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@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+july3.xlsx filter=lfs diff=lfs merge=lfs -text

july3.xlsx

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+version https://git-lfs.github.com/spec/v1
+oid sha256:2fc4f44468eaf6f73112a550fcc058c200f617394bdad9f3db45a09293c0eec1
+size 100575

main.py

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+# ================================================================
+# Self-Sensing Concrete Assistant — Hybrid RAG + XGB + (opt) GPT-5
+# FIXED for Windows/Conda import issues (transformers/quantizers)
+# - Pins compatible versions (transformers 4.44.2, sbert 2.7.0, torch 2.x)
+# - Disables TF/Flax backends; safe fallbacks if dense fails
+# - Hybrid retrieval (BM25 + TF-IDF + Dense*) + MMR sentence selection
+# - Optional OA PDF harvest (Crossref + Unpaywall) OR local folder
+# - Optional GPT-5 synthesis strictly from selected cited sentences
+# - Gradio UI with Prediction + Literature Q&A tabs
+# ================================================================
+
+# ---------------------- MUST RUN THESE FLAGS FIRST ----------------------
+import os
+os.environ["TRANSFORMERS_NO_TF"] = "1"      # don't import TensorFlow
+os.environ["TRANSFORMERS_NO_FLAX"] = "1"    # don't import Flax/JAX
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# ------------------------------- Imports -----------------------------------
+import re, json, time, joblib, warnings, math, hashlib, urllib.parse, requests
+from pathlib import Path
+from typing import List, Dict
+import numpy as np
+import pandas as pd
+
+from sklearn.model_selection import train_test_split
+from sklearn.impute import SimpleImputer
+from sklearn.pipeline import Pipeline
+from sklearn.compose import ColumnTransformer
+from sklearn.preprocessing import RobustScaler, OneHotEncoder
+from sklearn.preprocessing import normalize as sk_normalize
+from sklearn.metrics import r2_score, mean_absolute_error, mean_squared_error
+from sklearn.feature_selection import VarianceThreshold
+from sklearn.feature_extraction.text import TfidfVectorizer
+
+from xgboost import XGBRegressor
+from pypdf import PdfReader
+import fitz  # PyMuPDF
+import gradio as gr
+
+USE_DENSE = True
+try:
+    from sentence_transformers import SentenceTransformer
+except Exception as e:
+    USE_DENSE = False
+    print("⚠️ sentence-transformers unavailable; continuing with TF-IDF + BM25 only.\n", e)
+
+from rank_bm25 import BM25Okapi
+from openai import OpenAI
+
+warnings.filterwarnings("ignore", category=UserWarning)
+
+# ============================ Config =======================================
+# --- Data & model paths ---
+DATA_PATH       = r"C:\Users\nmoha13\OneDrive - Louisiana State University\School\Grad School\ChatBot\LLM\july3.xlsx"   # <- update if needed
+LOCAL_PDF_DIR   = Path(r"C:\Users\nmoha13\OneDrive - Louisiana State University\School\Grad School\ChatBot\LLM") # <- optional local folder
+
+# --- RAG artifacts (kept in working dir) ---
+ARTIFACT_DIR    = Path("rag_artifacts"); ARTIFACT_DIR.mkdir(exist_ok=True)
+MODEL_OUT       = "stress_gf_xgb.joblib"
+TFIDF_VECT_PATH = ARTIFACT_DIR / "tfidf_vectorizer.joblib"
+TFIDF_MAT_PATH  = ARTIFACT_DIR / "tfidf_matrix.joblib"
+BM25_TOK_PATH   = ARTIFACT_DIR / "bm25_tokens.joblib"
+EMB_NPY_PATH    = ARTIFACT_DIR / "chunk_embeddings.npy"
+RAG_META_PATH   = ARTIFACT_DIR / "chunks.parquet"
+
+# --- Online OA sourcing (set USE_ONLINE_SOURCES=False to rely only on local PDFs) ---
+USE_ONLINE_SOURCES = True
+DOWNLOAD_DIR       = Path("oa_pdfs"); DOWNLOAD_DIR.mkdir(exist_ok=True)
+
+KEYWORDS = [
+    "self-sensing concrete gauge factor",
+    "piezoresistive cementitious composite",
+    "carbon nanotube cement gauge factor",
+    "graphene nanoplatelet self-sensing mortar",
+]
+YEAR_FROM, YEAR_TO = 2010, 2025
+MAX_DOIS_PER_QUERY = 25
+
+# Required identifiers for APIs (use institutional email)
