scripts/deeppurpose002.py

import os
import json
import math
import time
import argparse
from datetime import datetime
import matplotlib.pyplot as plt
from datetime import datetime


import numpy as np
import pandas as pd

from tdc.multi_pred import DTI
from DeepPurpose import utils
from DeepPurpose import DTI as dp_models


# -------------------------
# Metrics (régression)
# -------------------------
def mse(y_true, y_pred):
    y_true = np.asarray(y_true, dtype=float).reshape(-1)
    y_pred = np.asarray(y_pred, dtype=float).reshape(-1)
    return float(np.mean((y_true - y_pred) ** 2))

def mae(y_true, y_pred):
    y_true = np.asarray(y_true, dtype=float).reshape(-1)
    y_pred = np.asarray(y_pred, dtype=float).reshape(-1)
    return float(np.mean(np.abs(y_true - y_pred)))

def pearson(y_true, y_pred):
    y_true = np.asarray(y_true, dtype=float).reshape(-1)
    y_pred = np.asarray(y_pred, dtype=float).reshape(-1)
    if y_true.size < 2 or np.std(y_true) == 0 or np.std(y_pred) == 0:
        return float("nan")
    return float(np.corrcoef(y_true, y_pred)[0, 1])

def spearman(y_true, y_pred):
    a = pd.Series(np.asarray(y_true, dtype=float).reshape(-1)).rank(method="average").to_numpy()
    b = pd.Series(np.asarray(y_pred, dtype=float).reshape(-1)).rank(method="average").to_numpy()
    return pearson(a, b)

def concordance_index_approx(y_true, y_pred, max_n=2000, seed=0):
    """
    CI approximatif (échantillonné si trop grand).
    """
    y_true = np.asarray(y_true, dtype=float).reshape(-1)
    y_pred = np.asarray(y_pred, dtype=float).reshape(-1)
    n = len(y_true)
    if n < 2:
        return float("nan")

    if n > max_n:
        rng = np.random.default_rng(seed)
        idx = rng.choice(n, size=max_n, replace=False)
        y_true = y_true[idx]
        y_pred = y_pred[idx]
        n = max_n

    conc = 0.0
    total = 0.0
    for i in range(n):
        for j in range(i + 1, n):
            if y_true[i] == y_true[j]:
                continue
            total += 1.0
            dt = y_true[i] - y_true[j]
            dp = y_pred[i] - y_pred[j]
            prod = dt * dp
            if prod > 0:
                conc += 1.0
            elif prod == 0:
                conc += 0.5
    if total == 0:
        return float("nan")
    return float(conc / total)


# -------------------------
# Utils
# -------------------------
def log_section(title):
    bar = "=" * 70
    print("\n" + bar)
    print(title)
    print(bar)

def detect_cols(df):
    cols = df.columns.tolist()
    # TDC DTI: souvent Drug, Target, Y
    drug_col = "Drug" if "Drug" in cols else None
    target_col = "Target" if "Target" in cols else None
    y_col = "Y" if "Y" in cols else None

    # fallback "best effort"
    if drug_col is None:
        for c in cols:
            if "smiles" in c.lower() or "drug" in c.lower():
                drug_col = c
                break
    if target_col is None:
        for c in cols:
            if "sequence" in c.lower() or "target" in c.lower() or "protein" in c.lower():
                target_col = c
                break
    if y_col is None:
        for c in cols:
            if c.lower() in {"y", "label", "labels", "affinity"}:
                y_col = c
                break

