diff --git a/README.md b/README.md
index a77f005..71d103a 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,17 @@
-
Genomic Embedding Benchmark
+Diverse Genomic Embedding Benchmark
-
-
+
+
-
-
+
+
-
-
+
+
@@ -19,53 +19,51 @@
Installation |
Usage |
- Leaderboard |
+ Leaderboard |
Documentation |
Citing
-
+
## Installation
TODO(joshua):
+
```bash
-pip install geb
+pip install dgeb
```
## Usage
-- Using the python script (see [run_geb.py](https://github.com/tattabio/geb/blob/main/run_geb.py)):
+- Using the python script (see [run_dgeb.py](https://github.com/tattabio/geb/blob/main/run_geb.py)):
```bash
-python run_geb.py --model facebook/esm2_t6_8M_UR50D
+python run_dgeb.py --model facebook/esm2_t6_8M_UR50D
```
-
- Using the python API:
```py
-import geb
+import dgeb
-model = geb.get_model("facebook/esm2_t6_8M_UR50D")
-tasks = geb.get_tasks_by_modality(geb.Modality.PROTEIN)
-evaluation = geb.GEB(tasks=tasks)
+model = dgeb.get_model("facebook/esm2_t6_8M_UR50D")
+tasks = dgeb.get_tasks_by_modality(geb.Modality.PROTEIN)
+evaluation = dgeb.DGEB(tasks=tasks)
evaluation.run(model, output_folder="results")
```
-
### Using a custom model
-Custom models should be wrapped with the `geb.models.BioSeqTransformer` abstract class, and specify the modality, number of layers, and embedding dimension. See see [models.py](https://github.com/tattabio/geb/blob/main/geb/models.py) for additional examples on custom model loading and inference.
-
+Custom models should be wrapped with the `dgeb.models.BioSeqTransformer` abstract class, and specify the modality, number of layers, and embedding dimension. See see [models.py](https://github.com/tattabio/geb/blob/main/geb/models.py) for additional examples on custom model loading and inference.
```python
-import geb
-from geb.models import BioSeqTransformer
-from geb.modality import Modality
+import dgeb
+from dgeb.models import BioSeqTransformer
+from dgeb.modality import Modality
class MyModel(BioSeqTransformer):
@@ -83,20 +81,20 @@ class MyModel(BioSeqTransformer):
model = MyModel()
-tasks = geb.get_tasks_by_modality(model.modality)
+tasks = dgeb.get_tasks_by_modality(model.modality)
evaluation = MTEB(tasks=tasks)
evaluation.run(model)
```
### Evaluating on a custom dataset
-TODO(andre): Update this section
+TODO(andre): Update this section
To evaluate on a custom task, you can run the following code on your custom task.
```python
-import geb
-from geb.tasks import AbsTask
+import dgeb
+from dgeb.tasks import AbsTask
class MyCustomTask(AbsTask):
def run(
@@ -104,8 +102,8 @@ class MyCustomTask(AbsTask):
) -> TaskResult:
pass
-model = geb.models.ESM("facebook/esm2_t6_8M_UR50D")
-evaluation = geb.GEB(tasks=[MyCustomTask()])
+model = dgeb.models.ESM("facebook/esm2_t6_8M_UR50D")
+evaluation = dgeb.DGEB(tasks=[MyCustomTask()])
evaluation.run(model)
```
@@ -113,8 +111,8 @@ evaluation.run(model)
## Citing
-GEB was introduced in "[GEB: Genomic Embedding Benchmark]()", feel free to cite:
+dgeb was introduced in "[DGEB: Diverse Genomic Embedding Benchmark]()", feel free to cite:
TODO(andre): bibtex
-For works that have used GEB for benchmarking, you can find them on the [leaderboard](https://huggingface.co/spaces/tattabio/GEB/leaderboard).
+For works that have used dgeb for benchmarking, you can find them on the [leaderboard](https://huggingface.co/spaces/tattabio/DGEB/leaderboard).
diff --git a/geb/__init__.py b/dgeb/__init__.py
similarity index 100%
rename from geb/__init__.py
rename to dgeb/__init__.py
diff --git a/geb/geb.py b/dgeb/dgeb.py
similarity index 100%
rename from geb/geb.py
rename to dgeb/dgeb.py
diff --git a/geb/eval_utils.py b/dgeb/eval_utils.py
similarity index 100%
rename from geb/eval_utils.py
rename to dgeb/eval_utils.py
diff --git a/geb/evaluators.py b/dgeb/evaluators.py
similarity index 100%
rename from geb/evaluators.py
rename to dgeb/evaluators.py
diff --git a/geb/modality.py b/dgeb/modality.py
similarity index 100%
rename from geb/modality.py
rename to dgeb/modality.py
diff --git a/geb/models.py b/dgeb/models.py
similarity index 100%
rename from geb/models.py
rename to dgeb/models.py
diff --git a/geb/results.py b/dgeb/results.py
similarity index 100%
rename from geb/results.py
rename to dgeb/results.py
diff --git a/geb/tasks/__init__.py b/dgeb/tasks/__init__.py
similarity index 100%
rename from geb/tasks/__init__.py
rename to dgeb/tasks/__init__.py
diff --git a/geb/tasks/bigene_mining_tasks.py b/dgeb/tasks/bigene_mining_tasks.py
similarity index 100%
rename from geb/tasks/bigene_mining_tasks.py
rename to dgeb/tasks/bigene_mining_tasks.py
diff --git a/geb/tasks/classification_tasks.py b/dgeb/tasks/classification_tasks.py
similarity index 100%
rename from geb/tasks/classification_tasks.py
rename to dgeb/tasks/classification_tasks.py
diff --git a/geb/tasks/clustering_tasks.py b/dgeb/tasks/clustering_tasks.py
similarity index 100%
rename from geb/tasks/clustering_tasks.py
rename to dgeb/tasks/clustering_tasks.py
diff --git a/geb/tasks/eds_tasks.py b/dgeb/tasks/eds_tasks.py
similarity index 100%
rename from geb/tasks/eds_tasks.py
rename to dgeb/tasks/eds_tasks.py
diff --git a/geb/tasks/pair_classification_tasks.py b/dgeb/tasks/pair_classification_tasks.py
similarity index 100%
rename from geb/tasks/pair_classification_tasks.py
rename to dgeb/tasks/pair_classification_tasks.py
diff --git a/geb/tasks/retrieval_tasks.py b/dgeb/tasks/retrieval_tasks.py
similarity index 100%
rename from geb/tasks/retrieval_tasks.py
rename to dgeb/tasks/retrieval_tasks.py
diff --git a/geb/tasks/tasks.py b/dgeb/tasks/tasks.py
similarity index 100%
rename from geb/tasks/tasks.py
rename to dgeb/tasks/tasks.py
diff --git a/plot_benchmarks.py b/plot_benchmarks.py
index 1d75ceb..7de5e30 100644
--- a/plot_benchmarks.py
+++ b/plot_benchmarks.py
@@ -10,8 +10,8 @@
import pandas as pd
import seaborn as sns
-from geb.geb import get_all_tasks, get_output_folder, get_tasks_by_name
-from geb.tasks.tasks import TaskResult
+from dgeb.geb import get_all_tasks, get_output_folder, get_tasks_by_name
+from dgeb.tasks.tasks import TaskResult
ALL_TASKS = [task.metadata.id for task in get_all_tasks()]
diff --git a/run_geb.py b/run_dgeb.py
similarity index 100%
rename from run_geb.py
rename to run_dgeb.py