+UNPAYWALL_EMAIL   = os.getenv("UNPAYWALL_EMAIL", "your_email@lsu.edu")
+CROSSREF_MAILTO   = os.getenv("CROSSREF_MAILTO", "your_email@lsu.edu")
+
+# --- Embedding model (fast CPU) ---
+EMB_MODEL_NAME    = os.getenv("EMB_MODEL_NAME", "sentence-transformers/all-MiniLM-L6-v2")
+
+# --- OpenAI (optional LLM synthesis) ---
+OPENAI_MODEL      = os.getenv("OPENAI_MODEL", "gpt-5")  # e.g., "gpt-5-mini"
+OPENAI_API_KEY    = os.getenv("OPENAI_API_KEY", None)   # set env var to enable LLM
+
+# --- Retrieval weights (UI defaults adapt if dense disabled) ---
+W_TFIDF_DEFAULT = 0.50 if not USE_DENSE else 0.30
+W_BM25_DEFAULT  = 0.50 if not USE_DENSE else 0.30
+W_EMB_DEFAULT   = 0.00 if not USE_DENSE else 0.40
+
+RANDOM_SEED = 42
+
+# ====================== OA PDF Harvesting (Crossref + Unpaywall) ===========
+def crossref_search_dois(query, year_from=YEAR_FROM, year_to=YEAR_TO, rows=MAX_DOIS_PER_QUERY):
+    base = "https://api.crossref.org/works"
+    params = {
+        "query": query,
+        "filter": f"type:journal-article,from-pub-date:{year_from}-01-01,until-pub-date:{year_to}-12-31",
+        "rows": rows,
+        "mailto": CROSSREF_MAILTO
+    }
+    r = requests.get(base, params=params, timeout=30)
+    r.raise_for_status()
+    items = r.json().get("message", {}).get("items", [])
+    dois = []
+    for it in items:
+        doi = it.get("DOI")
+        title = " ".join(it.get("title", [])[:1]).strip() if it.get("title") else ""
+        if doi:
+            dois.append((doi, title))
+    return dois
+
+def unpaywall_pdf_url(doi, email=UNPAYWALL_EMAIL):
+    url = f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi)}?email={urllib.parse.quote(email)}"
+    r = requests.get(url, timeout=30)
+    if r.status_code != 200:
+        return None
+    data = r.json()
+    loc = data.get("best_oa_location") or {}
+    return loc.get("url_for_pdf") or loc.get("url")
+
+def _sanitize_filename(s):
+    return "".join(c for c in s if c.isalnum() or c in "._- ()").strip()[:180] or "paper"
+
+def fetch_oa_pdfs(keywords=KEYWORDS, out_dir=DOWNLOAD_DIR, throttle=1.2):
+    saved = []
+    for q in keywords:
+        try:
+            dois = crossref_search_dois(q)
+        except Exception as e:
+            print(f"[Crossref] {q}: {e}")
+            continue
+        for doi, title in dois:
+            try:
+                pdf_url = unpaywall_pdf_url(doi)
+            except Exception as e:
+                print(f"[Unpaywall] {doi}: {e}")
+                pdf_url = None
+            time.sleep(throttle)
+            if not pdf_url:
+                continue
+            fname = _sanitize_filename(f"{title or doi}.pdf")
+            fp = out_dir / fname
+            if fp.exists():
+                saved.append(fp); continue
+            try:
+                rr = requests.get(pdf_url, timeout=60)
+                ctype = rr.headers.get("Content-Type", "")
+                if rr.status_code == 200 and "pdf" in ctype.lower():
+                    with open(fp, "wb") as f:
+                        f.write(rr.content)
+                    print(f"Saved: {fp.name}")
+                    saved.append(fp)
+                else:
+                    print(f"Skipped (not pdf): {pdf_url}")
+            except Exception as e:
+                print(f"[Download] {pdf_url}: {e}")
+    print(f"Total OA PDFs cached: {len(saved)}")
+    return saved
+
+def get_pdf_source_dir():
+    if USE_ONLINE_SOURCES:
+        fetch_oa_pdfs()  # idempotent; skips existing
+        return DOWNLOAD_DIR
+    else:
+        return LOCAL_PDF_DIR
+
+# ==================== XGB Pipeline (Prediction) ============================
+def make_onehot():
+    try:
+        return OneHotEncoder(handle_unknown="ignore", sparse_output=False)
+    except TypeError:
+        return OneHotEncoder(handle_unknown="ignore", sparse=False)
+
+def rmse(y_true, y_pred):
+    return mean_squared_error(y_true, y_pred)
+
+def evaluate(m, X, y_log, name="Model"):
