Adding more detailed references/citations

Author: niklases

pypef/llm/esm_lora_tune.py

@@ -5,10 +5,15 @@
 # MIT License
 # Copyright (c) Meta Platforms, Inc. and affiliates.
 # https://github.com/facebookresearch/esm
+# ESM1v model publication:
+# Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu, Alexander Rives
+# Language models enable zero-shot prediction of the effects of mutations on protein function
+# bioRxiv 2021.07.09.450648; doi: https://doi.org/10.1101/2021.07.09.450648 
 
 # Inspired by ConFit
 # https://github.com/luo-group/ConFit
 
+
 from __future__ import annotations
 
 import torch

pypef/llm/prosst_lora_tune.py

@@ -3,9 +3,11 @@
 
 # Using (training, testing/infering) ProSST model(s) published under 
 # GNU GENERAL PUBLIC LICENSE: GPL-3.0 license
-# https://github.com/ai4protein/ProSST
-#import warnings
-#warnings.filterwarnings('error')
+# Code repository: https://github.com/ai4protein/ProSST
+# Mingchen Li, Pan Tan, Xinzhu Ma, Bozitao Zhong, Huiqun Yu, Ziyi Zhou, Wanli Ouyang, Bingxin Zhou, Liang Hong, Yang Tan
+# ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention
+# bioRxiv 2024.04.15.589672; doi: https://doi.org/10.1101/2024.04.15.589672 
+
 
 from sys import path
 import os

pypef/llm/prosst_structure/encoder/gvp.py

@@ -4,7 +4,10 @@
 
 # Using (training, testing/infering) ProSST model(s) published under 
 # GNU GENERAL PUBLIC LICENSE: GPL-3.0 license
-# https://github.com/ai4protein/ProSST
+# Code repository: https://github.com/ai4protein/ProSST
+# Mingchen Li, Pan Tan, Xinzhu Ma, Bozitao Zhong, Huiqun Yu, Ziyi Zhou, Wanli Ouyang, Bingxin Zhou, Liang Hong, Yang Tan
+# ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention
+# bioRxiv 2024.04.15.589672; doi: https://doi.org/10.1101/2024.04.15.589672 
 
 
 import torch

pypef/llm/prosst_structure/encoder/layer.py

@@ -4,7 +4,10 @@
 
 # Using (training, testing/infering) ProSST model(s) published under 
 # GNU GENERAL PUBLIC LICENSE: GPL-3.0 license
-# https://github.com/ai4protein/ProSST
+# Code repository: https://github.com/ai4protein/ProSST
+# Mingchen Li, Pan Tan, Xinzhu Ma, Bozitao Zhong, Huiqun Yu, Ziyi Zhou, Wanli Ouyang, Bingxin Zhou, Liang Hong, Yang Tan
+# ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention
+# bioRxiv 2024.04.15.589672; doi: https://doi.org/10.1101/2024.04.15.589672 
 
 
 import torch, functools

pypef/llm/prosst_structure/quantizer.py

@@ -4,7 +4,10 @@
 
 # Using (training, testing/infering) ProSST model(s) published under 
 # GNU GENERAL PUBLIC LICENSE: GPL-3.0 license
-# https://github.com/ai4protein/ProSST
+# Code repository: https://github.com/ai4protein/ProSST
+# Mingchen Li, Pan Tan, Xinzhu Ma, Bozitao Zhong, Huiqun Yu, Ziyi Zhou, Wanli Ouyang, Bingxin Zhou, Liang Hong, Yang Tan
+# ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention
+# bioRxiv 2024.04.15.589672; doi: https://doi.org/10.1101/2024.04.15.589672 
 
 
 import biotite