| --- |
| license: apache-2.0 |
| library_name: pytorch |
| tags: |
| - protein |
| - protein-protein-interaction |
| - esm2 |
| - bernett |
| - biology |
| --- |
| |
| # LoGoPPI Bernett |
|
|
| LoGoPPI is a protein–protein interaction prediction model built on ESM-2. It combines a Global sequence representation with a residue-level Maxsim score. The two calibrated scores are combined with fixed weights of 0.5 and 0.5. |
|
|
| ## Model overview |
|
|
| This checkpoint was trained independently on the Bernett human PPI benchmark. It does not load or continue training from the LoGoPPI Cross-species checkpoint. |
|
|
| ## Training and evaluation data |
|
|
| The data originate from the [Bernett human PPI benchmark, Figshare version 3](https://doi.org/10.6084/m9.figshare.21591618.v3), which is based on high-confidence human interactions from HIPPIE v2.3 and uses leakage-controlled dataset construction. |
|
|
| The `data/bernett/` directory contains `proteins.fasta` and `query,text,label` CSV files for training, checkpoint selection, calibration, and testing. |
|
|
| | Split | Pairs | |
| |---|---:| |
| | Training | 163,192 | |
| | Validation selection | 29,630 | |
| | Validation calibration | 29,630 | |
| | Test | 52,048 | |
|
|
| ## Results |
|
|
| | Metric | Value | |
| |---|---:| |
| | AUPR | 0.684319 | |
| | AUROC | 0.701470 | |
| | NLL | 0.632073 | |
| | F1 | 0.673916 | |
|
|
| ## Usage |
|
|
| Install [LoGoPPI v2.0.0](https://github.com/netbiolab/LoGoPPI/tree/v2.0.0) and download the model files: |
|
|
| ```bash |
| git clone https://github.com/netbiolab/LoGoPPI.git |
| cd LoGoPPI |
| conda env create -f environment.yml |
| conda activate logoppi |
| |
| python - <<'PY' |
| from huggingface_hub import snapshot_download |
| |
| snapshot_download( |
| "netbiolab/LoGoPPI-Bernett", |
| revision="v2.0.0", |
| local_dir="models/bernett", |
| ignore_patterns=["data/*"], |
| ) |
| PY |
| ``` |
|
|
| Run inference with a FASTA file and a `query,text` pair CSV: |
|
|
| ```bash |
| python inference.py \ |
| --model_dir models/bernett \ |
| --fasta_path proteins.fasta \ |
| --pair_csv pairs.csv \ |
| --output_path predictions.csv \ |
| --gpus 0 |
| ``` |
|
|
| Training, testing, sequence-only input, and embedding reuse are documented in the [GitHub repository](https://github.com/netbiolab/LoGoPPI). |
|
|
| ## License and citation |
|
|
| LoGoPPI is released under the Apache License 2.0. Please cite the accompanying LoGoPPI study and the [Bernett benchmark](https://doi.org/10.1093/bioinformatics/btaf192) when using this model or the distributed data. |
|
|