    # dernier fallback: 0,1,2
    if drug_col is None and len(cols) >= 1:
        drug_col = cols[0]
    if target_col is None and len(cols) >= 2:
        target_col = cols[1]
    if y_col is None and len(cols) >= 3:
        y_col = cols[2]

    return drug_col, target_col, y_col

def label_transform(y, mode, dataset_name):
    """
    mode:
      - none
      - paffinity_nm : suppose y en nM -> p = 9 - log10(nM)
      - auto : BindingDB_* -> paffinity_nm, sinon none
    """
    y = np.asarray(y, dtype=float)

    if mode == "auto":
        if dataset_name.startswith("BindingDB_"):
            mode = "paffinity_nm"
        else:
            mode = "none"

    if mode == "none":
        return y, "none"

    if mode == "paffinity_nm":
        y = np.where(y <= 0, np.nan, y)
        y = 9.0 - np.log10(y)
        return y, "paffinity_nm"

    raise ValueError(f"Unknown label_transform: {mode}")

def make_run_dir(base_dir, dataset):
    ts = datetime.now().strftime("%Y%m%d_%H%M%S")
    run_id = f"{ts}_{dataset}"
    run_dir = os.path.join(base_dir, run_id)
    os.makedirs(run_dir, exist_ok=True)
    return run_id, run_dir


def main():
    ap = argparse.ArgumentParser()
    ap.add_argument("--dataset", default="DAVIS", help="DAVIS | KIBA | BindingDB_Kd | BindingDB_Ki | BindingDB_IC50")
    ap.add_argument("--drug_enc", default="Morgan")
    ap.add_argument("--target_enc", default="CNN")
    ap.add_argument("--epochs", type=int, default=10)
    ap.add_argument("--batch", type=int, default=256)
    ap.add_argument("--lr", type=float, default=1e-4)
    ap.add_argument("--seed", type=int, default=1)
    ap.add_argument("--split", default="random", help="DeepPurpose split_method (random recommandé ici)")
    ap.add_argument("--frac_train", type=float, default=0.8)
    ap.add_argument("--frac_val", type=float, default=0.1)
    ap.add_argument("--frac_test", type=float, default=0.1)
    ap.add_argument("--label_transform", default="auto", help="auto | none | paffinity_nm")
    ap.add_argument("--harmonize", default="none", help="none | mean | max_affinity (utile surtout BindingDB_*)")
    ap.add_argument("--runs_dir", default="runs")
    ap.add_argument("--dry_run", action="store_true", help="Charge dataset + prints info, sans training")
    args = ap.parse_args()

    np.random.seed(args.seed)

    run_id, run_dir = make_run_dir(args.runs_dir, args.dataset)
    pred_path = os.path.join(run_dir, "predictions_test.csv")
    summary_path = os.path.join(run_dir, "run_summary.json")

    # -------------------------
    # 1) LOAD DATA (TDC)
    # -------------------------
    log_section("[1] LOAD DATASET (TDC)")
    print(f"[RUN] run_id={run_id}")
    print(f"[RUN] dataset={args.dataset}")
    print(f"[RUN] cache=PyTDC (download auto si nécessaire)")

    t0 = time.time()
    data = DTI(name=args.dataset)

    if args.harmonize != "none" and args.dataset.startswith("BindingDB_"):
        mode = args.harmonize
        print(f"[TDC] harmonize_affinities(mode='{mode}')")
        data.harmonize_affinities(mode=mode)

    # PyTDC renvoie un DataFrame via get_data() (selon version, get_data(format='df') existe aussi)
    try:
        df = data.get_data()
    except TypeError:
        df = data.get_data(format="df")

    print(f"[INPUT] raw_shape={df.shape}")
    drug_col, target_col, y_col = detect_cols(df)
    print(f"[INPUT] detected_cols: drug='{drug_col}', target='{target_col}', label='{y_col}'")

    # -------------------------
    # 2) CLEAN + PREP
    # -------------------------
    log_section("[2] CLEAN + PREP (Input DeepPurpose)")
    df = df[[drug_col, target_col, y_col]].copy()
    df.columns = ["Drug", "Target", "Y"]

    n0 = len(df)
    df = df.dropna()
    df["Drug"] = df["Drug"].astype(str).str.strip()
    df["Target"] = df["Target"].astype(str).str.strip()
    df = df[(df["Drug"] != "") & (df["Target"] != "")]
    df["Y"] = pd.to_numeric(df["Y"], errors="coerce")
    df = df.dropna()
    n1 = len(df)

    y_raw = df["Y"].astype(float).values
    y_trans, used_transform = label_transform(y_raw, args.label_transform, args.dataset)
    df["Y"] = y_trans
    df = df.dropna()
    n2 = len(df)

