├── .gitmodules ├── Benchmark ├── ProtAlbert.ipynb ├── ProtBert.ipynb ├── ProtElectra.ipynb └── ProtXLNet.ipynb ├── Embedding ├── Onnx │ └── ProtBert-BFD.ipynb ├── PyTorch │ ├── Advanced │ │ ├── ProtAlbert.ipynb │ │ ├── ProtBert-BFD.ipynb │ │ ├── ProtBert.ipynb │ │ ├── ProtElectra.ipynb │ │ ├── ProtT5-XL-BFD.ipynb │ │ ├── ProtT5-XL-UniRef50.ipynb │ │ └── ProtXLNet.ipynb │ ├── Basic │ │ ├── ProtAlbert.ipynb │ │ ├── ProtBert-BFD.ipynb │ │ ├── ProtBert.ipynb │ │ ├── ProtElectra.ipynb │ │ └── ProtXLNet.ipynb │ └── Use_Case:NetSurfp_Dataset_Secondary_Structure_Prediction_(3_States)_Feature_Extraction.ipynb └── TensorFlow │ └── Advanced │ ├── ProtAlbert.ipynb │ ├── ProtBert-BFD.ipynb │ ├── ProtBert.ipynb │ ├── ProtT5-XL-BFD.ipynb │ ├── ProtT5-XL-UniRef50.ipynb │ └── ProtXLNet.ipynb ├── Fine-Tuning ├── ProtBert-BFD-FineTune-SS3.ipynb ├── ProtBert-BFD-FineTuning-PyTorchLightning-Localization.ipynb ├── ProtBert-BFD-FineTuning-PyTorchLightning-MS.ipynb ├── ProtBert_BFD_FineTuning_MS.ipynb ├── README.md └── protBERT-BFD-lightning-multitasks.ipynb ├── Generate └── ProtXLNet.ipynb ├── LICENSE.md ├── Prediction ├── ProtBert-BFD-Predict-SS3.ipynb └── ProtBert_BFD_Predict_MS.ipynb ├── README.md ├── Visualization ├── ProtAlbert_attention_head_view.ipynb ├── ProtBert_attention_head_view.ipynb ├── ProtElectra_attention_head_view.ipynb └── ProtXLNet_attention_head_view.ipynb └── images ├── 1200px-Nvidia_image_logo.svg.png ├── 471px-Google_"G"_Logo.svg.png ├── B.Rost.jpg ├── Christoph-Angerer.jpg ├── Debsindhu-Bhowmik.jpg ├── ElnaggarAhmend.jpg ├── Google-Logo.jpg ├── Llion-Jones.jpg ├── Martin-Steinegger.png ├── MichaelHeinzinger-2.jpg ├── Oak_Ridge_National_Laboratory_logo.svg.png ├── SOFTWARE_CAMPUS_logo_cmyk.jpg ├── Tamas-Feher.jpeg ├── Tom-Gibbs.png ├── christiandallago.png ├── female.png ├── google-cloud-logo.jpg ├── tfrc.png ├── transformers_attention.png └── yu-wang.jpeg /.gitmodules: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Benchmark/ProtAlbert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Benchmark/ProtAlbert.ipynb -------------------------------------------------------------------------------- /Benchmark/ProtBert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Benchmark/ProtBert.ipynb -------------------------------------------------------------------------------- /Benchmark/ProtElectra.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Benchmark/ProtElectra.ipynb -------------------------------------------------------------------------------- /Benchmark/ProtXLNet.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Benchmark/ProtXLNet.ipynb -------------------------------------------------------------------------------- /Embedding/Onnx/ProtBert-BFD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/Onnx/ProtBert-BFD.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtAlbert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtAlbert.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtBert-BFD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtBert-BFD.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtBert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtBert.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtElectra.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtElectra.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtT5-XL-BFD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtT5-XL-BFD.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtT5-XL-UniRef50.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtT5-XL-UniRef50.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Advanced/ProtXLNet.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Advanced/ProtXLNet.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Basic/ProtAlbert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Basic/ProtAlbert.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Basic/ProtBert-BFD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Basic/ProtBert-BFD.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Basic/ProtBert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Basic/ProtBert.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Basic/ProtElectra.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Basic/ProtElectra.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Basic/ProtXLNet.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Basic/ProtXLNet.ipynb -------------------------------------------------------------------------------- /Embedding/PyTorch/Use_Case:NetSurfp_Dataset_Secondary_Structure_Prediction_(3_States)_Feature_Extraction.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/PyTorch/Use_Case:NetSurfp_Dataset_Secondary_Structure_Prediction_(3_States)_Feature_Extraction.ipynb -------------------------------------------------------------------------------- /Embedding/TensorFlow/Advanced/ProtAlbert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/TensorFlow/Advanced/ProtAlbert.ipynb -------------------------------------------------------------------------------- /Embedding/TensorFlow/Advanced/ProtBert-BFD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/TensorFlow/Advanced/ProtBert-BFD.ipynb -------------------------------------------------------------------------------- /Embedding/TensorFlow/Advanced/ProtBert.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/TensorFlow/Advanced/ProtBert.ipynb -------------------------------------------------------------------------------- /Embedding/TensorFlow/Advanced/ProtT5-XL-BFD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/TensorFlow/Advanced/ProtT5-XL-BFD.ipynb -------------------------------------------------------------------------------- /Embedding/TensorFlow/Advanced/ProtT5-XL-UniRef50.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/TensorFlow/Advanced/ProtT5-XL-UniRef50.ipynb -------------------------------------------------------------------------------- /Embedding/TensorFlow/Advanced/ProtXLNet.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Embedding/TensorFlow/Advanced/ProtXLNet.ipynb -------------------------------------------------------------------------------- /Fine-Tuning/ProtBert-BFD-FineTune-SS3.