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Linear-chain conditional random fields (CRF) for natural language processing

Home Page: https://severinsimmler.github.io/chaine

Python 11.62% C 81.40% C++ 5.31% Cython 1.67%

machine-learning conditional-random-fields natural-language-processing named-entity-recognition sequence-labeling crf

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adam444555

chaine's Issues

More restrictions for input data

The restrictions for input data are to loose, something like the following is allowed:

>>> import chaine
>>> tokens = [["John", "Lennon", "was", "born", "in", "Liverpool"]]
>>> labels = [["B-PER", "I-PER", "O", "O", "O", "B-LOC"]]
>>> model = chaine.train(tokens, labels, max_iterations=5)
>>> model.predict(["John", "Lennon", "was", "born", "in", "Liverpool"])
[['O', 'O', 'O', 'O'], ['O', 'O', 'O', 'O', 'O', 'O'], ['O', 'O', 'O'], ['O', 'O', 'O', 'O'], ['O', 'O'], ['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']]

This human error, where the person forgot the outer brackets, leads to bad predictions. The "correct code" would be:

>>> import chaine
>>> tokens = [["John", "Lennon", "was", "born", "in", "Liverpool"]]
>>> labels = [["B-PER", "I-PER", "O", "O", "O", "B-LOC"]]
>>> model = chaine.train(tokens, labels, max_iterations=5)
>>> model.predict([["John", "Lennon", "was", "born", "in", "Liverpool"]])
[['B-PER', 'I-PER', 'O', 'O', 'O', 'B-LOC']]

Predict next most likely state

Similar to Hidden Markov Models

Add docs to gh-pages

https://www.mkdocs.org/

Import model from plain text

Like #12, only the other way round

Cythonize and build wheels

Add logging

pip installation failed (macOS)

macOS Catalina 10.15.7

jan@iMac:~$ pip3.9 install chaine
Collecting chaine
  Using cached chaine-0.1.0.tar.gz (7.8 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Building wheels for collected packages: chaine
  Building wheel for chaine (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/local/opt/[email protected]/bin/python3.9 /usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/tmpnfwxnwmi
       cwd: /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine
  Complete output (50 lines):
  A setup.py file already exists. Using it.
  warning: chaine/crfsuite_api.pxd:53:4: 'messagefunc' redeclared
  running build
  running build_py
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/__init__.py -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/core.py -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/utils.py -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/typing.py -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/data.py -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/trainer_wrapper.hpp -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/model.pyx -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/tagger_wrapper.hpp -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/model.cpp -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/crfsuite_api.pxd -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  copying chaine/trainer_wrapper.cpp -> /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/lib.macosx-10.15-x86_64-3.9/chaine
  running build_ext
  building 'chaine.model' extension
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9/chaine
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9/chaine/crfsuite
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9/chaine/crfsuite/lib
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9/chaine/crfsuite/lib/cqdb
  creating /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9/chaine/crfsuite/lib/cqdb/src
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -Ichaine/crfsuite/include/ -Ichaine/crfsuite/lib/cqdb/include -Ichaine/liblbfgs/include -Ichaine -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/[email protected]/3.9.0_2/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c -std=c99 chaine/crfsuite/lib/cqdb/src/cqdb.c -o /private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build/temp.macosx-10.15-x86_64-3.9/chaine/crfsuite/lib/cqdb/src/cqdb.o
  clang: error: no such file or directory: 'chaine/crfsuite/lib/cqdb/src/cqdb.c'
  clang: error: no input files
  error: command '/usr/bin/clang' failed with exit code 1
  Traceback (most recent call last):
    File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
      main()
    File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 204, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
    File "/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-build-env-s4rurxcv/overlay/lib/python3.9/site-packages/poetry/core/masonry/api.py", line 57, in build_wheel
      return unicode(WheelBuilder.make_in(poetry, Path(wheel_directory)))
    File "/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-build-env-s4rurxcv/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 59, in make_in
      wb.build()
    File "/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-build-env-s4rurxcv/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 89, in build
      self._build(zip_file)
    File "/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-build-env-s4rurxcv/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 121, in _build
      self._run_build_command(setup)
    File "/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-build-env-s4rurxcv/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 149, in _run_build_command
      subprocess.check_call(
    File "/usr/local/Cellar/[email protected]/3.9.0_2/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 373, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['/usr/local/Cellar/[email protected]/3.9.0_2/bin/python3.9', '/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/setup.py', 'build', '-b', '/private/var/folders/y9/8ddvkkvs3r783w2v7l_hnm2c0000gn/T/pip-install-8m0zcihl/chaine/build']' returned non-zero exit status 1.
  ----------------------------------------
  ERROR: Failed building wheel for chaine
Failed to build chaine
ERROR: Could not build wheels for chaine which use PEP 517 and cannot be installed directly

