Update README.md
Browse files
README.md
CHANGED
|
@@ -13,7 +13,7 @@ pipeline_tag: token-classification
|
|
| 13 |
# 🦠 MicrobELP — Microbiome Entity Recognition
|
| 14 |
|
| 15 |
MicrobELP is a deep learning model for Microbiome Entity Recognition, identifying microbial entities (bacteria, archaea, fungi) in biomedical and scientific text.
|
| 16 |
-
It is part of the [microbELP](https://github.com/omicsNLP/microbELP) toolkit and has been optimised for GPU inference.
|
| 17 |
|
| 18 |
This model enables automated extraction of microbiome names from unstructured text, facilitating microbiome-related text mining and literature curation.
|
| 19 |
|
|
@@ -68,7 +68,7 @@ pip install ./microbELP
|
|
| 68 |
|
| 69 |
It is recommended to install in an isolated environment due to dependencies.
|
| 70 |
|
| 71 |
-
Example Usage
|
| 72 |
|
| 73 |
```python
|
| 74 |
from microbELP import microbiome_DL_ner
|
|
@@ -103,6 +103,8 @@ Output:
|
|
| 103 |
```
|
| 104 |
Each element in the output corresponds to one input text, containing recognised microbiome entities and their text locations.
|
| 105 |
|
|
|
|
|
|
|
| 106 |
---
|
| 107 |
|
| 108 |
## 📘 Model Details
|
|
|
|
| 13 |
# 🦠 MicrobELP — Microbiome Entity Recognition
|
| 14 |
|
| 15 |
MicrobELP is a deep learning model for Microbiome Entity Recognition, identifying microbial entities (bacteria, archaea, fungi) in biomedical and scientific text.
|
| 16 |
+
It is part of the [microbELP](https://github.com/omicsNLP/microbELP) toolkit and has been optimised for CPU and GPU inference.
|
| 17 |
|
| 18 |
This model enables automated extraction of microbiome names from unstructured text, facilitating microbiome-related text mining and literature curation.
|
| 19 |
|
|
|
|
| 68 |
|
| 69 |
It is recommended to install in an isolated environment due to dependencies.
|
| 70 |
|
| 71 |
+
Example Usage
|
| 72 |
|
| 73 |
```python
|
| 74 |
from microbELP import microbiome_DL_ner
|
|
|
|
| 103 |
```
|
| 104 |
Each element in the output corresponds to one input text, containing recognised microbiome entities and their text locations.
|
| 105 |
|
| 106 |
+
There is one optional parameter to this function called `cpu` <type 'bool'>, the default value is False, i.e. runs on a GPU if any are available. If you want to force the usage of the CPU, you will need to use `microbiome_DL_ner(input_list, cpu = True)`.
|
| 107 |
+
|
| 108 |
---
|
| 109 |
|
| 110 |
## 📘 Model Details
|