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RSchmirler · Jun 3, 2024 · 0719329 · 0719329
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diff --git a/MIT-LICENSE.txt b/MIT-LICENSE.txt
@@ -0,0 +1,20 @@
+Copyright 2024 Robert Schmirler and others
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
@@ -16,4 +16,6 @@ We also provide Notebooks to reproduce our work, inlcuding examples.
 
 **License**
 
-   This data repository is released under terms of the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/).
+   The data in this repository is released under terms of the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/).
+
+   The source code in this repository is licensed under the MIT license, which you can find in the MIT-LICENSE.txt file.
diff --git a/SOM data/Figure S1 top level upper bound.csv b/SOM data/Figure S1 top level upper bound.csv
diff --git a/SOM data/Figure S2 ESM650 finetune vs PEFT.csv b/SOM data/Figure S2 ESM650 finetune vs PEFT.csv
diff --git a/SOM data/Table S10 & S12 finetune agg upper bound.csv b/SOM data/Table S10 & S12 finetune agg upper bound.csv
diff --git a/SOM data/Table S2 finetuning.csv b/SOM data/Table S2 finetuning.csv
diff --git a/SOM data/Table S4 & S6 finetuning aggregated.csv b/SOM data/Table S4 & S6 finetuning aggregated.csv
diff --git a/SOM data/Table S8 finetuning parameter.csv b/SOM data/Table S8 finetuning parameter.csv
diff --git a/data/Figure 1 top level.csv b/data/Figure 1 top level.csv
diff --git a/notebooks/embedding/README.md b/notebooks/embedding/README.md
@@ -38,4 +38,6 @@ Important Notes:
 
 7. **License**
 
-   This repository is released under terms of the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/).
+   The data in this repository is released under terms of the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/).
+
+   The source code in this repository is licensed under the MIT license, which you can find in the MIT-LICENSE.txt file.
diff --git a/notebooks/finetune/README.md b/notebooks/finetune/README.md
@@ -32,7 +32,7 @@ Important Notes:
 5. **Advice for memory efficient use**
     - always use mixed precision training 
     - if GPU memory overflow occurs, reduce batch size to 1 and simulated the desired batch size using gradient accumulation
-    - if GPU memory still overflows, enable deepspeed to utilize cpu offloading
+    - if GPU memory still overflows, enable DeepSpeed to utilize CPU offloading
     - if GPU memory still overflows, remove(or truncate) long sequences
 
 6. **Cite**
@@ -41,4 +41,6 @@ Important Notes:
 
 7. **License**
 
-   This repository is released under terms of the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/).
+   The data in this repository is released under terms of the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/).
+
+   The source code in this repository is licensed under the MIT license, which you can find in the MIT-LICENSE.txt file.
diff --git a/source_data_SOM/Figure S1_GPU requirements - embedding creation.csv b/source_data_SOM/Figure S1_GPU requirements - embedding creation.csv
@@ -0,0 +1,9 @@
+Model;8GB;16GB;24GB
+ESM2 8M;9500;10000;
+ESM2 35M;9500;10000;
+ESM2 150M;9500;10000;
+ESM2 650M;7000;10000;
+Ankh Base;5000;7000;8500
+ProtT5;3000;5000;8500
+Ankh Large;5000;7000;8500
+ESM2 3B;2500;7500;10000
diff --git a/source_data_SOM/Figure S2_LoRA compared to fine-tuning full models.csv b/source_data_SOM/Figure S2_LoRA compared to fine-tuning full models.csv
@@ -0,0 +1,10 @@
+;ESM2 8M;CI ESM2 8M;ESM2 35M;CI ESM2 35M;ESM2 150M;CI ESM2 150M;ESM2 650M;CI ESM2 650M
+Stability;0,2;5,1;-2,1;1,9;6,3;2;5,7;5,8
+GFP;0,2;0,5;0,4;0,3;0,5;0,4;0,6;0,5
+AAV;-3;4,7;-0,3;6,5;-1,2;3,1;3,3;5,8
+GB1;-3,6;1,8;-0,9;1,1;-0,5;0,9;0,3;1,6
+Meltome;-1,2;2,9;-1,9;3,9;-3,6;2,6;-4;3,4
+Subcellular location;0;2,1;-0,2;1,9;-1,2;2;0,1;1,9
+Disorder;-4,9;1,9;-4,4;1,6;-4,7;1,7;-0,3;0,9
+Secondary structure;-0,2;0,2;-0,3;0,1;-0,4;0,2;-0,1;0,1
+Mean;-1,6;;-1,2;;-0,6;;0,7;