import gradio as gr import joblib from huggingface_hub import hf_hub_download import pandas as pd import numpy as np from collections import Counter import os os.environ["GRADIO_SSR_MODE"] = "false" os.environ["GRADIO_ANALYTICS_ENABLED"] = "false" import time print("STARTING APP...") time.sleep(2) print("APP READY") # ➕ ADDED: placeholders (instead of loading at startup) model_dict = None feature_columns = None model_package = None # ❌ REMOVED: direct model loading at startup # repo_id = "Ym420/Peptide-Function" # model_filename = "xgb_multilabel_model_full.pkl" # model_path = hf_hub_download(repo_id=repo_id, filename=model_filename) # model_package = joblib.load(model_path) # model_dict = model_package['model'] # feature_columns = model_package['feature_columns'] # ➕ ADDED: lazy loader function def init_model(): global model_dict, feature_columns, model_package if model_dict is None: repo_id = "Ym420/Peptide-Function" model_filename = "xgb_multilabel_model_full.pkl" model_path = hf_hub_download(repo_id=repo_id, filename=model_filename) model_package = joblib.load(model_path) model_dict = model_package['model'] feature_columns = model_package['feature_columns'] # 🔁 MOVED: metadata loading (was global before) global aa_list, dipeptides, hydrophobicity_scale, eisenberg_scale global aa_mass, aa_charge, aa_boman, aa_flexibility global aa_polarizability, aa_aliphatic, aa_deltaG, aa_pucker aa_list = model_package.get('aa_list', []) dipeptides = model_package.get('dipeptides', []) hydrophobicity_scale = model_package.get('hydrophobicity_scale', {}) eisenberg_scale = model_package.get('eisenberg_scale', {}) aa_mass = model_package.get('aa_mass', {}) aa_charge = model_package.get('aa_charge', {}) aa_boman = model_package.get('aa_boman', {}) aa_flexibility = model_package.get('aa_flexibility', {}) aa_polarizability = model_package.get('aa_polarizability', {}) aa_aliphatic = model_package.get('aa_aliphatic', {}) aa_deltaG = model_package.get('aa_deltaG', {}) aa_pucker = model_package.get('aa_pucker', {}) # --- Target cells --- TARGET_CELLS = ["Gram+", "Fungus", "Mammalian Cell", "Cancer", "Gram-"] # --- Feature extraction --- def extract_features_app(seq: str) -> pd.DataFrame: seq = seq.upper() count = Counter([seq[i:i+2] for i in range(len(seq)-1)]) total = max(len(seq)-1, 1) dipep_features = [count.get(dp, 0) / total for dp in dipeptides] def g(aa, table): return table.get(aa, 0) def h(dp, table): return (g(dp[0], table) + g(dp[1], table)) / 2.0 dipeptides_seq = [seq[i:i+2] for i in range(len(seq)-1)] if len(seq) < 2: physchem_features = [0]*13 else: mw = np.mean([h(dp, aa_mass) for dp in dipeptides_seq]) charge = np.mean([h(dp, aa_charge) for dp in dipeptides_seq]) hydro = np.mean([h(dp, hydrophobicity_scale) for dp in dipeptides_seq]) aromatic = np.mean([(dp[0] in 'FWY') + (dp[1] in 'FWY') for dp in dipeptides_seq]) / 2.0 pI = np.mean([h(dp, {aa: 7 + (int(aa in 'KRH') - int(aa in 'DE')) for aa in aa_list}) for dp in dipeptides_seq]) instability = np.mean([((dp[0] in 'DEKR') + (dp[1] in 'DEKR')) / 2.0 for dp in dipeptides_seq]) hydro_moment = np.sqrt(np.mean([(h(dp, eisenberg_scale))**2 for dp in dipeptides_seq])) aliphatic = np.mean([h(dp, aa_aliphatic) for dp in dipeptides_seq]) boman = np.mean([h(dp, aa_boman) for dp in dipeptides_seq]) flexibility = np.mean([h(dp, aa_flexibility) for dp in dipeptides_seq]) polarizability = np.mean([h(dp, aa_polarizability) for dp in dipeptides_seq]) deltag = np.mean([h(dp, aa_deltaG) for dp in dipeptides_seq]) pucker = np.mean([h(dp, aa_pucker) for dp in dipeptides_seq]) physchem_features = [mw, charge, hydro, aromatic, pI, instability, hydro_moment, aliphatic, boman, flexibility, polarizability, deltag, pucker] features = dipep_features + physchem_features df = pd.DataFrame([features], columns=feature_columns) df = df.astype('float32') return df # --- Prediction function --- def predict_peptide(sequence: str): init_model() # ➕ ADDED: ensures model loads only when needed seq = "".join(sequence.split()).upper() if not seq: return [] X = extract_features_app(seq) table = [] for target in TARGET_CELLS: clf = model_dict.get(target) if clf is not None: prob = clf.predict_proba(X)[0][1] table.append([target, round(float(prob), 4)]) else: table.append([target, None]) return table # --- Gradio Interface --- custom_css = """ footer, .footer {display:none !important;} """ #with gr.Blocks(css=custom_css, theme="default") as demo: with gr.Blocks(css=custom_css) as demo: gr.Markdown("## AMP Spectrum") seq_input = gr.Textbox(label="Enter Peptide Sequence") with gr.Row(): predict_btn = gr.Button("Predict", variant="primary") clear_btn = gr.Button("Clear") table_output = gr.Dataframe( headers=["Target", "Confidence"], datatype=["str","number"], interactive=False ) predict_btn.click(fn=predict_peptide, inputs=seq_input, outputs=table_output) clear_btn.click(fn=lambda: ("", []), outputs=[seq_input, table_output]) gr.api(predict_peptide, api_name="predict_peptide") if __name__ == "__main__": demo.launch( server_name="0.0.0.0", server_port=7860, root_path="/", show_error=True, ssr_mode=False )