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Fine-Tuning/ProtBert-BFD-FineTune-SS3.ipynb -------------------------------------------------------------------------------- /Fine-Tuning/ProtBert-BFD-FineTuning-PyTorchLightning-Localization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Fine-Tuning/ProtBert-BFD-FineTuning-PyTorchLightning-Localization.ipynb -------------------------------------------------------------------------------- /Fine-Tuning/ProtBert-BFD-FineTuning-PyTorchLightning-MS.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Fine-Tuning/ProtBert-BFD-FineTuning-PyTorchLightning-MS.ipynb -------------------------------------------------------------------------------- /Fine-Tuning/ProtBert_BFD_FineTuning_MS.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Fine-Tuning/ProtBert_BFD_FineTuning_MS.ipynb -------------------------------------------------------------------------------- /Fine-Tuning/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Fine-Tuning/README.md -------------------------------------------------------------------------------- /Fine-Tuning/protBERT-BFD-lightning-multitasks.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Fine-Tuning/protBERT-BFD-lightning-multitasks.ipynb -------------------------------------------------------------------------------- /Generate/ProtXLNet.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Generate/ProtXLNet.ipynb -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/LICENSE.md -------------------------------------------------------------------------------- /Prediction/ProtBert-BFD-Predict-SS3.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Prediction/ProtBert-BFD-Predict-SS3.ipynb -------------------------------------------------------------------------------- /Prediction/ProtBert_BFD_Predict_MS.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Prediction/ProtBert_BFD_Predict_MS.ipynb -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/README.md -------------------------------------------------------------------------------- /Visualization/ProtAlbert_attention_head_view.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Visualization/ProtAlbert_attention_head_view.ipynb -------------------------------------------------------------------------------- /Visualization/ProtBert_attention_head_view.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Visualization/ProtBert_attention_head_view.ipynb -------------------------------------------------------------------------------- /Visualization/ProtElectra_attention_head_view.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Visualization/ProtElectra_attention_head_view.ipynb -------------------------------------------------------------------------------- /Visualization/ProtXLNet_attention_head_view.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/Visualization/ProtXLNet_attention_head_view.ipynb -------------------------------------------------------------------------------- /images/1200px-Nvidia_image_logo.svg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/1200px-Nvidia_image_logo.svg.png -------------------------------------------------------------------------------- /images/471px-Google_"G"_Logo.svg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/471px-Google_"G"_Logo.svg.png -------------------------------------------------------------------------------- /images/B.Rost.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/B.Rost.jpg -------------------------------------------------------------------------------- /images/Christoph-Angerer.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Christoph-Angerer.jpg -------------------------------------------------------------------------------- /images/Debsindhu-Bhowmik.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Debsindhu-Bhowmik.jpg -------------------------------------------------------------------------------- /images/ElnaggarAhmend.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/ElnaggarAhmend.jpg -------------------------------------------------------------------------------- /images/Google-Logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Google-Logo.jpg -------------------------------------------------------------------------------- /images/Llion-Jones.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Llion-Jones.jpg -------------------------------------------------------------------------------- /images/Martin-Steinegger.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Martin-Steinegger.png -------------------------------------------------------------------------------- /images/MichaelHeinzinger-2.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/MichaelHeinzinger-2.jpg -------------------------------------------------------------------------------- /images/Oak_Ridge_National_Laboratory_logo.svg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Oak_Ridge_National_Laboratory_logo.svg.png -------------------------------------------------------------------------------- /images/SOFTWARE_CAMPUS_logo_cmyk.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/SOFTWARE_CAMPUS_logo_cmyk.jpg -------------------------------------------------------------------------------- /images/Tamas-Feher.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Tamas-Feher.jpeg -------------------------------------------------------------------------------- /images/Tom-Gibbs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/Tom-Gibbs.png -------------------------------------------------------------------------------- /images/christiandallago.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/christiandallago.png -------------------------------------------------------------------------------- /images/female.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/female.png -------------------------------------------------------------------------------- /images/google-cloud-logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/google-cloud-logo.jpg -------------------------------------------------------------------------------- /images/tfrc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/tfrc.png -------------------------------------------------------------------------------- /images/transformers_attention.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/transformers_attention.png -------------------------------------------------------------------------------- /images/yu-wang.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Rostlab/ProtTrans/HEAD/images/yu-wang.jpeg --------------------------------------------------------------------------------