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import pandas as pd
import streamlit as st
from sidebar import sidebar
from model_utils import load_model, load_model_ensemble, ensemble_predict, get_latest_model_name_hf
from preprocess_utils import load_train_features
from preprocess_utils import preprocess_pipeline as preprocess
from inference_utils import add_predictions
import numpy as np
import matplotlib.pyplot as plt
import sys
from pathlib import Path
import shap
from inference_utils import ensemble_shap
ROOT = Path(__file__).resolve().parents[1] # /app
if str(ROOT) not in sys.path:
sys.path.insert(0, str(ROOT))
from src.survival_utils import prepare_cox_df, fit_cox, make_patient_design_row, predict_patient_survival
from src.cox_persist import load_cox_artifacts, ensure_cox_artifacts_available
@st.cache_resource
def get_or_load_cox():
"""
Load Cox artifacts trained in Bulk page.
If running on Spaces without persistence, download from HF dataset repo when missing.
"""
# Ensure artifacts exist locally (downloads to /tmp/saved_models by default)
ensure_cox_artifacts_available() # downloads cox_os_model.joblib + cox_os_meta.json
payload, meta = load_cox_artifacts(prefix="cox_os") # loads from DEFAULT_DIR (/tmp/saved_models)
cph = payload["cph"]
design_cols = payload["design_cols"]
cat_cols = payload["cat_cols"]
return cph, design_cols, cat_cols, meta
# --- Country options for UI (pycountry backed) ---
try:
import pycountry
COUNTRY_OPTIONS = sorted({c.name for c in pycountry.countries})
COUNTRY_OPTIONS = sorted(set(COUNTRY_OPTIONS) | {"UAE", "KSA", "UK", "USA", "US", "RUSSIA", "IRAN", "SYRIA", "PALESTINE"})
except Exception:
COUNTRY_OPTIONS = sorted(["UAE", "KSA", "UK", "USA", "INDIA", "PAKISTAN", "EGYPT", "SAUDI ARABIA", "UNITED ARAB EMIRATES"])
st.set_page_config(
page_title="GVHD-Intel | Individual Prediction",
page_icon="🧬",
layout="wide",
initial_sidebar_state="expanded",
)
st.markdown(
"""
<style>
/* Hide the first page in the sidebar navigation (this is typically the main app.py page) */
[data-testid="stSidebarNav"] ul li:first-child {display: none;}
</style>
""",
unsafe_allow_html=True
)
# ---------- App Header ----------
st.markdown(
"""
<h1 style='text-align: center; margin-bottom: 10px;'>
GVHD-Intel Pro
</h1>
""",
unsafe_allow_html=True
)
st.markdown(
"""
<div style='font-size:16px; line-height:1.6;'>
A modular clinical decision-support framework for predicting <b>Acute GVHD</b> and <b>Chronic GVHD</b> risk after HSCT using machine learning models trained on transplant datasets.<br><br>
<b>Prediction workflow:</b><br>
• Use the <b>Acute GVHD</b> or <b>Chronic GVHD</b> tab below and click the corresponding <b>Predict</b> button.<br>
• The app will automatically use the <b>latest ensemble model</b> available for the selected outcome (Acute = <b>A</b>, Chronic = <b>C</b>) based on the timestamp in the model name.<br>
• Admin use: The sidebar model selector remains available for browsing models, but tab-based prediction will prioritize the latest outcome-specific ensemble.<br><br>
<b>Explainability:</b><br>
• Displays the <b>top 20 risk factors</b> contributing to each prediction.<br>
• Provides a <b>SHAP waterfall plot</b> for the individual patient (for ensemble models, SHAP values are averaged across models).<br><br>
<b>Survival module:</b><br>
• Supports adjusted overall survival (all-cause mortality) risk estimation using <b>Cox Proportional Hazards</b> analysis.<br>
• Generates an individualized adjusted survival curve with landmark estimates (e.g., 3-, 5-, and 10-year survival).<br><br>
Enter recipient and donor details below to generate individualized risk predictions.<br><br>
<b>Research tool only — not validated for clinical use.</b>
</div>
""",
unsafe_allow_html=True
)
st.divider()
def two_alleles_number_inputs(label: str, key_prefix: str, max_allele: int = 500, disabled: bool = False):
"""
Two numeric allele inputs. 0 = not provided.