+    y_pred_log = m.predict(X)
+    y_pred = np.expm1(y_pred_log)
+    y_true = np.expm1(y_log)
+    r2  = r2_score(y_true, y_pred)
+    r   = rmse(y_true, y_pred)
+    mae = mean_absolute_error(y_true, y_pred)
+    print(f"{name}: R²={r2:.3f}, RMSE={r:.3f}, MAE={mae:.3f}")
+    return r2, r, mae
+
+# --- Load data
+df = pd.read_excel(DATA_PATH)
+df.columns = df.columns.str.strip()
+
+drop_cols = [
+    'Loading rate (MPa/s)', 'Voltage (V) AC\\DC', 'Elastic Modulus (GPa)', 'Duration (hrs) of Dying Method'
+]
+df = df.drop(columns=[c for c in drop_cols if c in df.columns], errors='ignore')
+
+main_variables = [
+    'Filler1_Type', 'Filler1_Diameter_um', 'Filler1_Length_mm',
+    'AvgFiller_Density_g/cm3', 'AvgFiller_weight_%', 'AvgFiller_Volume_%',
+    'Filler1_Dimensions', 'Filler2_Type', 'Filler2_Diameter_um', 'Filler2_Length_mm',
+    'Filler2_Dimensions', 'Sample_Volume_mm3', 'Electrode/Probe_Count', 'Electrode/Probe_Material',
+    'W/B', 'S/B', 'GaugeLength_mm', 'Curing_Conditions', 'Num_ConductiveFillers',
+    'DryingTemperature_C', 'DryingDuration_hrs', 'LoadingRate_MPa/s',
+    'ElasticModulus_Gpa', 'Voltage_Type', 'Applied_Voltage_V'
+]
+target_col = 'Stress_GF_Mpa'
+
+df = df[main_variables + [target_col]].copy()
+df = df.dropna(subset=[target_col])
+df = df[df[target_col] > 0]
+
+numeric_cols = [
+    'Filler1_Diameter_um', 'Filler1_Length_mm', 'AvgFiller_Density_g/cm3',
+    'AvgFiller_weight_%', 'AvgFiller_Volume_%', 'Filler2_Diameter_um',
+    'Filler2_Length_mm', 'Sample_Volume_mm3', 'Electrode/Probe_Count',
+    'W/B', 'S/B', 'GaugeLength_mm', 'Num_ConductiveFillers',
+    'DryingTemperature_C', 'DryingDuration_hrs', 'LoadingRate_MPa/s',
+    'ElasticModulus_Gpa', 'Applied_Voltage_V'
+]
+categorical_cols = [
+    'Filler1_Type', 'Filler1_Dimensions', 'Filler2_Type', 'Filler2_Dimensions',
+    'Electrode/Probe_Material', 'Curing_Conditions', 'Voltage_Type'
+]
+
+for c in numeric_cols:
+    df[c] = pd.to_numeric(df[c], errors='coerce')
+for c in categorical_cols:
+    df[c] = df[c].astype(str)
+
+vt = VarianceThreshold(threshold=1e-3)
+vt.fit(df[numeric_cols])
+numeric_cols = [c for c in numeric_cols if c not in df[numeric_cols].columns[vt.variances_ < 1e-3]]
+
+corr = df[numeric_cols].corr().abs()
+upper = corr.where(np.triu(np.ones(corr.shape), k=1).astype(bool))
+to_drop = [c for c in upper.columns if any(upper[c] > 0.95)]
+numeric_cols = [c for c in numeric_cols if c not in to_drop]
+
+X = df[main_variables].copy()
+y = np.log1p(df[target_col])
+
+X_train, X_test, y_train, y_test = train_test_split(
+    X, y, test_size=0.2, random_state=RANDOM_SEED
+)
+
+BEST_PARAMS = {
+    "regressor__subsample":        1.0,
+    "regressor__reg_lambda":       5,
+    "regressor__reg_alpha":        0.05,
+    "regressor__n_estimators":     300,
+    "regressor__max_depth":        6,
+    "regressor__learning_rate":    0.1,
+    "regressor__gamma":            0,
+    "regressor__colsample_bytree": 1.0
+}
+
+def train_and_save_model():
+    num_tf = Pipeline([('imputer', SimpleImputer(strategy='median')),
+                       ('scaler', RobustScaler())])
+    cat_tf = Pipeline([('imputer', SimpleImputer(strategy='most_frequent')),
+                       ('onehot', make_onehot())])
+
+    preprocessor = ColumnTransformer([
+        ('num', num_tf, numeric_cols),
+        ('cat', cat_tf, categorical_cols)
+    ])
+
+    xgb_pipe = Pipeline([
+        ('preprocessor', preprocessor),
+        ('regressor', XGBRegressor(random_state=RANDOM_SEED, n_jobs=-1, verbosity=0))
+    ])
+    xgb_pipe.set_params(**BEST_PARAMS).fit(X_train, y_train)
+
+    joblib.dump(xgb_pipe, MODEL_OUT)
+    print(f"✅ Trained new model and saved → {MODEL_OUT}")
+    return xgb_pipe
+
+def load_or_train_model():
+    if os.path.exists(MODEL_OUT):
+        print(f"📂 Loading existing model from {MODEL_OUT}")
+        return joblib.load(MODEL_OUT)
+    else:
+        print("⚠️ No saved model found. Training a new one...")
