Gabriel Altay

Removing (token level) entity information from doc.

2

## How to reproduce the behaviour EntityRuler is run as in example from docs here https://spacy.io/usage/rule-based-matching#entityruler-ent-ids Suppose someone has a series of pipeline components that run after some entities are...

Hello, neo4j version: 3.5.25 spatial jar file: neo4j-spatial-0.26.2-neo4j-3.5.2-server-plugin.jar I seem to be getting inconsistent results (or I'm not understanding the procedures) from `spatial.closest` and `spatial.withinDistance`. If I load the following...

Create methods to randomly sample distances along the curve and to randomly sample points in the n-d space.

Create a unit test that assert bibtex citations exist and that they can be parsed correctly.

chemdner kb implementation needs normalizations

1

https://github.com/bigscience-workshop/biomedical/blob/master/bigbio/biodatasets/chemdner/chemdner.py https://github.com/bigscience-workshop/biomedical/pull/326 the current implementation says it supports the text classification and named entity recognition tasks. the text classification tasks has MESH codes but the NER task does not. this...

https://github.com/bigscience-workshop/biomedical/blob/master/bigbio/biodatasets/ntcir_13_medweb/ntcir_13_medweb.py this is a text classification on tweets task for config = `ntcir_13_medweb_classification_en_bigbio_text` it appears that all tweets with a given label are in one sample this issue is to...

``` In [3]: dsd = load_dataset('bigbio/biodatasets/psytar/psytar.py', name='psytar_bigbio_text', data_dir='/home/galtay/data/ ...: bigbio/psytar/PsyTAR_dataset.xlsx') Using custom data configuration psytar_bigbio_text-7247dd615c830efa Reusing dataset psy_tar_dataset (/home/galtay/.cache/huggingface/datasets/psy_tar_dataset/psytar_bigbio_text-7247dd615c830efa/1.0.0/149b2465b2445f8a388bc2f7af48f0d136d246f718f59743564f154ea3c2dfbf) 100%|████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00

What exactly are the differences between the gnormplus dataset and the biocreative II datasets (BC2GM & BC2GN) * https://biocreative.bioinformatics.udel.edu/resources/corpora/biocreative-ii-corpus/ * https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/ currently only gnormplus is implemented https://github.com/bigscience-workshop/biomedical/blob/master/bigbio/biodatasets/gnormplus/gnormplus.py but BLURB uses...

bc5cdr drug/chemical counts dont match paper

3

When I count the number of chemical and disease entities in the different splits of bc5cdr, I get different numbers than what is reported in the paper and in BLURB...