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...
This is of low priority, but eventually we would need to support multiple types of input format (BioC, Standoff, etc). What this really means, is that we need to convert...
With the web-service, you can provide a `PMID` which will be fetched and annotated. You cannot currently do this with `Saber.annotate()`. Fix!
It would be useful if saber came with a default dataset (pointed to by the default config file). This would make it easier to follow along with the notebook (which...
It would be useful to add more performance metrics like AuROC, AuPR, TP, FP, FN. These should be printed by default in the table displayed after each epoch. **TODO** -...
Currently, 'loading' a model loads its architecture and its weights, which is useful for transfer learning. However, a mechanism for loading the entire model, including the state of the optimizer,...
Implement some mechanism for freezing certain layers during a transfer (i.e., learned weights are transferred but not updated) and another mechanism for loading only the weights from certain layers. **TODOS**...
For now, this is low on the priority scale, but is something we will likely have to implement. Many text-mining tools include simple web interfaces for annotating text ([ex](http://agathon.sista.arizona.edu:8080/odinweb/bio/enterText), [ex](http://bioinformatics.ua.pt/becas/#!/),...
I tried using `pip install git+https://github.com/BaderLab/saber.git` and got the following response: ```pip install git+https://github.com/BaderLab/saber.git Collecting git+https://github.com/BaderLab/saber.git Cloning https://github.com/BaderLab/saber.git to c:\users\deploy\appdata\local\temp\pip-req-build-cao6qk8t Running command git clone --filter=blob:none --quiet https://github.com/BaderLab/saber.git 'C:\Users\deploy\AppData\Local\Temp\pip-req-build-cao6qk8t' Resolved https://github.com/BaderLab/saber.git...
