andrewdalpino commited on
Commit
896c05d
·
verified ·
1 Parent(s): d30614e

Update README.md

Browse files
Files changed (1) hide show
  1. README.md +10 -2
README.md CHANGED
@@ -16,7 +16,7 @@ pipeline_tag: text-classification
16
 
17
  # ESM2 Protein Function Caller
18
 
19
- An Evolutionary-scale Model (ESM) for protein function calling from amino acid sequences. Based on the ESM2 architecture and fine-tuned on the [CAFA 5](https://huggingface.co/datasets/andrewdalpino/CAFA5) dataset, this model predicts the gene ontology (GO) subgraph for a particular protein sequence - giving you insight into the molecular function, biological process, and location of the activity inside the cell.
20
 
21
  **Note**: This model specilizes on the `celluar component` subgraph of the gene ontology.
22
 
@@ -84,4 +84,12 @@ print(f"{probability:.4f}: {term}")
84
  - **Epochs**: 20
85
  - **Test F1**: 0.63
86
  - **Test Precision**: 0.78
87
- - **Test Recall**: 0.53
 
 
 
 
 
 
 
 
 
16
 
17
  # ESM2 Protein Function Caller
18
 
19
+ An Evolutionary-scale Model (ESM) for protein function calling from amino acid sequences. Based on the ESM2 Transformer architecture and fine-tuned on the [CAFA 5](https://huggingface.co/datasets/andrewdalpino/CAFA5) dataset, this model predicts the gene ontology (GO) subgraph for a particular protein sequence - giving you insight into the molecular function, biological process, and location of the activity inside the cell.
20
 
21
  **Note**: This model specilizes on the `celluar component` subgraph of the gene ontology.
22
 
 
84
  - **Epochs**: 20
85
  - **Test F1**: 0.63
86
  - **Test Precision**: 0.78
87
+ - **Test Recall**: 0.53
88
+
89
+ ## References:
90
+
91
+ >- A. Rives, et al. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences, 2021.
92
+ >- Z. Lin, et al. Evolutionary-scale prediction of atomic level protein structure with a language model, 2022.
93
+ >- G. A. Merino, et al. Hierarchical deep learning for predicting GO annotations by integrating protein knowledge, 2022.
94
+ >- I. Friedberg, et al. CAFA 5 Protein Function Prediction. https://kaggle.com/competitions/cafa-5-protein-function-prediction, 2023.
95
+ >- M. Ashburner, et al. Gene Ontology: tool for the unification of biology, 2000.