Progress bar

https://github.com/verigak/progress

Build wheels for macOS and Windows

Check if this is also free on GitHub Actions for Open Source projects?
Add a workflow to build wheels for macOS
Add a workflow to build wheels for Windows

Refactor C logging and remove Python log parser

High-level function to load dataset

Improve errors messages

When e.g. data is not in the correct format

Wrong wheels being built

We used to

chaine-1.1.0-cp38-cp38-manylinux2014_x86_64.whl

but now

chaine-1.1.1-cp38-cp38-manylinux_2_27_x86_64.whl

which seems to be broken on some machines.

Model output path as argument

It would be helpful to have an option to define the output path of the model.crf.

Fix Python 3.10 wheel for Windows

For some reason the wheel build process fails for Python 3.10 on Windows: https://github.com/severinsimmler/chaine/runs/5529016996?check_suite_focus=true

Add support for Python 3.10

Where to set verbosity

Extend README

Export learned parameters to plain text

Parse binary model file
Write content to a human-readable format (e.g. JSON)

Drop support for Python 3.8

And update type hints

Improve release workflow

Manually increment version
Merge dev to master
Tag release
Automatic release by tag build

Write documentation for the Cython part

Refactor logger

Add info about features and learned weights

Set up GitHub pages with documentation

Allow int/float types as direct input features

int/float features like this [1, 19, 4, 0, 0, 0] are currently not supported by chaine. crfsuite_api.hpp only allows double at the moment, see:

chaine/chaine/crfsuite/include/crfsuite_api.hpp

Line 148 in 852ff92

Attribute(const std::string &name, double val) : attr(name), value(val)

EDIT: string types also work.
EDIT: float types doesn't work.

Make Cython module private

And create a high-level Python module using the private module. I think this is best practice.

Introduce data structure for labels

E.g. LabelSequence as a pendant to TokenSequence/Sequence

Make the high-level API more user friendly

Think about real-world scenarios how the library might be used

Error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1

Initial position:

Installing dependencies with poetry using poetry install (on WSL Ubuntu).

Error:

error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1

Solution:

sudo apt-get install build-essential

Improve build process

Commit the C++ files

Missing GLIBC_2.29

ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by /opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/chaine/crf.cpython-38-x86_64-linux-gnu.so)

Use POS tagger to extract features

Add POS tagger for realistic feature extraction: https://stanfordnlp.github.io/stanza/pos.html

Add LICENSE

Sample/label weighting to handle class imbalance

Resources:

Move ItemSequence class to its own file

Set up GitHub Actions

Run unit tests
Deploy wheels for Python 3.8 and 3.9 to PyPI
Tag and release snapshot on GitHub

