Singh-Lab/bom-pooling

Implementation of ISMB-25 Paper: Locality-aware pooling enhances protein language model performance across varied applications

Python

4 commits

updated Aug 17, 2025

See the code

README

This is the official implementation of ISMB 2025 Paper: Locality-aware pooling enhances protein language model performance across varied applications (Minh Hoang, Mona Singh)

Fig2

Data used in the paper can be obtained at the following sites:

Fluorescence and Beta-Lactamase dataset: https://deepprotein.readthedocs.io/en/latest/notes/download.html
SCOPe meta file: https://scop.berkeley.edu/downloads/parse/dir.cla.scope.2.08-stable.txt
SCOPe download script is provided in get_scope_data.py
Signaling protein interaction detection dataset: https://figshare.com/articles/dataset/Predictions_-_Domain-Peptide_and_Protein-Protein_Interactions_-_HSM/10084745

Significant stargazers

Logan Hallee

33 followers · starred Apr 2026

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Singh-Lab/bom-pooling

Implementation of ISMB-25 Paper: Locality-aware pooling enhances protein language model performance across varied applications

Python

4 commits

updated Aug 17, 2025

See the code

README

This is the official implementation of ISMB 2025 Paper: Locality-aware pooling enhances protein language model performance across varied applications (Minh Hoang, Mona Singh)

Fig2

Data used in the paper can be obtained at the following sites:

Fluorescence and Beta-Lactamase dataset: https://deepprotein.readthedocs.io/en/latest/notes/download.html
SCOPe meta file: https://scop.berkeley.edu/downloads/parse/dir.cla.scope.2.08-stable.txt
SCOPe download script is provided in get_scope_data.py
Signaling protein interaction detection dataset: https://figshare.com/articles/dataset/Predictions_-_Domain-Peptide_and_Protein-Protein_Interactions_-_HSM/10084745

Significant stargazers

Logan Hallee

33 followers · starred Apr 2026

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This dataset is associated with the paper Rethinking Text-based Protein Understanding: Retrieval or…

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