+        return train_and_save_model()
+
+xgb_pipe = load_or_train_model()
+
+
+# ======================= Hybrid RAG Indexing ================================
+_SENT_SPLIT_RE = re.compile(r"(?<=[.!?])\s+|\n+")
+TOKEN_RE = re.compile(r"[A-Za-z0-9_#+\-/\.%]+")
+
+def sent_split(text: str) -> List[str]:
+    sents = [s.strip() for s in _SENT_SPLIT_RE.split(text) if s.strip()]
+    return [s for s in sents if len(s.split()) >= 5]
+
+def tokenize(text: str) -> List[str]:
+    return [t.lower() for t in TOKEN_RE.findall(text)]
+
+def extract_text_pymupdf(pdf_path: Path) -> str:
+    try:
+        doc = fitz.open(pdf_path)
+        buff = []
+        for i, page in enumerate(doc):
+            txt = page.get_text("text") or ""
+            buff.append(f"[[PAGE={i+1}]]\n{txt}")
+        return "\n\n".join(buff)
+    except Exception:
+        # Fallback to PyPDF
+        try:
+            reader = PdfReader(str(pdf_path))
+            buff = []
+            for i, p in enumerate(reader.pages):
+                txt = p.extract_text() or ""
+                buff.append(f"[[PAGE={i+1}]]\n{txt}")
+            return "\n\n".join(buff)
+        except Exception as e:
+            print(f"PDF read error ({pdf_path}): {e}")
+            return ""
+
+def chunk_by_sentence_windows(text: str, win_size=8, overlap=2) -> List[str]:
+    sents = sent_split(text)
+    chunks = []
+    step = max(1, win_size - overlap)
+    for i in range(0, len(sents), step):
+        window = sents[i:i+win_size]
+        if not window: break
+        chunks.append(" ".join(window))
+    return chunks
+
+def _safe_init_st_model(name: str):
+    """Try to init SentenceTransformer; on failure, disable dense and return None."""
+    global USE_DENSE
+    if not USE_DENSE:
+        return None
+    try:
+        m = SentenceTransformer(name)
+        return m
+    except Exception as e:
+        print("⚠️ Could not initialize SentenceTransformer; disabling dense embeddings.\n", e)
+        USE_DENSE = False
+        return None
+
+def build_or_load_hybrid(pdf_dir: Path):
+    have_cache = (TFIDF_VECT_PATH.exists() and TFIDF_MAT_PATH.exists()
+                  and BM25_TOK_PATH.exists() and RAG_META_PATH.exists()
+                  and (EMB_NPY_PATH.exists() or not USE_DENSE))
+    if have_cache:
+        vectorizer = joblib.load(TFIDF_VECT_PATH)
+        X_tfidf    = joblib.load(TFIDF_MAT_PATH)
+        meta       = pd.read_parquet(RAG_META_PATH)
+        bm25_toks  = joblib.load(BM25_TOK_PATH)
+        emb        = np.load(EMB_NPY_PATH) if (USE_DENSE and EMB_NPY_PATH.exists()) else None
+        print("Loaded hybrid index.")
+        return vectorizer, X_tfidf, meta, bm25_toks, emb
+
+    rows, all_tokens = [], []
+    pdf_paths = list(Path(pdf_dir).glob("**/*.pdf"))
+    if LOCAL_PDF_DIR.exists() and LOCAL_PDF_DIR != pdf_dir:
+        pdf_paths += list(LOCAL_PDF_DIR.glob("**/*.pdf"))
+
+    print(f"Indexing PDFs from {pdf_dir} (+ local merge if present). Found {len(pdf_paths)} files.")
+    for pdf in pdf_paths:
+        raw = extract_text_pymupdf(pdf)
+        if not raw.strip():
+            continue
+        for i, ch in enumerate(chunk_by_sentence_windows(raw, win_size=8, overlap=2)):
+            rows.append({"doc_path": str(pdf), "chunk_id": i, "text": ch})
+            all_tokens.append(tokenize(ch))
+
+    if not rows:
+        raise RuntimeError(f"No PDF text found under: {pdf_dir}")
+
+    meta = pd.DataFrame(rows)
+
+    # TF-IDF
+    vectorizer = TfidfVectorizer(
+        ngram_range=(1,2),
+        min_df=1, max_df=0.95,
+        sublinear_tf=True, smooth_idf=True,
+        lowercase=True,
+        token_pattern=r"(?u)\b\w[\w\-\./%+#]*\b"
+    )
+    X_tfidf = vectorizer.fit_transform(meta["text"].tolist())
+
+    # Dense (optional)
+    emb = None
+    if USE_DENSE:
+        try:
+            st_model_tmp = _safe_init_st_model(EMB_MODEL_NAME)
+            if st_model_tmp is not None:
+                em = st_model_tmp.encode(meta["text"].tolist(), batch_size=64, show_progress_bar=False, convert_to_numpy=True)
+                emb = sk_normalize(em)
+                np.save(EMB_NPY_PATH, emb)
+        except Exception as e:
+            emb = None
+            print("⚠️ Dense embeddings failed; continuing without them.\n", e)
+
+    # Save artifacts
+    joblib.dump(vectorizer, TFIDF_VECT_PATH)
+    joblib.dump(X_tfidf, TFIDF_MAT_PATH)
+    joblib.dump(all_tokens, BM25_TOK_PATH)
+    meta.to_parquet(RAG_META_PATH, index=False)
+
+    print(f"Indexed {len(meta)} chunks from {meta['doc_path'].nunique()} PDFs.")