Use own metrics for hyperparameter optimization

Accept a callable instead of a string

Add more pandas example

Write unit tests

Lightweight progress bar

Or something that displays loading data and current iteration + loss

Clean up the C libraries and resolve warnings

warning: chaine/crfsuite_api.pxd:53:4: 'messagefunc' redeclared
chaine/crfsuite/lib/cqdb/src/cqdb.c: In function ‘cqdb_to_id’:
chaine/crfsuite/lib/cqdb/src/cqdb.c:600:26: warning: variable ‘ksize’ set but not used [-Wunused-but-set-variable]
  600 |                 uint32_t ksize;
      |                          ^~~~~
In file included from /usr/include/string.h:519,
                 from chaine/crfsuite/lib/cqdb/src/cqdb.c:37:
In function ‘strncpy’,
    inlined from ‘cqdb_writer_close’ at chaine/crfsuite/lib/cqdb/src/cqdb.c:287:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘cqdb_reader’ at chaine/crfsuite/lib/cqdb/src/cqdb.c:503:9:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/crf1d_context.c:47:
chaine/crfsuite/lib/crf/src/vecmath.h: In function ‘_aligned_malloc’:
chaine/crfsuite/lib/crf/src/vecmath.h:50:15: warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
   50 |     int ret = posix_memalign(&p, alignment, size);
      |               ^~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/crf1d_context.c: In function ‘crf1dc_new’:
chaine/crfsuite/lib/crf/src/crf1d_context.c:74:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   74 |         if (ret = crf1dc_set_num_items(ctx, T))
      |             ^~~
chaine/crfsuite/lib/crf/src/crf1d_context.c: In function ‘crf1dc_score’:
chaine/crfsuite/lib/crf/src/crf1d_context.c:468:15: warning: unused variable ‘L’ [-Wunused-variable]
  468 |     const int L = ctx->num_labels;
      |               ^
chaine/crfsuite/lib/crf/src/crf1d_context.c:466:38: warning: unused variable ‘cur’ [-Wunused-variable]
  466 |     const floatval_t *state = NULL, *cur = NULL, *trans = NULL;
      |                                      ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_state_score’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:141:15: warning: unused variable ‘L’ [-Wunused-variable]
  141 |     const int L = crf1de->num_labels;
      |               ^
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_state_score_scaled’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:179:15: warning: unused variable ‘L’ [-Wunused-variable]
  179 |     const int L = crf1de->num_labels;
      |               ^
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_features_on_path’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:281:15: warning: unused variable ‘L’ [-Wunused-variable]
  281 |     const int L = crf1de->num_labels;
      |               ^
chaine/crfsuite/lib/crf/src/crf1d_encode.c:279:22: warning: unused variable ‘ctx’ [-Wunused-variable]
  279 |     crf1d_context_t *ctx = crf1de->ctx;
      |                      ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_observation_expectation’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:340:15: warning: unused variable ‘L’ [-Wunused-variable]
  340 |     const int L = crf1de->num_labels;
      |               ^
chaine/crfsuite/lib/crf/src/crf1d_encode.c:338:22: warning: unused variable ‘ctx’ [-Wunused-variable]
  338 |     crf1d_context_t *ctx = crf1de->ctx;
      |                      ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_model_expectation’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:397:41: warning: unused variable ‘trans’ [-Wunused-variable]
  397 |     const feature_refs_t *attr = NULL, *trans = NULL;
      |                                         ^~~~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_set_data’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:449:13: warning: variable ‘begin’ set but not used [-Wunused-but-set-variable]
  449 |     clock_t begin = 0;
      |             ^~~~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_save_model’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:583:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  583 |     if (ret = crf1dmw_open_features(writer))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:624:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  624 |             if (ret = crf1dmw_put_feature(writer, fmap[k], &feat))
