/usr/lib/libcblas.3.dylib' (no such file)

System info

• How you installed Snorkel (conda, pip, source): conda
• OS: MacOS 12.6
• Python version: 3.9
• Snorkel version: 0.9.9

Additional context

I did the following test:

install NumPy before installing the snorkel, the NumPy can work.

After installing the snorkel, the NumPy will downgrade to 1.19.5, then the NumPy can not work.

Bumps pyspark from 3.1.3 to 3.2.2.

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Does Snorkel have probabilistic weight for each labelling function accounting for predicted label ? For example, suppose we have three labeling function resulting in a particular label output as 1. Does snorkel provide the weights corresponding to each labelling function resulting in a particular prediction? If yes, Can you please point out to the correct direction.

Issue description

I tried Snorkel on five different problems and while the framework does work... MajorityLabelVoter and / or MajorityClassVoter outperformed the LabelModel on every problem. This problem has been noted in the past. In frustration, I asked around and found the secret to using Snorkel from two different people:

Snorkel's LabelModel doesn't work with broad coverage LabelingFunctions

This is the key to making the LabelModel work. You have to write fairly narrow LabelingFunctions that can work in combination to achieve the coverage you need. A 50% coverage LF will break the LabelModel.

For me it is good for a 3% performance bump across two classification problems using this method.

Big Question

Where do I make this contribution? This will make Snorkel much more useful to its users, many of whom had the same frustrations that I did. I would like it to get picked up in the website, and the tutorials haven't been updated in a while. Is that still the right place for this PR? https://github.com/snorkel-team/snorkel-tutorials

cc @ajratner @henryre

Issue description

In the logistic regression model when I run code i face Attribute erorr. A clear and concise description of what the bug is.

Code example/repro steps

from sklearn.model_selection import GridSearchCV
from sklearn.pipeline import Pipeline
from sklearn.linear_model import LogisticRegression
from sklearn.feature_extraction.text import TfidfVectorizer



tfidf = TfidfVectorizer(strip_accents=None,
                        lowercase=False,
                        preprocessor=None)

param_grid = [{'vect__ngram_range': [(1, 1)],
               'vect__stop_words': [stop_words, None],
               'vect__tokenizer': [tokenizer, tokenizer_porter],
               'vect__preprocessor': [None, preprocessor],
               'clf__penalty': ['l1', 'l2'],
               'clf__C': [1.0, 10.0, 100.0]},
              {'vect__ngram_range': [(1,1)],
               'vect__stop_words': [stop_words, None],
               'vect__tokenizer': [tokenizer, tokenizer_porter],
               'vect__preprocessor': [None, preprocessor],
               'vect__use_idf':[False],
               'vect__norm':[None],
               'clf__penalty': ['l1', 'l2'],
               'clf__C': [1.0, 10.0, 100.0]},
              ]

lr_tfidf = Pipeline([('vect', tfidf),
                     ('clf', LogisticRegression(random_state=0))])
#The parameters of the estimator used to apply these methods are optimized by cross-validated grid-search over a parameter grid
gs_lr_tfidf = GridSearchCV(lr_tfidf, param_grid,
                           scoring='accuracy',
                           cv=5,
                           verbose=1,
                           n_jobs=-1)
gs_lr_tfidf.fit(X_train, y_train)

after run this code I face the split not found error. Please try to provide a minimal example to repro the bug. Error messages and stack traces are also helpful.

AttributeError: split not found

Problem I Want To solve

I've found it easy to generate millions of labels with label functions, but loading them into Snorkel is hard. The problem is the conversion to augmented format and (for training) the calculation of the O matrix.

Describe the solution you'd like

In addition to letting the user load the full label matrix (n_docs,n_funcs), we can let the user load the indicator matrix (n_docs,n_funcsn_labels) in sparse format. e.g. user would input a list of tuples (doc_id,func_idnum_labels+label_id) and populate a sparse matrix. This makes the L.T@L calculation cheap, and saves lots of time and memory building indicator matrix.

Torch supports Sparse matrices, so we could even do training and inference without the memory hassle of the dense L matrix.

Example:

I calculate and store the label functions in SQL, so it's easy to generate that list of tuples.

Caveat

This would make modelling dependencies between LFs harder, but since _create_tree is degenerate that doesn't seem to be an issue in practice.

Describe alternatives you've considered

The other alternative is some "big-data" solution, but that's a lot of friction for something I can do so simply.

Additional context

I'm implementing this anyway for my own fun, happy to contribute it back if theirs interest