Returns [] if both 0 else list of strings, e.g. ["12","24"].
"""
c1, c2 = st.columns(2)
with c1:
a1 = st.number_input(
f"{label} allele 1",
min_value=0, max_value=max_allele, step=1,
value=0,
key=f"{key_prefix}_1",
disabled=disabled,
)
with c2:
a2 = st.number_input(
f"{label} allele 2",
min_value=0, max_value=max_allele, step=1,
value=0,
key=f"{key_prefix}_2",
disabled=disabled,
)
a1, a2 = int(a1), int(a2)
out = []
if a1 != 0:
out.append(str(a1))
if a2 != 0 and a2 != a1:
out.append(str(a2))
return out
def hla_block(person: str, key_prefix: str, enabled: bool):
if not enabled:
return {
f"{key_prefix}_A": ["Unknown"],
f"{key_prefix}_B": ["Unknown"],
f"{key_prefix}_C": ["Unknown"],
f"{key_prefix}_DR": ["Unknown"],
f"{key_prefix}_DQ": ["Unknown"],
}
st.markdown(f"###### {person} HLA Alleles")
def _val(x):
return x if (x and len(x) > 0) else ["Unknown"]
return {
f"{key_prefix}_A": _val(two_alleles_number_inputs(f"{person} HLA-A", f"{key_prefix}_A")),
f"{key_prefix}_B": _val(two_alleles_number_inputs(f"{person} HLA-B", f"{key_prefix}_B")),
f"{key_prefix}_C": _val(two_alleles_number_inputs(f"{person} HLA-C", f"{key_prefix}_C")),
f"{key_prefix}_DR": _val(two_alleles_number_inputs(f"{person} HLA-DR", f"{key_prefix}_DR")),
f"{key_prefix}_DQ": _val(two_alleles_number_inputs(f"{person} HLA-DQ", f"{key_prefix}_DQ")),
}
# Initialize sidebar (model/target/threshold defaults etc.)
sidebar()
st.title("👤 Individual Patient Risk Prediction")
st.caption("Enter recipient, donor, and transplant variables including HLA alleles to generate individualized risk estimates")
# Ensure this exists so add_predictions() can join safely
st.session_state.targets_df = pd.DataFrame()
min_d = dt.date(1950, 1, 1)
max_d = dt.date(2050, 12, 31)
with st.container():
st.subheader("Recepient Information", divider=True)
gender = st.radio("Recepient Gender", ["MALE", "FEMALE"], index=None)
dob = st.date_input(
"Recepient DOB",
value=dt.date(2000, 1, 31),
min_value=min_d,
max_value=max_d,
format="DD/MM/YYYY",
)
nationality = st.selectbox(
"Recepient Nationality (Country)",
COUNTRY_OPTIONS,
index=None,
)
diagnosis = st.selectbox(
"Hematological Diagnosis",
sorted([
"ACUTE MYELOID LEUKEMIA", "ALPHA THALSSEMIA", "AMYLOIDOSIS",
"APLASTIC ANEMIA", "BALL", "BETA THALESSEMIA",
"BLASTIC PLASMACYTOID DENDRITRIC CELL NEOPLASM",
"CHRONIC GRANULOMATOUS DISEASE", "CHRONIC LYMPHOCYTIC LEUKEMIA",
"CML", "COMBINED VARIABLE IMMUNODEFICIENCY",
"DYSKERATOSIS CONGENTIA", "FANCONI ANEMIA",
"GLANZMANN THROMBASTHENIA",
"HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS (HLH)",
"HEREDITARY SPHEROCYTOSIS", "HODGKIN LYMPHOMA",
"HYPOGAMMAGLOBULINEMIA", "LANGERHANS CELL HISTIOCYTOSIS",
"MYELODYSPLASTIC SYNDROME", "MEDULLOBLASTOMA", "MULTIPLE MYELOMA",