+    return vectorizer, X_tfidf, meta, all_tokens, emb
+
+# Build hybrid index
+pdf_source_dir = get_pdf_source_dir()
+tfidf_vectorizer, tfidf_matrix, rag_meta, bm25_tokens, emb_matrix = build_or_load_hybrid(pdf_source_dir)
+bm25 = BM25Okapi(bm25_tokens)
+st_query_model = _safe_init_st_model(EMB_MODEL_NAME)  # safe init; may set USE_DENSE=False
+
+# If dense failed at runtime, update default weights in case UI uses them
+if not USE_DENSE:
+    W_TFIDF_DEFAULT, W_BM25_DEFAULT, W_EMB_DEFAULT = 0.50, 0.50, 0.00
+
+def _extract_page(text_chunk: str) -> str:
+    m = list(re.finditer(r"\[\[PAGE=(\d+)\]\]", text_chunk))
+    return (m[-1].group(1) if m else "?")
+
+# ---------------------- Hybrid search --------------------------------------
+def hybrid_search(query: str, k=8, w_tfidf=W_TFIDF_DEFAULT, w_bm25=W_BM25_DEFAULT, w_emb=W_EMB_DEFAULT):
+    # Dense (optional)
+    if USE_DENSE and st_query_model is not None and emb_matrix is not None and w_emb > 0:
+        try:
+            q_emb = st_query_model.encode([query], convert_to_numpy=True)
+            q_emb = sk_normalize(q_emb)[0]
+            dense_scores = emb_matrix @ q_emb
+        except Exception as e:
+            print("⚠️ Dense query encoding failed; ignoring dense this run.\n", e)
+            dense_scores = np.zeros(len(rag_meta), dtype=float)
+            w_emb = 0.0
+    else:
+        dense_scores = np.zeros(len(rag_meta), dtype=float)
+        w_emb = 0.0  # force off
+
+    # TF-IDF
+    q_vec = tfidf_vectorizer.transform([query])
+    tfidf_scores = (tfidf_matrix @ q_vec.T).toarray().ravel()
+
+    # BM25
+    q_tokens = [t.lower() for t in TOKEN_RE.findall(query)]
+    bm25_scores = np.array(bm25.get_scores(q_tokens), dtype=float)
+
+    def _norm(x):
+        x = np.asarray(x, dtype=float)
+        if np.allclose(x.max(), x.min()):
+            return np.zeros_like(x)
+        return (x - x.min()) / (x.max() - x.min())
+
+    s_dense = _norm(dense_scores)
+    s_tfidf = _norm(tfidf_scores)
+    s_bm25  = _norm(bm25_scores)
+
+    total_w = (w_tfidf + w_bm25 + w_emb) or 1.0
+    w_tfidf, w_bm25, w_emb = w_tfidf/total_w, w_bm25/total_w, w_emb/total_w
+
+    combo = w_emb * s_dense + w_tfidf * s_tfidf + w_bm25 * s_bm25
+    idx = np.argsort(-combo)[:k]
+    hits = rag_meta.iloc[idx].copy()
+    hits["score_dense"] = s_dense[idx]
+    hits["score_tfidf"] = s_tfidf[idx]
+    hits["score_bm25"]  = s_bm25[idx]
+    hits["score"]       = combo[idx]
+    return hits.reset_index(drop=True)
+
+# -------------- Sentence selection with MMR (diversity) --------------------
+def split_sentences(text: str) -> List[str]:
+    sents = sent_split(text)
+    return [s for s in sents if 6 <= len(s.split()) <= 60]
+
+def mmr_select_sentences(question: str, hits: pd.DataFrame, top_n=4, pool_per_chunk=6, lambda_div=0.7):
+    pool = []
+    for _, row in hits.iterrows():
+        doc = Path(row["doc_path"]).name
+        page = _extract_page(row["text"])
+        for s in split_sentences(row["text"])[:pool_per_chunk]:
+            pool.append({"sent": s, "doc": doc, "page": page})
+    if not pool:
+        return []
+
+    sent_texts = [p["sent"] for p in pool]
+
+    if USE_DENSE and st_query_model is not None:
+        try:
+            texts = [question] + sent_texts
+            enc = st_query_model.encode(texts, convert_to_numpy=True)
+            q_vec = sk_normalize(enc[:1])[0]
+            S    = sk_normalize(enc[1:])
+            rel = (S @ q_vec)
+            def sim_fn(i, j): return float(S[i] @ S[j])
+        except Exception as e:
+            print("⚠️ Dense sentence encoding failed; falling back to TF-IDF for MMR.\n", e)
+            Q = tfidf_vectorizer.transform([question])
+            S = tfidf_vectorizer.transform(sent_texts)