    # drop duplicates (Drug,Target) -> keep first
    df = df.drop_duplicates(subset=["Drug", "Target"], keep="first").reset_index(drop=True)
    n3 = len(df)

    print(f"[CLEAN] start={n0} -> after_na/parse={n1} -> after_transform={n2} -> after_dedup={n3}")
    print(f"[LABEL] transform={used_transform}")
    y = df["Y"].astype(float).values
    print(f"[LABEL] stats: min={np.min(y):.6f} | mean={np.mean(y):.6f} | median={np.median(y):.6f} | max={np.max(y):.6f}")
    print("[SAMPLE] first_rows:")
    print(df.head(3).to_string(index=False))

    if args.dry_run:
        print(f"\n[DRY_RUN] stop ici. (Aucun training lancé)")
        return

    # -------------------------
    # 3) SPLIT + ENCODE (DeepPurpose)
    # -------------------------
    log_section("[3] DATA_PROCESS (DeepPurpose)")
    frac = [args.frac_train, args.frac_val, args.frac_test]
    print(f"[SPLIT] method={args.split} | frac={frac} | seed={args.seed}")
    X_drugs = df["Drug"].values
    X_targets = df["Target"].values
    y = df["Y"].values

    train, val, test = utils.data_process(
        X_drugs, X_targets, y,
        drug_encoding=args.drug_enc,
        target_encoding=args.target_enc,
        split_method=args.split,
        frac=frac,
        random_seed=args.seed
    )

    # tailles (DeepPurpose objects ont souvent .Label)
    try:
        n_train, n_val, n_test = len(train.Label), len(val.Label), len(test.Label)
    except Exception:
        # fallback: len(obj)
        n_train, n_val, n_test = len(train), len(val), len(test)

    print(f"[SPLIT] sizes: train={n_train} | val={n_val} | test={n_test}")
    print(f"[ENC] drug_encoding={args.drug_enc} | target_encoding={args.target_enc}")

    # -------------------------
    # 4) MODEL INIT + TRAIN
    # -------------------------
    log_section("[4] MODEL INIT + TRAIN")
    config = utils.generate_config(
        drug_encoding=args.drug_enc,
        target_encoding=args.target_enc,
        cls_hidden_dims=[1024, 1024, 512],
        train_epoch=args.epochs,
        batch_size=args.batch,
        LR=args.lr,
        result_folder=run_dir
    )

    print("[MODEL] config:")
    print(f"  epochs={args.epochs} | batch={args.batch} | lr={args.lr}")
    print(f"  hidden=[1024,1024,512] | result_dir={run_dir}")

    model = dp_models.model_initialize(**config)

    t_train0 = time.time()
    try:
        model.train(train, val, test)
    except TypeError:
        model.train(train, val)
    t_train1 = time.time()
    print(f"[TIME] train_seconds={t_train1 - t_train0:.1f}")

    # -------------------------
    # 5) EVAL + EXPORT
    # -------------------------
    log_section("[5] EVAL + EXPORT")
    print("[PREDICT] predicting on test...")
    y_true = np.asarray(test.Label.values, dtype=float).reshape(-1)
    y_pred = np.asarray(model.predict(test), dtype=float).reshape(-1)

    m_mse = mse(y_true, y_pred)
    m_rmse = float(math.sqrt(m_mse))
    m_mae = mae(y_true, y_pred)
    m_p = pearson(y_true, y_pred)
    m_s = spearman(y_true, y_pred)
    m_ci = concordance_index_approx(y_true, y_pred, max_n=2000, seed=args.seed)

    print("[METRICS] test:")
    print(f"  MSE   = {m_mse:.6f}")
    print(f"  RMSE  = {m_rmse:.6f}")
    print(f"  MAE   = {m_mae:.6f}")
    print(f"  Pearson  = {m_p:.6f}")
    print(f"  Spearman = {m_s:.6f}")
    print(f"  CI(approx) = {m_ci:.6f}")

