saber
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BaderLab
Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not st...
Need to train models for each major entity class: `PRGE`, `LIVB`, `DISO`, `CHED`. The first three are fairly straight-forward. As for the last, there are multiple levels of granularity to...
Updates the requirements on [spacy](https://github.com/explosion/spaCy) to permit the latest version. Release notes Sourced from spacy's releases. v2.3.2: Improved Korean tokenizer speed, experimental character-based pretraining and bug fixes ✨ New features...
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Bumps [keras](https://github.com/keras-team/keras) from 2.2.4 to 2.4.3. Release notes Sourced from keras's releases. Keras 2.4.0 As previously announced, we have discontinued multi-backend Keras to refocus exclusively on the TensorFlow implementation of...
Bumps [msgpack](https://github.com/msgpack/msgpack-python) from 0.5.6 to 1.0.0. Changelog Sourced from msgpack's changelog. 1.0.0 Release Date: 2020-02-17 Remove Python 2 support from the msgpack/_cmsgpack. msgpack/fallback still supports Python 2. Remove encoding option...
The PyTorch Transformer library recently added a new `AutoModel` API, which lets you instantiate one of the many pre-trained transformers that are available (BERT, GPT-2, RoBERTa, etc.). We should switch...
When batching data, Saber truncates / right-pads each sequence to match a length of `saber.constants.MAX_SENT_LEN`. Truncating sequences should only happen on the train set, ensuring that we don't drop examples...
Currently, we are using `keras.preprocessing.text` to pad sequences. This function is easy to use and convenient, but given that we have dropped Keras support (#157) we will need to find...
There is currently no easy way to evaluate a trained model. There should be some kind of interface for this, e.g. ```python from saber import Saber sb = Saber() sb.load('path/to/some/model')...
Use a decorator to time functions in saber class. https://realpython.com/primer-on-python-decorators/
In the docs, models for each major entity type are listed, but not all of them are implemented. The user should get an error when they try to load these...