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| import gradio as gr | |
| from gradio_leaderboard import Leaderboard | |
| from pathlib import Path | |
| import pandas as pd | |
| import os | |
| import json | |
| from envs import API, EVAL_REQUESTS_PATH, TOKEN, QUEUE_REPO | |
| def submit(model_name, model_id, challenge, submission_id, paper_link, architecture, license): | |
| if model_name == "" or model_id == "" or challenge == "" or architecture == "" or license == "": | |
| gr.Error("Please fill all the fields") | |
| return | |
| if submission_id == "" and paper_link =="": | |
| gr.Error("Provide either a link to a paper describing the method or a submission ID for the MLSB workshop.") | |
| return | |
| try: | |
| user_name = "" | |
| if "/" in model_id: | |
| user_name = model_id.split("/")[0] | |
| model_path = model_id.split("/")[1] | |
| eval_entry = { | |
| "model_name": model_name, | |
| "model_id": model_id, | |
| "challenge": challenge, | |
| "submission_id": submission_id, | |
| "architecture": architecture, | |
| "license": license | |
| } | |
| OUT_DIR = f"{EVAL_REQUESTS_PATH}/{user_name}" | |
| os.makedirs(OUT_DIR, exist_ok=True) | |
| out_path = f"{OUT_DIR}/{user_name}_{model_path}.json" | |
| with open(out_path, "w") as f: | |
| f.write(json.dumps(eval_entry)) | |
| print("Uploading eval file") | |
| API.upload_file( | |
| path_or_fileobj=out_path, | |
| path_in_repo=out_path.split("eval-queue/")[1], | |
| repo_id=QUEUE_REPO, | |
| repo_type="dataset", | |
| commit_message=f"Add {model_name} to eval queue", | |
| ) | |
| gr.Info("Successfully submitted", duration=10) | |
| # Remove the local file | |
| os.remove(out_path) | |
| except: | |
| gr.Error("Error submitting the model") | |
| abs_path = Path(__file__).parent | |
| # Any pandas-compatible data | |
| pinder_df = pd.read_json(str(abs_path / "leaderboard_pinder.json")) | |
| plinder_df = pd.read_json(str(abs_path / "leaderboard_plinder.json")) | |
| with gr.Blocks() as demo: | |
| gr.Markdown(""" | |
| # MLSB 2024 Leaderboard | |
| """) | |
| with gr.Tab("🎖️ PINDER Leaderboard"): | |
| gr.Markdown("""## PINDER Leaderboard | |
| Evaluating Protein-Protein interaction prediction | |
| """) | |
| Leaderboard( | |
| value=pinder_df, | |
| select_columns=["Arch", "Model", "L_rms", "I_rms", | |
| "F_nat", "DOCKQ", "CAPRI"], | |
| search_columns=["model_name_for_query"], | |
| hide_columns=["model_name_for_query",], | |
| filter_columns=["Arch"], | |
| ) | |
| with gr.Tab("🥇 PLINDER Leaderboard"): | |
| gr.Markdown("""## PLINDER Leaderboard | |
| Evaluating Protein-Ligand prediction | |
| """) | |
| Leaderboard( | |
| value=plinder_df, | |
| select_columns=["Arch", "Model", "Mean lDDT-PLI", "Mean lDDT-LP", | |
| "Median RMSD", "% lDDT-PLI >= 0.5", "% pass PoseBusters"], | |
| search_columns=["model_name_for_query"], | |
| hide_columns=["model_name_for_query",], | |
| filter_columns=["Arch"], | |
| ) | |
| with gr.Tab("✉️ Submit"): | |
| gr.Markdown("""## Submit your model | |
| Submit your model to the leaderboard using the below form AFTER following the following steps: | |
| - Create a HuggingFace account and request to join the [MLSB organization](https://huggingface.co/MLSB) | |
| - Create a new space in the MLSB organization and add your model using the inference templates: https://huggingface.co/new-space?owner=MLSB | |
| - Fill the submission form. | |
| ## Prerequisites: | |
| To qualify for submission, each team must: | |
| - Provide an MLSB submission ID (find it on CMT) or a link to a preprint/paper describing their methodology. This publication does not have to specifically report training or evaluation on the P(L)INDER dataset. Previously published methods, such as DiffDock, only need to link their existing paper. Note that entry into this competition does not equate to an MLSB workshop paper submission. | |
| - Create a copy of the provided [inference templates](https://huggingface.co/MLSB/). | |
| - Go to the top right corner of the page of the respective inference template and click on the drop-down menu (vertical ellipsis) right next to the “Community”, then select “Duplicate this space”. | |
| - Change files in the newly create space to reflect the peculiarities of your model | |
| - Edit `requirements.txt` to capture all python dependencies. | |
| - Modify the Dockerfile as appropriate (including selecting the right base image) | |
| - Include a `inference_app.py` file. This contains a `predict` function that should be modified to reflect the specifics of inference using their model. | |
| - Include a `train.py` file to ensure that training and model selection use only the PINDER/PLINDER datasets and to clearly show any additional hyperparameters used. | |
| - Provide a LICENSE file that allows for reuse, derivative works, and distribution of the provided software and weights (e.g., MIT or Apache2 license). | |
| - Submit to the leaderboard via the [form below](https://huggingface.co/spaces/MLSB/leaderboard2024). | |
| - On submission page, add reference to the newly created space in the format username/space (e.g mlsb/alphafold3). You can create the space on your personal Huggingface account and transfer it to MLSB for the submission to get a GPU assigned. | |
| After a brief technical review by our organizers we will grant you a free GPU until MLSB so that anyone can play with the model and we will run the evaluation. | |
| If you have a questions please email: workshopmlsb@gmail.com | |
| """) | |
| model_name = gr.Textbox(label="Model name") | |
| model_id = gr.Textbox(label="username/space e.g mlsb/alphafold3") | |
| challenge = gr.Radio(choices=["PINDER", "PLINDER"],label="Challenge") | |
| gr.Markdown("Either give a submission id if you submitted to the MLSB workshop or provide a link to the preprint/paper describing the method.") | |
| with gr.Row(): | |
| submission_id = gr.Textbox(label="Submission ID on CMT") | |
| paper_link = gr.Textbox(label="Preprint or Paper link") | |
| architecture = gr.Dropdown(choices=["GNN", "CNN", "Physics-based", "Other"],label="Model architecture") | |
| license = gr.Dropdown(choices=["mit", "apache-2.0", "gplv2", "gplv3", "lgpl", "mozilla", "bsd", "other"],label="License") | |
| submit_btn = gr.Button("Submit") | |
| submit_btn.click(submit, inputs=[model_name, model_id, challenge, submission_id, paper_link, architecture, license], outputs=[]) | |
| gr.Markdown(""" | |
| Please find more information about the challenges on [mlsb.io/#challenge](https://mlsb.io/#challenge)""") | |
| if __name__ == "__main__": | |
| demo.launch() |