      |                 ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:632:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  632 |     if (ret = crf1dmw_close_features(writer))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:638:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  638 |     if (ret = crf1dmw_open_labels(writer, L))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:648:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  648 |             if (ret = crf1dmw_put_label(writer, l, str))
      |                 ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:655:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  655 |     if (ret = crf1dmw_close_labels(writer))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:661:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  661 |     if (ret = crf1dmw_open_attrs(writer, B))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:673:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  673 |                 if (ret = crf1dmw_put_attr(writer, amap[a], str))
      |                     ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:681:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  681 |     if (ret = crf1dmw_close_attrs(writer))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:687:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  687 |     if (ret = crf1dmw_open_labelrefs(writer, L + 2))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:694:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  694 |         if (ret = crf1dmw_put_labelref(writer, l, edge, fmap))
      |             ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:699:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  699 |     if (ret = crf1dmw_close_labelrefs(writer))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:705:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  705 |     if (ret = crf1dmw_open_attrrefs(writer, B))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:714:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  714 |             if (ret = crf1dmw_put_attrref(writer, amap[a], attr, fmap))
      |                 ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:720:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  720 |     if (ret = crf1dmw_close_attrrefs(writer))
      |         ^~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:533:22: warning: unused variable ‘threshold’ [-Wunused-variable]
  533 |     const floatval_t threshold = 0.01;
      |                      ^~~~~~~~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:529:13: warning: variable ‘begin’ set but not used [-Wunused-but-set-variable]
  529 |     clock_t begin;
      |             ^~~~~
In file included from chaine/crfsuite/lib/crf/src/crf1d_encode.c:47:
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘crf1de_exchange_options’:
chaine/crfsuite/lib/crf/src/params.h:51:13: warning: variable ‘__ret’ set but not used [-Wunused-but-set-variable]
   51 |         int __ret = 0;                \
      |             ^~~~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c:750:5: note: in expansion of macro ‘BEGIN_PARAM_MAP’
  750 |     BEGIN_PARAM_MAP(params, mode)
      |     ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘encoder_viterbi’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:953:9: warning: unused variable ‘i’ [-Wunused-variable]
  953 |     int i;
      |         ^
chaine/crfsuite/lib/crf/src/crf1d_encode.c: In function ‘encoder_save_model’:
chaine/crfsuite/lib/crf/src/crf1d_encode.c:920:12: warning: ‘ret’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  920 |     return crf1de_save_model(crf1de, filename, w, self->ds->data->attrs, self->ds->data->labels, lg);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/crf1d_model.c: In function ‘crf1dmw_put_labelref’:
chaine/crfsuite/lib/crf/src/crf1d_model.c:521:21: warning: unused variable ‘offset’ [-Wunused-variable]
  521 |     uint32_t n = 0, offset = 0;
      |                     ^~~~~~
chaine/crfsuite/lib/crf/src/crf1d_model.c: In function ‘crf1dmw_put_attrref’:
chaine/crfsuite/lib/crf/src/crf1d_model.c:638:21: warning: unused variable ‘offset’ [-Wunused-variable]
  638 |     uint32_t n = 0, offset = 0;
      |                     ^~~~~~
chaine/crfsuite/lib/crf/src/crf1d_model.c: In function ‘crf1dmw_put_feature’:
chaine/crfsuite/lib/crf/src/crf1d_model.c:744:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
  744 |     if (fid != hfeat->num)
      |             ^~
In function ‘read_uint8’,
    inlined from ‘read_uint8_array’ at chaine/crfsuite/lib/crf/src/crf1d_model.c:173:20,
    inlined from ‘crf1dm_new_impl’ at chaine/crfsuite/lib/crf/src/crf1d_model.c:786:10:
chaine/crfsuite/lib/crf/src/crf1d_model.c:133:12: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=]
  133 |     *value = *buffer;
      |     ~~~~~~~^~~~~~~~~
chaine/crfsuite/lib/crf/src/crf1d_model.c: In function ‘crf1dm_new_impl’:
chaine/crfsuite/lib/crf/src/crf1d_model.c:66:13: note: at offset 0 to object ‘magic’ with size 4 declared here
   66 |     uint8_t magic[4];       /* File magic. */
      |             ^~~~~
chaine/crfsuite/lib/crf/src/crf1d_tag.c: In function ‘crf1dt_state_score’:
chaine/crfsuite/lib/crf/src/crf1d_tag.c:74:15: warning: unused variable ‘L’ [-Wunused-variable]
   74 |     const int L = crf1dt->num_labels;
      |               ^
chaine/crfsuite/lib/crf/src/crfsuite.c: In function ‘crfsuite_evaluation_output’:
chaine/crfsuite/lib/crf/src/crfsuite.c:482:44: warning: unused variable ‘lev’ [-Wunused-variable]
  482 |         const crfsuite_label_evaluation_t *lev = &eval->tbl[i];
      |                                            ^~~
chaine/crfsuite/lib/crf/src/crfsuite.c:475:15: warning: variable ‘lg’ set but not used [-Wunused-but-set-variable]
  475 |     logging_t lg;
      |               ^~
At top level:
chaine/crfsuite/lib/crf/src/crfsuite.c:325:14: warning: ‘safe_strncpy’ defined but not used [-Wunused-function]
  325 | static char *safe_strncpy(char *dst, const char *src, size_t n)
      |              ^~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/crfsuite_train.c: In function ‘crfsuite_train_train’:
chaine/crfsuite/lib/crf/src/crfsuite_train.c:140:11: warning: unused variable ‘algorithm’ [-Wunused-variable]
  140 |     char *algorithm = NULL;
      |           ^~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_arow.c:47:
chaine/crfsuite/lib/crf/src/vecmath.h: In function ‘_aligned_malloc’:
chaine/crfsuite/lib/crf/src/vecmath.h:50:15: warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
   50 |     int ret = posix_memalign(&p, alignment, size);
      |               ^~~~~~~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_arow.c:46:
chaine/crfsuite/lib/crf/src/train_arow.c: In function ‘exchange_options’:
chaine/crfsuite/lib/crf/src/params.h:51:13: warning: variable ‘__ret’ set but not used [-Wunused-but-set-variable]
   51 |         int __ret = 0;                \
      |             ^~~~~
chaine/crfsuite/lib/crf/src/train_arow.c:219:5: note: in expansion of macro ‘BEGIN_PARAM_MAP’
  219 |     BEGIN_PARAM_MAP(params, mode)
      |     ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_arow.c: In function ‘crfsuite_train_arow’:
chaine/crfsuite/lib/crf/src/train_arow.c:292:17: warning: unused variable ‘iteration_begin’ [-Wunused-variable]
  292 |         clock_t iteration_begin = clock();
      |                 ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_arow.c:291:20: warning: unused variable ‘norm’ [-Wunused-variable]
  291 |         floatval_t norm = 0., sum_loss = 0.;
      |                    ^~~~
chaine/crfsuite/lib/crf/src/train_arow.c:259:13: warning: unused variable ‘begin’ [-Wunused-variable]
  259 |     clock_t begin = clock();
      |             ^~~~~
chaine/crfsuite/lib/crf/src/train_arow.c:252:16: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable]
  252 |     floatval_t beta;
      |                ^~~~
At top level:
chaine/crfsuite/lib/crf/src/train_arow.c:212:19: warning: ‘tau2’ defined but not used [-Wunused-function]
  212 | static floatval_t tau2(floatval_t cost, floatval_t norm, floatval_t c)
      |                   ^~~~
chaine/crfsuite/lib/crf/src/train_arow.c:207:19: warning: ‘tau1’ defined but not used [-Wunused-function]
  207 | static floatval_t tau1(floatval_t cost, floatval_t norm, floatval_t c)
      |                   ^~~~
chaine/crfsuite/lib/crf/src/train_arow.c:202:19: warning: ‘tau0’ defined but not used [-Wunused-function]
  202 | static floatval_t tau0(floatval_t cost, floatval_t norm, floatval_t c)
      |                   ^~~~