+            rel = (S @ Q.T).toarray().ravel()
+            def sim_fn(i, j): return float((S[i] @ S[j].T).toarray()[0, 0])
+    else:
+        Q = tfidf_vectorizer.transform([question])
+        S = tfidf_vectorizer.transform(sent_texts)
+        rel = (S @ Q.T).toarray().ravel()
+        def sim_fn(i, j): return float((S[i] @ S[j].T).toarray()[0, 0])
+
+    selected, selected_idx = [], []
+    remain = list(range(len(pool)))
+    first = int(np.argmax(rel))
+    selected.append(pool[first]); selected_idx.append(first); remain.remove(first)
+
+    while len(selected) < top_n and remain:
+        cand_scores = []
+        for i in remain:
+            sim_to_sel = max(sim_fn(i, j) for j in selected_idx) if selected_idx else 0.0
+            score = lambda_div * rel[i] - (1 - lambda_div) * sim_to_sel
+            cand_scores.append((score, i))
+        cand_scores.sort(reverse=True)
+        best_i = cand_scores[0][1]
+        selected.append(pool[best_i]); selected_idx.append(best_i); remain.remove(best_i)
+    return selected
+
+def compose_extractive(selected: List[Dict]) -> str:
+    if not selected:
+        return ""
+    lines = [f"{s['sent']} ({s['doc']}, p.{s['page']})" for s in selected]
+    return " ".join(lines)
+
+# ------------------- Optional GPT-5 synthesis ------------------------------
+def synthesize_with_llm(question: str, sentence_lines: List[str], model: str = None, temperature: float = 0.2) -> str:
+    if OPENAI_API_KEY is None:
+        return None  # not configured → skip synthesis
+    client = OpenAI(api_key=OPENAI_API_KEY)
+    if model is None:
+        model = OPENAI_MODEL
+
+    SYSTEM_PROMPT = (
+        "You are a scientific assistant for self-sensing cementitious materials.\n"
+        "Answer STRICTLY using the provided sentences.\n"
+        "Do not invent facts. Keep it concise (3–6 sentences).\n"
+        "Retain inline citations like (Doc.pdf, p.X) exactly as given."
+    )
+    user_prompt = (
+        f"Question: {question}\n\n"
+        f"Use ONLY these sentences to answer; keep their inline citations:\n" +
+        "\n".join(f"- {s}" for s in sentence_lines)
+    )
+    try:
+        resp = client.responses.create(
+            model=model,
+            input=[
+                {"role": "system", "content": SYSTEM_PROMPT},
+                {"role": "user", "content": user_prompt},
+            ],
+            temperature=temperature,
+        )
+        return getattr(resp, "output_text", None) or str(resp)
+    except Exception:
+        return None
+
+# ------------------------ RAG reply ----------------------------------------
+def rag_reply(
+    question: str,
+    k: int = 8,
+    n_sentences: int = 4,
+    include_passages: bool = False,
+    use_llm: bool = False,
+    model: str = None,
+    temperature: float = 0.2,
+    strict_quotes_only: bool = False,
+    w_tfidf: float = W_TFIDF_DEFAULT,
+    w_bm25: float  = W_BM25_DEFAULT,
+    w_emb: float   = W_EMB_DEFAULT
+) -> str:
+    hits = hybrid_search(question, k=k, w_tfidf=w_tfidf, w_bm25=w_bm25, w_emb=w_emb)
+    if hits.empty:
+        return "No relevant passages found. Try rephrasing or adding more PDFs."
+
+    selected = mmr_select_sentences(question, hits, top_n=int(n_sentences), pool_per_chunk=6, lambda_div=0.7)
+    header_cites = "; ".join(
+        f"{Path(r['doc_path']).name} (p.{_extract_page(r['text'])})" for _, r in hits.head(6).iterrows()
+    )
+    # Coverage note (helps debugging thin answers)
+    srcs = {Path(r['doc_path']).name for _, r in hits.iterrows()}
+    coverage_note = ""
+    if len(srcs) < 3:
+        coverage_note = f"\n\n> Note: Only {len(srcs)} unique source(s) contributed. Add more PDFs or increase Top-K."
