app.py

import gradio as gr
import joblib
import numpy as np
import pandas as pd
from propy import AAComposition, Autocorrelation, CTD, PseudoAAC
from sklearn.preprocessing import MinMaxScaler
import torch
from transformers import BertTokenizer, BertModel
from math import expm1

# Load AMP Classifier
model = joblib.load("RF.joblib")
scaler = joblib.load("norm (4).joblib")

# Load ProtBert Globally
tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False)
protbert_model = BertModel.from_pretrained("Rostlab/prot_bert")
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
protbert_model = protbert_model.to(device).eval()

# Selected Features
selected_features = [
    "_SolventAccessibilityC3", "_SecondaryStrC1", "_SecondaryStrC3", "_ChargeC1", "_PolarityC1",
    "_NormalizedVDWVC1", "_HydrophobicityC3", "_SecondaryStrT23", "_PolarizabilityD1001",
    "_PolarizabilityD2001", "_PolarizabilityD3001", "_SolventAccessibilityD1001",
    "_SolventAccessibilityD2001", "_SolventAccessibilityD3001", "_SecondaryStrD1001",
    "_SecondaryStrD1075", "_SecondaryStrD2001", "_SecondaryStrD3001", "_ChargeD1001",
    "_ChargeD1025", "_ChargeD2001", "_ChargeD3075", "_ChargeD3100", "_PolarityD1001",
    "_PolarityD1050", "_PolarityD2001", "_PolarityD3001", "_NormalizedVDWVD1001",
    "_NormalizedVDWVD2001", "_NormalizedVDWVD2025", "_NormalizedVDWVD2050", "_NormalizedVDWVD3001",
    "_HydrophobicityD1001", "_HydrophobicityD2001", "_HydrophobicityD3001", "_HydrophobicityD3025",
    "A", "R", "D", "C", "E", "Q", "H", "I", "M", "P", "Y", "V",
    "AR", "AV", "RC", "RL", "RV", "CR", "CC", "CL", "CK", "EE", "EI", "EL",
    "HC", "IA", "IL", "IV", "LA", "LC", "LE", "LI", "LT", "LV", "KC", "MA",
    "MS", "SC", "TC", "TV", "YC", "VC", "VE", "VL", "VK", "VV",
    "MoreauBrotoAuto_FreeEnergy30", "MoranAuto_Hydrophobicity2", "MoranAuto_Hydrophobicity4",
    "GearyAuto_Hydrophobicity20", "GearyAuto_Hydrophobicity24", "GearyAuto_Hydrophobicity26",
    "GearyAuto_Hydrophobicity27", "GearyAuto_Hydrophobicity28", "GearyAuto_Hydrophobicity29",
    "GearyAuto_Hydrophobicity30", "GearyAuto_AvFlexibility22", "GearyAuto_AvFlexibility26",
    "GearyAuto_AvFlexibility27", "GearyAuto_AvFlexibility28", "GearyAuto_AvFlexibility29",
    "GearyAuto_AvFlexibility30", "GearyAuto_Polarizability22", "GearyAuto_Polarizability24",
    "GearyAuto_Polarizability25", "GearyAuto_Polarizability27", "GearyAuto_Polarizability28",
    "GearyAuto_Polarizability29", "GearyAuto_Polarizability30", "GearyAuto_FreeEnergy24",
    "GearyAuto_FreeEnergy25", "GearyAuto_FreeEnergy30", "GearyAuto_ResidueASA21",
    "GearyAuto_ResidueASA22", "GearyAuto_ResidueASA23", "GearyAuto_ResidueASA24",
    "GearyAuto_ResidueASA30", "GearyAuto_ResidueVol21", "GearyAuto_ResidueVol24",
    "GearyAuto_ResidueVol25", "GearyAuto_ResidueVol26", "GearyAuto_ResidueVol28",
    "GearyAuto_ResidueVol29", "GearyAuto_ResidueVol30", "GearyAuto_Steric18",
    "GearyAuto_Steric21", "GearyAuto_Steric26", "GearyAuto_Steric27", "GearyAuto_Steric28",
    "GearyAuto_Steric29", "GearyAuto_Steric30", "GearyAuto_Mutability23", "GearyAuto_Mutability25",
    "GearyAuto_Mutability26", "GearyAuto_Mutability27", "GearyAuto_Mutability28",
    "GearyAuto_Mutability29", "GearyAuto_Mutability30", "APAAC1", "APAAC4", "APAAC5",
    "APAAC6", "APAAC8", "APAAC9", "APAAC12", "APAAC13", "APAAC15", "APAAC18", "APAAC19",
    "APAAC24"
]

