Datasets:
add strand numbers and citation
Browse files
README.md
CHANGED
|
@@ -129,8 +129,6 @@ ExomeBench includes **five supervised tasks**, each framed as a classification p
|
|
| 129 |
|
| 130 |
## 4. SOTA Model Performances
|
| 131 |
|
| 132 |
-
<div align="center">
|
| 133 |
-
|
| 134 |
<table border="1" cellspacing="0" cellpadding="8">
|
| 135 |
<thead>
|
| 136 |
<tr>
|
|
@@ -146,37 +144,44 @@ ExomeBench includes **five supervised tasks**, each framed as a classification p
|
|
| 146 |
</tr>
|
| 147 |
</thead>
|
| 148 |
<tbody>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 149 |
<tr>
|
| 150 |
<td>DNABERT-2</td>
|
| 151 |
-
<td align="center">0.
|
| 152 |
-
<td align="center">0.
|
| 153 |
-
<td align="center">0.
|
| 154 |
-
<td align="center">0.
|
| 155 |
-
<td align="center">0.
|
| 156 |
</tr>
|
| 157 |
<tr>
|
| 158 |
<td>HyenaDNA</td>
|
| 159 |
-
<td align="center">0.
|
| 160 |
-
<td align="center">0.
|
| 161 |
-
<td align="center">0.
|
| 162 |
-
<td align="center">0.
|
| 163 |
-
<td align="center">0.
|
| 164 |
</tr>
|
| 165 |
<tr>
|
| 166 |
<td>NT-Multispecies-2.5B</td>
|
| 167 |
-
<td align="center">0.
|
| 168 |
-
<td align="center">0.
|
| 169 |
-
<td align="center">0.
|
| 170 |
-
<td align="center">0.
|
| 171 |
-
<td align="center">0.
|
| 172 |
</tr>
|
| 173 |
</tbody>
|
| 174 |
</table>
|
| 175 |
|
| 176 |
</div>
|
| 177 |
|
| 178 |
-
> **Note**: For some models and tasks, the seed settings in the [STRAND paper](https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5183178) were slightly different from those used in this repository, which may lead to minor variations in the reported results.
|
| 179 |
-
|
| 180 |
|
| 181 |
## 5. Usage
|
| 182 |
```python
|
|
|
|
| 129 |
|
| 130 |
## 4. SOTA Model Performances
|
| 131 |
|
|
|
|
|
|
|
| 132 |
<table border="1" cellspacing="0" cellpadding="8">
|
| 133 |
<thead>
|
| 134 |
<tr>
|
|
|
|
| 144 |
</tr>
|
| 145 |
</thead>
|
| 146 |
<tbody>
|
| 147 |
+
<tr>
|
| 148 |
+
<td>STRAND<sup><a href="#citation">[1]</a></sup></td>
|
| 149 |
+
<td align="center"><strong>0.360</strong></td>
|
| 150 |
+
<td align="center"><strong>0.937</strong></td>
|
| 151 |
+
<td align="center"><strong>0.774</strong></td>
|
| 152 |
+
<td align="center"><strong>0.877</strong></td>
|
| 153 |
+
<td align="center"><strong>0.996</strong></td>
|
| 154 |
+
</tr>
|
| 155 |
<tr>
|
| 156 |
<td>DNABERT-2</td>
|
| 157 |
+
<td align="center">0.162</td>
|
| 158 |
+
<td align="center">0.876</td>
|
| 159 |
+
<td align="center">0.549</td>
|
| 160 |
+
<td align="center">0.552</td>
|
| 161 |
+
<td align="center">0.996</td>
|
| 162 |
</tr>
|
| 163 |
<tr>
|
| 164 |
<td>HyenaDNA</td>
|
| 165 |
+
<td align="center">0.135</td>
|
| 166 |
+
<td align="center">0.816</td>
|
| 167 |
+
<td align="center">0.445</td>
|
| 168 |
+
<td align="center">0.700</td>
|
| 169 |
+
<td align="center">0.994</td>
|
| 170 |
</tr>
|
| 171 |
<tr>
|
| 172 |
<td>NT-Multispecies-2.5B</td>
|
| 173 |
+
<td align="center">0.306</td>
|
| 174 |
+
<td align="center">0.624</td>
|
| 175 |
+
<td align="center">0.293</td>
|
| 176 |
+
<td align="center">0.422</td>
|
| 177 |
+
<td align="center">0.991</td>
|
| 178 |
</tr>
|
| 179 |
</tbody>
|
| 180 |
</table>
|
| 181 |
|
| 182 |
</div>
|
| 183 |
|
| 184 |
+
> **Note**: For some models and tasks, the seed settings in the [STRAND paper](https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5183178) were slightly different from those used in this repository, which may lead to minor variations in the reported results. Due to this, on an overly saturated tasks like TFG, you might observe a small discrepancy in the ordering of models based on MCC values compared to those reported in the paper.
|
|
|
|
| 185 |
|
| 186 |
## 5. Usage
|
| 187 |
```python
|