    out_pred = pd.DataFrame({"y_true": y_true, "y_pred": y_pred})
    out_pred.to_csv(pred_path, index=False)
    print(f"[FILE] saved predictions: {pred_path}")

    summary = {
        "run_id": run_id,
        "dataset": args.dataset,
        "drug_encoding": args.drug_enc,
        "target_encoding": args.target_enc,
        "epochs": args.epochs,
        "batch": args.batch,
        "lr": args.lr,
        "seed": args.seed,
        "split_method": args.split,
        "frac": [args.frac_train, args.frac_val, args.frac_test],
        "label_transform": used_transform,
        "harmonize": args.harmonize,
        "n_rows_after_clean": int(len(df)),
        "metrics_test": {
            "mse": m_mse,
            "rmse": m_rmse,
            "mae": m_mae,
            "pearson": m_p,
            "spearman": m_s,
            "ci_approx": m_ci,
        },
        "files": {
            "predictions_test_csv": pred_path,
        },
        "timing": {
            "load_seconds": time.time() - t0,
            "train_seconds": t_train1 - t_train0,
        }
    }
    with open(summary_path, "w", encoding="utf-8") as f:
        json.dump(summary, f, indent=2)
    print(f"[FILE] saved summary: {summary_path}")

    print("\n[DONE]")


if __name__ == "__main__":
    main()
# =========================
# VISUALISATION + EXPORTS
# =========================

# 0) Dossier de sortie (stable)
BASE_DIR = os.path.dirname(__file__)
RUNS_DIR = os.path.join(BASE_DIR, "runs")
os.makedirs(RUNS_DIR, exist_ok=True)

# si tu as déjà un run_dir dans ton code, il sera utilisé; sinon on en crée un
try:
    run_dir
except NameError:
    run_id = datetime.now().strftime("%Y%m%d_%H%M%S")
    run_dir = os.path.join(RUNS_DIR, run_id)
    os.makedirs(run_dir, exist_ok=True)

# 1) Récupère y_true / y_pred (sans retraining)
y_true = np.asarray(test.Label.values, dtype=float).reshape(-1)
y_pred = np.asarray(model.predict(test), dtype=float).reshape(-1)

# 2) Sauvegarde CSV predictions
pred_csv = os.path.join(run_dir, "predictions_test.csv")
pd.DataFrame({"y_true": y_true, "y_pred": y_pred}).to_csv(pred_csv, index=False)
print("[FILE] saved predictions:", pred_csv)

# 3) Scatter: y_true vs y_pred
scatter_png = os.path.join(run_dir, "scatter.png")
plt.figure()
plt.scatter(y_true, y_pred, s=8)
plt.xlabel("y_true")
plt.ylabel("y_pred")
plt.title("Test: y_true vs y_pred")
plt.tight_layout()
plt.savefig(scatter_png, dpi=200)
plt.close()
print("[PLOT] saved:", scatter_png)

# 4) Courbes triées: y_true et y_pred (tri par y_true)
curves_png = os.path.join(run_dir, "curves_sorted.png")
order = np.argsort(y_true)
plt.figure()
plt.plot(y_true[order], label="y_true")
plt.plot(y_pred[order], label="y_pred")
plt.xlabel("samples (sorted by y_true)")
plt.ylabel("value")
plt.title("Test: curves (sorted)")
plt.legend()
plt.tight_layout()
plt.savefig(curves_png, dpi=200)
plt.close()
print("[PLOT] saved:", curves_png)

# 5) Résidus: (y_pred - y_true) vs y_true
res_png = os.path.join(run_dir, "residuals.png")
res = y_pred - y_true
plt.figure()
plt.scatter(y_true, res, s=8)
plt.axhline(0)
plt.xlabel("y_true")
plt.ylabel("y_pred - y_true")
plt.title("Test: residuals")
plt.tight_layout()
plt.savefig(res_png, dpi=200)
plt.close()
print("[PLOT] saved:", res_png)