"MYELOFIBROSIS", "MYELOPROLIFERATIVE DISORDER", "NEUROBLASTOMA",
"NON HODGKIN LYMPHOMA", "OTHER",
"PAROXYSMAL NOCTURNAL HEMOGLOBINURIA", "PLASMA CELL LEUKEMIA",
"SCID", "SICKLE CELL DISEASE", "TALL",
"X-LINKED HYPER IGM SYNDROME",
]),
index=None,
)
diagnosis_date = st.date_input(
"Date of First Diagnosis / BMBx",
value=dt.date(2000, 1, 31),
min_value=min_d,
max_value=max_d,
format="DD/MM/YYYY",
)
recepient_blood_group = st.radio(
"Recepient Blood Group",
["A+", "A-", "B+", "B-", "O+", "O-", "AB+", "AB-", "Unknown"],
index=None,
key="recepient_blood_group",
)
st.subheader("Donor Information", divider=True)
donor_relation = st.radio(
"Donor Relation to Recepient",
["SELF", "SIBLING", "FIRST DEGREE RELATIVE", "SECOND DEGREE RELATIVE", "RELATED", "UNRELATED", "Unknown"],
index=None,
)
st.session_state.SELF = (donor_relation == "SELF")
donor_gender = st.radio("Donor Gender", ["MALE", "FEMALE"], index=None)
donor_dob = st.date_input(
"Donor DOB",
value=dt.date(2000, 1, 31),
min_value=min_d,
max_value=max_d,
format="DD/MM/YYYY",
)
donor_blood_group = st.radio(
"Donor Blood Group",
["A+", "A-", "B+", "B-", "O+", "O-", "AB+", "AB-", "Unknown"],
index=None,
key="donor_blood_group",
)
st.subheader("Treatment Details", divider=True)
lines_of_rx = st.selectbox("Number of Lines of Rx Before HSCT", [0, 1, 2, 3, 4, 5, 6, 7, "Unknown"], index=None)
conditioning = st.multiselect(
"Pre-HSCT Conditioning Regimen",
sorted([
"ALEMTUZUMAB", "ATG", "BEAM", "BUSULFAN", "CAMPATH", "CARMUSTINE",
"CLOFARABINE", "CYCLOPHOSPHAMIDE", "CYCLOSPORIN", "CYTARABINE",
"ETOPOSIDE", "FLUDARABINE", "GEMCITABINE", "MELPHALAN",
"METHOTREXATE", "OTHER", "RANIMUSTINE", "REDUCED_CONDITIONING",
"RITUXIMAB", "SIROLIMUS", "TBI", "THIOTEPA", "TREOSULFAN",
"UA", "VORINOSTAT",
]),
placeholder="Choose option(s)",
)
st.subheader("HSCT Details", divider=True)
hsct_date = st.date_input(
"HSCT Date",
value=dt.date(2000, 1, 31),
min_value=min_d,
max_value=max_d,
format="DD/MM/YYYY",
)
cell_source = st.radio(
"Source of Cells",
sorted(["BONE MARROW", "PERIPHERAL BLOOD", "UMBILICAL CORD", "PBSC", "Unknown"]),
index=None,
)
hla_match = st.radio("HLA Match Ratio", ["FULL", "PARTIAL", "HAPLOIDENTICAL", "Unknown"], index=None)
st.subheader("Transplant Risk Modifiers", divider=True)
donor_type = st.selectbox(
"Donor Type",
["MRD", "MMRD", "MUD", "MMUD", "HAPLOIDENTICAL", "CORD", "Unknown"],
index=None,
)
r_hla = {"R_HLA_A":["Unknown"], "R_HLA_B":["Unknown"], "R_HLA_C":["Unknown"], "R_HLA_DR":["Unknown"], "R_HLA_DQ":["Unknown"]}
d_hla = {"D_HLA_A":["Unknown"], "D_HLA_B":["Unknown"], "D_HLA_C":["Unknown"], "D_HLA_DR":["Unknown"], "D_HLA_DQ":["Unknown"]}
with st.expander("Enter: HLA Allele Details", expanded=True):
st.caption("Enter HLA allele data if available to enhance prediction accuracy.")