# AMP Feature Extractor
def extract_features(sequence):
    all_features_dict = {}
    sequence = ''.join([aa for aa in sequence.upper() if aa in "ACDEFGHIKLMNPQRSTVWY"])
    if len(sequence) < 10:
        return "Error: Sequence too short."
    dipeptide_features = AAComposition.CalculateAADipeptideComposition(sequence)
    filtered_dipeptide_features = {k: dipeptide_features[k] for k in list(dipeptide_features.keys())[:420]}
    ctd_features = CTD.CalculateCTD(sequence)
    auto_features = Autocorrelation.CalculateAutoTotal(sequence)
    pseudo_features = PseudoAAC.GetAPseudoAAC(sequence, lamda=9)
    all_features_dict.update(ctd_features)
    all_features_dict.update(filtered_dipeptide_features)
    all_features_dict.update(auto_features)
    all_features_dict.update(pseudo_features)
    feature_df_all = pd.DataFrame([all_features_dict])
    normalized_array = scaler.transform(feature_df_all.values)
    normalized_df = pd.DataFrame(normalized_array, columns=feature_df_all.columns)
    selected_df = normalized_df[selected_features].fillna(0)
    return selected_df.values

# MIC Predictor
def predictmic(sequence):
    sequence = ''.join([aa for aa in sequence.upper() if aa in "ACDEFGHIKLMNPQRSTVWY"])
    if len(sequence) < 10:
        return {"Error": "Sequence too short or invalid. Must contain at least 10 valid amino acids."}
    seq_spaced = ' '.join(list(sequence))
    tokens = tokenizer(seq_spaced, return_tensors="pt", padding='max_length', truncation=True, max_length=512)
    tokens = {k: v.to(device) for k, v in tokens.items()}
    with torch.no_grad():
        outputs = protbert_model(**tokens)
        embedding = outputs.last_hidden_state.mean(dim=1).squeeze().cpu().numpy().reshape(1, -1)
    bacteria_config = {
        "E.coli": {"model": "coli_xgboost_model.pkl", "scaler": "coli_scaler.pkl", "pca": None},
        "S.aureus": {"model": "aur_xgboost_model.pkl", "scaler": "aur_scaler.pkl", "pca": None},
        "P.aeruginosa": {"model": "arg_xgboost_model.pkl", "scaler": "arg_scaler.pkl", "pca": None},
        "K.Pneumonia": {"model": "pne_mlp_model.pkl", "scaler": "pne_scaler.pkl", "pca": "pne_pca.pkl"}
    }
    mic_results = {}
    for bacterium, cfg in bacteria_config.items():
        try:
            scaler = joblib.load(cfg["scaler"])
            scaled = scaler.transform(embedding)
            transformed = joblib.load(cfg["pca"]).transform(scaled) if cfg["pca"] else scaled
            model = joblib.load(cfg["model"])
            mic_log = model.predict(transformed)[0]
            mic = round(expm1(mic_log), 3)
            mic_results[bacterium] = mic
        except Exception as e:
            mic_results[bacterium] = f"Error: {str(e)}"
    return mic_results

# Combined Output as Single String
def full_prediction(sequence):
    features = extract_features(sequence)
    if isinstance(features, str):  # error message returned
        return features
    prediction = model.predict(features)[0]
    probabilities = model.predict_proba(features)[0]
    amp_result = "Antimicrobial Peptide (AMP)" if prediction == 0 else "Non-AMP"
    confidence = round(probabilities[0 if prediction == 0 else 1] * 100, 2)
    
    result = f"Prediction: {amp_result}\nConfidence: {confidence}%\n"
    
    if prediction == 0:  # only predict MIC if AMP
        mic_values = predictmic(sequence)
        result += "\nPredicted MIC Values (µM):\n"
        for organism, mic in mic_values.items():
            result += f"- {organism}: {mic}\n"
    else:
        result += "\nMIC prediction is not available because sequence is Non-AMP."
    
    return result


# Gradio Interface (Single Label Output)
iface = gr.Interface(
    fn=full_prediction,
    inputs=gr.Textbox(label="Enter Protein Sequence"),
    outputs=gr.Textbox(label="AMP & MIC Prediction Summary"),
    title="AMP & MIC Predictor",
    description="Enter an amino acid sequence (≥10 valid letters) to predict AMP class and MIC values."
)

iface.launch(share=True)