{"id":29569799,"url":"https://github.com/keiserlab/face-plm","last_synced_at":"2025-09-05T01:38:24.438Z","repository":{"id":302555277,"uuid":"939071711","full_name":"keiserlab/face-plm","owner":"keiserlab","description":null,"archived":false,"fork":false,"pushed_at":"2025-05-05T23:06:27.000Z","size":482,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-19T04:57:42.137Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/keiserlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-02-26T00:14:22.000Z","updated_at":"2025-05-06T02:38:00.000Z","dependencies_parsed_at":"2025-07-03T02:42:15.690Z","dependency_job_id":"03277b13-4b98-453b-902c-3e99ead19bd4","html_url":"https://github.com/keiserlab/face-plm","commit_stats":null,"previous_names":["keiserlab/face-plm"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/keiserlab/face-plm","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fface-plm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fface-plm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fface-plm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fface-plm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/keiserlab","download_url":"https://codeload.github.com/keiserlab/face-plm/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fface-plm/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273699716,"owners_count":25152284,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-04T02:00:08.968Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-07-19T02:06:53.693Z","updated_at":"2025-09-05T01:38:19.409Z","avatar_url":"https://github.com/keiserlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FACE-PLM\n**F**urther **A**ssessing **C**urrent **E**ndeavors in **PLM**s\n\n\u003cimg width=\"350\" alt=\"image\" src=\"https://github.com/user-attachments/assets/1493dc74-8eed-49b2-8792-d79dc870d008\" /\u003e\n\n\n[![](https://img.shields.io/badge/Python-3.10-blue.svg)](https://www.python.org/downloads/)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\n# Installation\n\n### Clone the repository\n\n    git clone git@github.com:keiserlab/face-plm.git\n\n### Navigate to the repository, create virtual conda environment  \n\n    cd face-plm\n\n    conda create -n face_plm python=3.10 -y\n\n    conda activate face_plm\n\n    pip install -e . \n\n    pip install pytorch-lightning\n\n# Getting Started\n\nIn order to get started with generating embeddings and training models you need to sign into HuggingFace and WandB.\n\n```bash\nhuggingface-cli login\n```\n```bash\nwandb login\n```\n\nAdditionally, you need to change the wandb config file at: training_probe/config/wandb_config/base_wandb.yaml\nThe entity and project need to be updated to properly log to the desired WandB location.\n\n```bash\n_target_: face_plm.probes.utils.WandbRunConfig\nrun_name: base_run+name\nentity: temp_entity  # CHANGEME\nproject: temp_project  # CHANGEME\n```\n\n# Generating the PLM Embeddings\n\n### Setup embedding generation env\n```bash\nbash scripts/setup_embed_env.sh\n```\n\n### Generating final layer embeddings for all PLMs\nWith ESM (requires ESMC/3 access)\n```bash\nbash scripts/get_all_plm_embedding.sh\n```\nWithout ESM\n```bash\nbash scripts/get_all_plm_embedding_no_esm.sh\n```\n\n### Generating all layer embeddings for all Ankh-base\n```bash\nbash scripts/get_all_layer_ankh_embedding.sh\n```\n\n# Training Probes\n### Training a single model (single probe type, single aggeregation type, final layer)\n```bash\nbash scripts/train_single_model.sh CONFIG_NAME\n```\nExample config: esmc_600m-agg_mlp\n\n### Training multiple models for cross-validation (single probe type, single aggregation, final layer)\n```bash\nbash scripts/train_cross_val_model.sh CONFIG_NAME\n```\nExample config: esmc_600m-agg_mlp\n\n### Training models on multiple layers (single probe type, single aggregation, all layers)\n```bash\nbash scripts/train_cross_val_model_ankh_multilayer.sh CONFIG_NAME\n```\nExample config: ankh_base_layer_specific_0-12\n\n\n# Masked Language Model Fine-tuning\n### EC 2.7.* Dataset Fine-tuning\n```bash\nbash scripts/finetune_mlm.sh ankh_large_ft_ec27\n```\n### ADK Dataset Fine-tuning\n```bash\nbash scripts/finetune_mlm.sh ankh_base_ft_kcat\n```\n\n# Direct Regression Fine-tuning\n```bash\nbash scripts/train_cross_val_direct_finetune.sh CONFIG_NAME\n```\nExample config: ankh_base_ft_kcat\n\n# No Torch Linear and Non-linear Probing\n```bash\nbash no_torch_probing.sh OUTPUT_DIR\n```\nexample output_dir: ./probe_outputs/\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeiserlab%2Fface-plm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkeiserlab%2Fface-plm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeiserlab%2Fface-plm/lists"}