enter_recipient_hla = st.toggle("Enter Recipient HLA alleles", value=False, key="enter_recipient_hla")
r_hla = hla_block("Recipient", "R_HLA", enabled=enter_recipient_hla)
enter_donor_hla = st.toggle("Enter Donor HLA alleles", value=False, key="enter_donor_hla")
d_hla = hla_block("Donor", "D_HLA", enabled=enter_donor_hla)
conditioning_intensity = st.radio("Conditioning Intensity", ["MAC", "RIC", "NMA", "Unknown"], index=None)
last_followup_date = st.date_input(
"Last Follow-up Date (optional)",
value=None,
min_value=min_d,
max_value=max_d,
format="DD/MM/YYYY",
)
date_of_death = st.date_input(
"Date of Death (optional)",
value=None,
min_value=min_d,
max_value=max_d,
format="DD/MM/YYYY",
)
gvhd_proph_cat = st.radio(
"GVHD Prophylaxis Category",
["CNI_BASED", "PTCY_BASED", "ATG_BASED", "TCD", "OTHER", "Unknown"],
index=None,
)
st.subheader("Post-HSCT Treatment and GVHD Prophylaxis", divider=True)
post_hsct_regimen = st.radio("Post-HSCT Regimen", ["YES", "NO", "IVIG", "Unknown"], index=None)
gvhd_prophylaxis = st.multiselect(
"First GVHD Prophylaxis",
sorted([
"ABATACEPT", "ALEMTUZUMAB", "ATG", "CYCLOPHOSPHAMIDE", "CYCLOSPORIN",
"IMATINIB", "LEFLUNOMIDE", "METHOTREXATE", "MMF", "NONE",
"RUXOLITINIB", "SIROLIMUS", "STEROID", "TAC", "TACROLIMUS",
]),
placeholder="Choose option(s)",
)
# --- Predict buttons as tabs (sidebar selection remains available) ---
tab_a, tab_c = st.tabs(["Acute GVHD", "Chronic GVHD"])
override_model_name = None
submitted = False
with tab_a:
if st.button("PREDICT ACUTE GVHD (latest ensemble)", type="primary", use_container_width=True, key="pred_acute"):
try:
override_model_name = get_latest_model_name_hf(
target_initial="A",
mode="ensemble",
name_contains= None,
)
submitted = True
except Exception as e:
st.error(f"Could not locate latest Acute ensemble model: {e}")
with tab_c:
if st.button("PREDICT CHRONIC GVHD (latest ensemble)", type="primary", use_container_width=True, key="pred_chronic"):
try:
override_model_name = get_latest_model_name_hf(
target_initial="C",
mode="ensemble",
name_contains= None,
)
submitted = True
except Exception as e:
st.error(f"Could not locate latest Chronic ensemble model: {e}")
if submitted:
# If user used tabs, override the sidebar-selected model for THIS run
model_to_use = override_model_name or st.session_state.selected_model
# Optional: show which model is being used (highly recommended)
st.caption(f"Model used: {model_to_use}")
# Collect input values in a dict
input_dict = {
"Recepient_gender": gender,
"Recepient_DOB": dob.strftime("%d/%m/%Y"),
"Recepient_Nationality": nationality if nationality else "X",
"Hematological Diagnosis": diagnosis,
"Date of first diagnosis/BMBx date": diagnosis_date.strftime("%d/%m/%Y"),
"Recepient_Blood group before HSCT": recepient_blood_group if recepient_blood_group != "Unknown" else "X",
"Donor_DOB": donor_dob.strftime("%d/%m/%Y"),
"Donor_gender": donor_gender,
"D_Blood group": donor_blood_group if donor_blood_group != "Unknown" else "X",
"R_HLA_A": r_hla["R_HLA_A"],
"R_HLA_B": r_hla["R_HLA_B"],
"R_HLA_C": r_hla["R_HLA_C"],
"R_HLA_DR": r_hla["R_HLA_DR"],
"R_HLA_DQ": r_hla["R_HLA_DQ"],
"D_HLA_A": d_hla["D_HLA_A"],
"D_HLA_B": d_hla["D_HLA_B"],
"D_HLA_C": d_hla["D_HLA_C"],
"D_HLA_DR": d_hla["D_HLA_DR"],
