David Kartchner

Have been using rmate for over a year and it suddenly stopped working on one of my remote servers. I get the error: "Exception: Could not connect to textmate: Connection...

## Describe the bug Some entity offsets for bc5cdr are off by a few characters ## Steps to reproduce the bug ```python from bigbio.dataloader import BigBioConfigHelpers data = conhelps.for_config_name("bc5cdr_bigbio_kb").load_dataset() for...

Closes #637

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Add the plant-phenotype dataset. Closes #637 New location for dataset (that corrects errors of nested/missing entities): https://github.com/davidkartchner/PPRcorpus ### Checkbox - [x] Confirm that this PR is linked to the dataset...

Create dataset loader for plant normalization

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## Adding a Dataset - **Name:** *PlantNorm* - **Description:** *Named entity disambiguation dataset for plants from PubMed abstracts* - **Task:** *NER, NED* - **Paper:** [*A method for named entity normalization...

Create dataset loader for Plant-Disease corpus

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## Adding a Dataset - **Name:** *plant-disease* - **Description:** *Dataset with tagged plant/disease entities, as well as relations on how the plants affect the tagged diseases* - **Task:** *NER, RE*...

Create dataset loader for PPR corpus

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## Adding a Dataset - **Name:** *PPR Plant Phenotype Relation corpus* - **Description:** *Dataset with plant and phenotype mentions, as well as relations of how plants/plant extracts affect the phenotypes*...

### Closes 912 - [x] Confirm that this PR is linked to the dataset issue. - [x] Create the dataloader script `hub/hub_repos/my_dataset/my_dataset.py` (please use only lowercase and underscore for dataset...

## Adding a Dataset - **Name:** *SourceData NLP* - **Description:** *SourceData-NLP is a named entity recognition and entity linking/disambiguation dataset produced through the routine curation of papers during the publication...

Error in text capture

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Hello and thank you for the great annotation tool! I am working on a biomedical annotation project with LEAN-LIFE but am encountering errors when I try to capture entity spans....

gemma-3-27b-it runs out of memory during warmup

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### System Info Using NC96ads node from Azure with 4 80 GB A100 GPUs and 866 GB RAM. Trying to host `google/gemma-3-27b-it` sharded across 4 nodes. ### Information - [x]...