chaine/crfsuite/lib/crf/src/train_arow.c:197:19: warning: ‘cost_sensitive’ defined but not used [-Wunused-function]
  197 | static floatval_t cost_sensitive(floatval_t err, floatval_t d)
      |                   ^~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_arow.c:192:19: warning: ‘cost_insensitive’ defined but not used [-Wunused-function]
  192 | static floatval_t cost_insensitive(floatval_t err, floatval_t d)
      |                   ^~~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_arow.c:166:13: warning: ‘delta_add’ defined but not used [-Wunused-function]
  166 | static void delta_add(delta_t *dc, floatval_t *w, floatval_t *ws, const floatval_t tau, const floatval_t u)
      |             ^~~~~~~~~
chaine/crfsuite/lib/crf/src/train_arow.c:153:19: warning: ‘delta_norm2’ defined but not used [-Wunused-function]
  153 | static floatval_t delta_norm2(delta_t *dc)
      |                   ^~~~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c:47:
chaine/crfsuite/lib/crf/src/vecmath.h: In function ‘_aligned_malloc’:
chaine/crfsuite/lib/crf/src/vecmath.h:50:15: warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
   50 |     int ret = posix_memalign(&p, alignment, size);
      |               ^~~~~~~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c:46:
chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c: In function ‘exchange_options’:
chaine/crfsuite/lib/crf/src/params.h:51:13: warning: variable ‘__ret’ set but not used [-Wunused-but-set-variable]
   51 |         int __ret = 0;                \
      |             ^~~~~
chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c:91:5: note: in expansion of macro ‘BEGIN_PARAM_MAP’
   91 |     BEGIN_PARAM_MAP(params, mode)
      |     ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c: In function ‘crfsuite_train_averaged_perceptron’:
chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c:156:17: warning: unused variable ‘iteration_begin’ [-Wunused-variabl]
  156 |         clock_t iteration_begin = clock();
      |                 ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c:155:20: warning: unused variable ‘norm’ [-Wunused-variable]
  155 |         floatval_t norm = 0., loss = 0.;
      |                    ^~~~
chaine/crfsuite/lib/crf/src/train_averaged_perceptron.c:126:13: warning: unused variable ‘begin’ [-Wunused-variable]
  126 |     clock_t begin = clock();
      |             ^~~~~
In file included from chaine/crfsuite/lib/crf/src/train_l2sgd.c:108:
chaine/crfsuite/lib/crf/src/vecmath.h: In function ‘_aligned_malloc’:
chaine/crfsuite/lib/crf/src/vecmath.h:50:15: warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
   50 |     int ret = posix_memalign(&p, alignment, size);
      |               ^~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c: In function ‘l2sgd’:
chaine/crfsuite/lib/crf/src/train_l2sgd.c:151:23: warning: unused variable ‘clk_begin’ [-Wunused-variable]
  151 |     clock_t clk_prev, clk_begin = clock();
      |                       ^~~~~~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c:151:13: warning: variable ‘clk_prev’ set but not used [-Wunused-but-set-variable]
  151 |     clock_t clk_prev, clk_begin = clock();
      |             ^~~~~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c: In function ‘l2sgd_calibration’:
chaine/crfsuite/lib/crf/src/train_l2sgd.c:296:13: warning: unused variable ‘clk_begin’ [-Wunused-variable]
  296 |     clock_t clk_begin = clock();
      |             ^~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_l2sgd.c:106:
chaine/crfsuite/lib/crf/src/train_l2sgd.c: In function ‘exchange_options’:
chaine/crfsuite/lib/crf/src/params.h:51:13: warning: variable ‘__ret’ set but not used [-Wunused-but-set-variable]
   51 |         int __ret = 0;                \
      |             ^~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c:393:5: note: in expansion of macro ‘BEGIN_PARAM_MAP’
  393 |     BEGIN_PARAM_MAP(params, mode)
      |     ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c: In function ‘crfsuite_train_l2sgd’:
chaine/crfsuite/lib/crf/src/train_l2sgd.c:447:15: warning: unused variable ‘T’ [-Wunused-variable]
  447 |     const int T = gm->cap_items;
      |               ^
chaine/crfsuite/lib/crf/src/train_l2sgd.c:443:13: warning: variable ‘clk_begin’ set but not used [-Wunused-but-set-variable]