"D_HLA_DQ": d_hla["D_HLA_DQ"],
"Number of lines of Rx before HSCT": lines_of_rx,
"PreHSCT conditioning regimen+/-ATG+/-TBI": conditioning,
"HSCT_date": hsct_date.strftime("%d/%m/%Y"),
"Last_followup_date": last_followup_date.strftime("%d/%m/%Y") if last_followup_date else "X",
"Date_of_death": date_of_death.strftime("%d/%m/%Y") if date_of_death else "X",
"Source of cells": cell_source,
"Donor_relation to recepient": donor_relation,
"HLA match ratio": hla_match,
"Donor_type": donor_type if (donor_type and donor_type != "Unknown") else "X",
"Conditioning_intensity": conditioning_intensity if (conditioning_intensity and conditioning_intensity != "Unknown") else "X",
"GVHD_Prophylaxis_Cat": gvhd_proph_cat if (gvhd_proph_cat and gvhd_proph_cat != "Unknown") else "X",
"Post HSCT regimen": post_hsct_regimen,
"First_GVHD prophylaxis": gvhd_prophylaxis,
}
X_raw = pd.DataFrame([input_dict])
# Preprocess
train_features, cat_features = load_train_features()
df_full, df_model = preprocess(X_raw)
X_model = df_model.reindex(columns=train_features, fill_value=0).copy()
# Ensure cat features are strings
for c in cat_features:
if c in X_model.columns:
X_model[c] = X_model[c].astype(str)
# Predict
if st.session_state.SELF:
pred_prob = 0.0
target_col = "GVHD"
else:
if model_to_use.endswith("ensemble"):
ensemble_data = load_model_ensemble(model_to_use)
target_col = ensemble_data.get("target_col", "UNKNOWN")
models = ensemble_data["model"]
pred_prob = float(ensemble_predict(models, X_model, cat_features)[0])
else:
model_dict = load_model(model_to_use)
target_col = model_dict.get("target_col", "UNKNOWN")
model = model_dict["model"]
pred_prob = float(model.predict_proba(X_model)[0][1])
st.session_state.target_col = target_col
st.info(
f"Model predicts target: **{target_col}**. "
f"Threshold: **{float(st.session_state.get('threshold', 0.5)):.2f}**."
)
# Display result
result_df = add_predictions(pd.DataFrame(index=[0]), [pred_prob])
st.subheader("Prediction")
st.dataframe(result_df, use_container_width=False, width=420)
st.divider()
st.header("Explainability (SHAP)")
try:
# For SHAP, use the same model object used for prediction
# If SELF donor case, prediction is forced to 0.0 and there is no meaningful SHAP
if st.session_state.SELF:
st.info("SHAP is not shown for SELF donor (prediction forced to 0).")
elif model_to_use.endswith("ensemble"):
ensemble_data = load_model_ensemble(model_to_use)
models = ensemble_data["model"]
# ensemble_shap() RETURNS shap.Explanation (already averaged across models)
ens_expl = ensemble_shap(models=models, X=X_model, positive_class=1)
one = ens_expl[0]
vals = one.values
feats = np.array(one.feature_names)
top_idx = np.argsort(np.abs(vals))[::-1][:20]
shap_table = pd.DataFrame({
"Feature": feats[top_idx],
"Feature value": X_model.iloc[0][feats[top_idx]].values,
"SHAP value (pushes risk ↑ / ↓)": vals[top_idx],
})
st.subheader("Top features driving this patient’s prediction (ensemble-mean)")
st.dataframe(shap_table, use_container_width=True)
st.subheader("Waterfall plot (single patient, ensemble-mean)")
plt.figure(figsize=(10, 6))
shap.plots.waterfall(one, max_display=20, show=False)
st.pyplot(plt.gcf(), bbox_inches="tight")
plt.clf()
st.caption("SHAP values shown are averaged across ensemble models.")