+
+    if strict_quotes_only:
+        if not selected:
+            return f"**Quoted Passages:**\n\n---\n" + "\n\n".join(hits["text"].tolist()[:2]) + \
+                   f"\n\n**Citations:** {header_cites}{coverage_note}"
+        msg = "**Quoted Passages:**\n- " + "\n- ".join(f"{s['sent']} ({s['doc']}, p.{s['page']})" for s in selected)
+        msg += f"\n\n**Citations:** {header_cites}{coverage_note}"
+        if include_passages:
+            msg += "\n\n---\n" + "\n\n".join(hits["text"].tolist()[:2])
+        return msg
+
+    # Extractive baseline
+    extractive = compose_extractive(selected)
+
+    # Optional LLM synthesis
+    if use_llm and selected:
+        lines = [f"{s['sent']} ({s['doc']}, p.{s['page']})" for s in selected]
+        llm_text = synthesize_with_llm(question, lines, model=model, temperature=temperature)
+        if llm_text:
+            msg = f"**Answer (GPT-5 synthesis):** {llm_text}\n\n**Citations:** {header_cites}{coverage_note}"
+            if include_passages:
+                msg += "\n\n---\n" + "\n\n".join(hits["text"].tolist()[:2])
+            return msg
+
+    # Fallback: purely extractive
+    if not extractive:
+        return f"**Answer:** Here are relevant passages.\n\n**Citations:** {header_cites}{coverage_note}\n\n---\n" + \
+               "\n\n".join(hits["text"].tolist()[:2])
+
+    msg = f"**Answer:** {extractive}\n\n**Citations:** {header_cites}{coverage_note}"
+    if include_passages:
+        msg += "\n\n---\n" + "\n\n".join(hits["text"].tolist()[:2])
+    return msg
+
+# =========================== Gradio UI =====================================
+INPUT_COLS = [
+    "Filler1_Type", "Filler1_Dimensions", "Filler1_Diameter_um", "Filler1_Length_mm",
+    "Filler2_Type", "Filler2_Dimensions", "Filler2_Diameter_um", "Filler2_Length_mm",
+    "AvgFiller_Density_g/cm3", "AvgFiller_weight_%", "AvgFiller_Volume_%",
+    "Sample_Volume_mm3", "Electrode/Probe_Count", "Electrode/Probe_Material",
+    "W/B", "S/B", "GaugeLength_mm", "Curing_Conditions", "Num_ConductiveFillers",
+    "DryingTemperature_C", "DryingDuration_hrs", "LoadingRate_MPa/s",
+    "ElasticModulus_Gpa", "Voltage_Type", "Applied_Voltage_V"
+]
+NUMERIC_INPUTS = {
+    "Filler1_Diameter_um","Filler1_Length_mm","Filler2_Diameter_um","Filler2_Length_mm",
+    "AvgFiller_Density_g/cm3","AvgFiller_weight_%","AvgFiller_Volume_%","Sample_Volume_mm3",
+    "Electrode/Probe_Count","W/B","S/B","GaugeLength_mm","Num_ConductiveFillers",
+    "DryingTemperature_C","DryingDuration_hrs","LoadingRate_MPa/s","ElasticModulus_Gpa",
+    "Applied_Voltage_V"
+}
+CAT_DIM_CHOICES = ["0D","1D","2D","3D","NA"]
+
+def _coerce_row(args):
+    row = {c: v for c, v in zip(INPUT_COLS, args)}
+    clean = {}
+    for k, v in row.items():
+        if k in NUMERIC_INPUTS:
+            if v in ("", None): clean[k] = None
+            else:
+                try: clean[k] = float(v)
+                except: clean[k] = None
+        else:
+            clean[k] = "" if v is None else str(v).strip()
+    return pd.DataFrame([clean], columns=INPUT_COLS)
+
+def _load_model():
+    if not os.path.exists(MODEL_OUT):
+        raise FileNotFoundError(f"Model file not found at '{MODEL_OUT}'. Retrain above.")
+    return joblib.load(MODEL_OUT)
+
+def predict_fn(*args):
+    try:
+        mdl = _load_model()
+        X_new = _coerce_row(args)
+        y_log = mdl.predict(X_new)
+        y = float(np.expm1(y_log)[0])
+        if -1e-8 < y < 0: y = 0.0
+        return y
+    except Exception as e:
+        return f"Error during prediction: {e}"
+
+def rag_chat_fn(message, history, top_k, n_sentences, include_passages,
+                use_llm, model_name, temperature, strict_quotes_only,
+                w_tfidf, w_bm25, w_emb):
+    if not message or not message.strip():
+        return "Ask a literature question (e.g., *How does CNT length affect gauge factor?*)"
+    try:
+        return rag_reply(
+            question=message,
+            k=int(top_k),
+            n_sentences=int(n_sentences),
+            include_passages=bool(include_passages),
+            use_llm=bool(use_llm),
+            model=(model_name or None),
+            temperature=float(temperature),
+            strict_quotes_only=bool(strict_quotes_only),
+            w_tfidf=float(w_tfidf),
+            w_bm25=float(w_bm25),
+            w_emb=float(w_emb),
+        )
+    except Exception as e:
+        return f"RAG error: {e}"
+
+with gr.Blocks() as demo:
+    gr.Markdown("# 🧪 Self-Sensing Concrete Assistant — Hybrid RAG (Accurate Q&A)")
+    gr.Markdown(
+        "- **Prediction**: XGBoost pipeline for **Stress Gauge Factor (MPa)**.\n"
+        "- **Literature (Hybrid RAG)**: BM25 + TF-IDF + Dense embeddings with **MMR** sentence selection.\n"
+        "- **Strict mode** shows only quoted sentences with citations; **GPT-5** can paraphrase strictly from those quotes.\n"
+        "- Toggle **online OA harvesting** in config (Crossref + Unpaywall) or use a local PDF folder."