  443 |     clock_t clk_begin;
      |             ^~~~~~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c:241:13: warning: ‘eta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  241 |             logging(lg, "Epoch %d, learning rate: %f, training loss: %f", epoch, eta, sum_loss);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_l2sgd.c:146:16: note: ‘eta’ was declared here
  146 |     floatval_t eta, gain, decay = 1.;
      |                ^~~
In file included from chaine/crfsuite/lib/crf/src/train_lbfgs.c:50:
chaine/crfsuite/lib/crf/src/vecmath.h: In function ‘_aligned_malloc’:
chaine/crfsuite/lib/crf/src/vecmath.h:50:15: warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
   50 |     int ret = posix_memalign(&p, alignment, size);
      |               ^~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_lbfgs.c: In function ‘lbfgs_progress’:
chaine/crfsuite/lib/crf/src/train_lbfgs.c:127:13: warning: variable ‘duration’ set but not used [-Wunused-but-set-variable]
  127 |     clock_t duration, clk = clock();
      |             ^~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_lbfgs.c:49:
chaine/crfsuite/lib/crf/src/train_lbfgs.c: In function ‘exchange_options’:
chaine/crfsuite/lib/crf/src/params.h:51:13: warning: variable ‘__ret’ set but not used [-Wunused-but-set-variable]
   51 |         int __ret = 0;                \
      |             ^~~~~
chaine/crfsuite/lib/crf/src/train_lbfgs.c:160:5: note: in expansion of macro ‘BEGIN_PARAM_MAP’
  160 |     BEGIN_PARAM_MAP(params, mode)
      |     ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_lbfgs.c: In function ‘crfsuite_train_lbfgs’:
chaine/crfsuite/lib/crf/src/train_lbfgs.c:217:15: warning: unused variable ‘A’ [-Wunused-variable]
  217 |     const int A = trainset->data->attrs->num(trainset->data->attrs);
      |               ^
chaine/crfsuite/lib/crf/src/train_lbfgs.c:216:15: warning: unused variable ‘L’ [-Wunused-variable]
  216 |     const int L = trainset->data->labels->num(trainset->data->labels);
      |               ^
chaine/crfsuite/lib/crf/src/train_lbfgs.c:215:15: warning: unused variable ‘N’ [-Wunused-variable]
  215 |     const int N = trainset->num_instances;
      |               ^
chaine/crfsuite/lib/crf/src/train_lbfgs.c:214:13: warning: unused variable ‘begin’ [-Wunused-variable]
  214 |     clock_t begin = clock();
      |             ^~~~~
In file included from chaine/crfsuite/lib/crf/src/train_passive_aggressive.c:47:
chaine/crfsuite/lib/crf/src/vecmath.h: In function ‘_aligned_malloc’:
chaine/crfsuite/lib/crf/src/vecmath.h:50:15: warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
   50 |     int ret = posix_memalign(&p, alignment, size);
      |               ^~~~~~~~~~~~~~
In file included from chaine/crfsuite/lib/crf/src/train_passive_aggressive.c:46:
chaine/crfsuite/lib/crf/src/train_passive_aggressive.c: In function ‘exchange_options’:
chaine/crfsuite/lib/crf/src/params.h:51:13: warning: variable ‘__ret’ set but not used [-Wunused-but-set-variable]
   51 |         int __ret = 0;                \
      |             ^~~~~
chaine/crfsuite/lib/crf/src/train_passive_aggressive.c:221:5: note: in expansion of macro ‘BEGIN_PARAM_MAP’
  221 |     BEGIN_PARAM_MAP(params, mode)
      |     ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_passive_aggressive.c: In function ‘crfsuite_train_passive_aggressive’:
chaine/crfsuite/lib/crf/src/train_passive_aggressive.c:328:17: warning: unused variable ‘iteration_begin’ [-Wunused-variable]
  328 |         clock_t iteration_begin = clock();
      |                 ^~~~~~~~~~~~~~~
chaine/crfsuite/lib/crf/src/train_passive_aggressive.c:327:20: warning: unused variable ‘norm’ [-Wunused-variable]
  327 |         floatval_t norm = 0., sum_loss = 0.;
      |                    ^~~~
chaine/crfsuite/lib/crf/src/train_passive_aggressive.c:270:13: warning: unused variable ‘begin’ [-Wunused-variable]
  270 |     clock_t begin = clock();
      |             ^~~~~

Extend high-level API

Add a chaine.load() function.

Stress test with a massive data set

And profile to identify bottlenecks (both speed and memory)

Add some real-world examples

Hyperparameter optimization

Add a module to optimize hyperparameters in a convenient way.

Make Cython module private

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