else:
model_dict = load_model(model_to_use)
model = model_dict["model"] # XGBoost model
explainer = shap.TreeExplainer(model)
shap_expl = explainer(X_model) # shap.Explanation for 1 row
# Handle possible 3D output (some wrappers return [n, p, classes])
if shap_expl.values.ndim == 3:
shap_expl = shap.Explanation(
values=shap_expl.values[:, :, 1],
base_values=shap_expl.base_values[:, 1] if np.ndim(shap_expl.base_values) == 2 else shap_expl.base_values,
data=X_model,
feature_names=X_model.columns,
)
one = shap_expl[0]
vals = one.values
feats = np.array(one.feature_names)
top_idx = np.argsort(np.abs(vals))[::-1][:20]
shap_table = pd.DataFrame({
"Feature": feats[top_idx],
"Feature value": X_model.iloc[0][feats[top_idx]].values,
"SHAP value (pushes risk ↑ / ↓)": vals[top_idx],
})
st.subheader("Top features driving this patient’s prediction")
st.dataframe(shap_table, use_container_width=True)
st.subheader("Waterfall plot (single patient)")
plt.figure(figsize=(10, 6))
shap.plots.waterfall(one, max_display=20, show=False)
st.pyplot(plt.gcf(), bbox_inches="tight")
plt.clf()
except Exception as e:
st.error(f"SHAP explanation failed: {e}")
st.divider()
st.header("Adjusted Overall Survival Prediction (Cox Proportional Hazards)")
# ---- load saved Cox artifacts (trained once in Bulk page) ----
try:
cph, design_cols, cat_cols, meta = get_or_load_cox()
st.success("Cox model ready (loaded from saved artifacts).")
covariates = meta["covariates"]
st.caption(f"N={meta['n']} | events={meta['n_events']} | C-index={meta['c_index']:.3f}")
except Exception as e:
st.error(f"Cox unavailable: {e}")
cph = None
if cph is not None:
# Build patient covariate row from THIS patient (df_full has preprocessed columns)
patient_cov = df_full.loc[[0], [c for c in covariates if c in df_full.columns]].copy()
patient_cov["Predicted_GVHD_Risk"] = float(pred_prob)
# Ensure missing covariates exist (type-safe defaults)
categorical_defaults = {
"Hematological Diagnosis_Grouped": "OTHER",
"Donor_relation to recepient": "Unknown",
"Source of cells": "Unknown",
"Donor_type": "Unknown",
"Conditioning_intensity": "Unknown",
"GVHD_Prophylaxis_Cat": "Unknown",
}
for c in covariates:
if c not in patient_cov.columns:
patient_cov[c] = categorical_defaults.get(c, 0)
try:
# Create one-hot design row matching training design columns
patient_design = make_patient_design_row(patient_cov, design_cols, cat_cols)
if isinstance(patient_design, tuple):
patient_design = patient_design[0] # keep only the DataFrame row
# Predict survival curve + landmarks
surv_fn, landmarks = predict_patient_survival(cph, patient_design, years=[3, 5, 10])
st.subheader("Individual adjusted survival curve")
# Convert days → years for plotting
surv_years = surv_fn.copy()
surv_years.index = surv_years.index / 365.25
fig, ax = plt.subplots(figsize=(8, 5))
surv_years.plot(ax=ax, legend=False)
ax.set_title("Predicted adjusted survival curve")
ax.set_xlabel("Years")
ax.set_ylabel("Survival probability")
# Optional: make ticks clean integers
ax.set_xlim(left=0)
ax.xaxis.set_major_locator(plt.MaxNLocator(integer=True))
st.pyplot(fig, bbox_inches="tight")
plt.clf()
st.write("Landmark survival probabilities:")
for y in [3, 5, 10]:
s = landmarks.get(y, None)
if s is not None:
st.write(f"{y}-year survival: {100*s:.1f}%")
except Exception as e:
st.error(f"Survival prediction failed: {e}")
st.caption(
"Use the tabs above to run prediction with the latest ensemble model "
"(Acute GVHD or Chronic GVHD). "
"The sidebar model selector remains available for manual model exploration if needed. "
"Model naming convention: A = Acute GVHD, C = Chronic GVHD, G = Overall GVHD "
"(e.g., 260222_062257A_Acute GVHD_ensemble)."
)
st.divider()
st.markdown(
"""
<div style="text-align:center; font-size:14px; color:grey; opacity:0.85; padding-top:20px; line-height:1.6;">
<br>
©2025 Department of Health – Abu Dhabi<br>
Partnership: SSMC (PureHealth) & MBZUAI<br>
Data Collaborators: SKMC, Tawam Hospital, KHCC (Jordan)<br><br>
<span style="font-size:13.5px;">
GVHD-Intel Pro — Developed and maintained by <b>Dr Syed Naveed</b><br>
Contact: <a href="mailto:naveed3642003@gmail.com" style="color:inherit; text-decoration:none;">
naveed3642003@gmail.com
</a>
</span>
</div>
""",
unsafe_allow_html=True
)
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