+    )
+
+    with gr.Tabs():
+        with gr.Tab("🔮 Predict Gauge Factor (XGB)"):
+            with gr.Row():
+                with gr.Column():
+                    inputs = [
+                        gr.Textbox(label="Filler1_Type", placeholder="e.g., CNT, Graphite, Steel fiber"),
+                        gr.Dropdown(CAT_DIM_CHOICES, label="Filler1_Dimensions", value="NA"),
+                        gr.Number(label="Filler1_Diameter_um"),
+                        gr.Number(label="Filler1_Length_mm"),
+                        gr.Textbox(label="Filler2_Type", placeholder="Optional"),
+                        gr.Dropdown(CAT_DIM_CHOICES, label="Filler2_Dimensions", value="NA"),
+                        gr.Number(label="Filler2_Diameter_um"),
+                        gr.Number(label="Filler2_Length_mm"),
+                        gr.Number(label="AvgFiller_Density_g/cm3"),
+                        gr.Number(label="AvgFiller_weight_%"),
+                        gr.Number(label="AvgFiller_Volume_%"),
+                        gr.Number(label="Sample_Volume_mm3"),
+                        gr.Number(label="Electrode/Probe_Count"),
+                        gr.Textbox(label="Electrode/Probe_Material", placeholder="e.g., Copper, Silver paste"),
+                        gr.Number(label="W/B"),
+                        gr.Number(label="S/B"),
+                        gr.Number(label="GaugeLength_mm"),
+                        gr.Textbox(label="Curing_Conditions", placeholder="e.g., 28d water, 20°C"),
+                        gr.Number(label="Num_ConductiveFillers"),
+                        gr.Number(label="DryingTemperature_C"),
+                        gr.Number(label="DryingDuration_hrs"),
+                        gr.Number(label="LoadingRate_MPa/s"),
+                        gr.Number(label="ElasticModulus_Gpa"),
+                        gr.Textbox(label="Voltage_Type", placeholder="AC / DC"),
+                        gr.Number(label="Applied_Voltage_V"),
+                    ]
+                with gr.Column():
+                    out_pred = gr.Number(label="Predicted Stress_GF (MPa)", precision=6)
+                    gr.Button("Predict", variant="primary").click(predict_fn, inputs, out_pred)
+
+        with gr.Tab("📚 Ask the Literature (Hybrid RAG + MMR)"):
+            with gr.Row():
+                top_k = gr.Slider(5, 12, value=8, step=1, label="Top-K chunks")
+                n_sentences = gr.Slider(2, 6, value=4, step=1, label="Answer length (sentences)")
+                include_passages = gr.Checkbox(value=False, label="Include supporting passages")
+            with gr.Accordion("Retriever weights (advanced)", open=False):
+                w_tfidf = gr.Slider(0.0, 1.0, value=W_TFIDF_DEFAULT, step=0.05, label="TF-IDF weight")
+                w_bm25  = gr.Slider(0.0, 1.0, value=W_BM25_DEFAULT,  step=0.05, label="BM25 weight")
+                w_emb   = gr.Slider(0.0, 1.0, value=W_EMB_DEFAULT,   step=0.05, label="Dense weight (set 0 if disabled)")
+            with gr.Accordion("LLM & Controls", open=False):
+                strict_quotes_only = gr.Checkbox(value=False, label="Strict quotes only (no paraphrasing)")
+                use_llm = gr.Checkbox(value=False, label="Use GPT-5 to paraphrase selected sentences")
+                model_name = gr.Textbox(value=os.getenv("OPENAI_MODEL", OPENAI_MODEL), label="LLM model", placeholder="e.g., gpt-5 or gpt-5-mini")
+                temperature = gr.Slider(0.0, 1.0, value=0.2, step=0.05, label="Temperature")
+            gr.ChatInterface(
+                fn=rag_chat_fn,
+                additional_inputs=[top_k, n_sentences, include_passages, use_llm, model_name, temperature, strict_quotes_only, w_tfidf, w_bm25, w_emb],
+                title="Literature Q&A",
+                description="Hybrid retrieval with diversity. Answers carry inline (Doc, p.X) citations. Toggle strict/LLM modes."
+            )
+
+# Note: add share=True to expose publicly (for iframe embedding)
+demo.queue().launch()

stress_gf_xgb.joblib

@@ -0,0 +1,3 @@
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+oid sha256:9bb87e629c6d09fcd4a0465ce7584fdecf4f90ac8363bad40458a4b19e855afa
+size 416235