import numpy as np import pandas as pd import statsmodels.api as sm from scipy import stats from scipy.optimize import linear_sum_assignment from sklearn.metrics import roc_auc_score, roc_curve from common import RES, SEED, hom, axes, centre, effects, sgd_labels, phenotypes CALIPERS = (0.05, 0.1, 0.25, 0.5) PRIMARY_CALIPER = 0.25 N_BOOT = 2000 N_ORDERS = 200 STRATA = {"all annotations": None, "small-scale studies only": ["classical genetics"]} Z = hom() ag, ox, os_, _ = axes(Z.columns) b = Z.median(axis=1) E = dict(zip(("oxidative", "osmotic"), effects(centre(Z), ox, os_))) N = {"oxidative": Z.loc[:, ox].mean(axis=1), "osmotic": Z.loc[:, os_].mean(axis=1)} rng = np.random.default_rng(SEED) src = phenotypes() for stress in ("oxidative", "osmotic"): terms = ("oxidative stress resistance",) if stress == "oxidative" else ("hyperosmotic stress resistance", "osmotic stress resistance") s = src[(src.mutant == "null") & src.phenotype.str.rsplit(": ", n=1).str[0].isin(terms)] s.groupby(["pmid", "exptype"]).size().rename("annotations").sort_values(ascending=False).to_csv( RES / f"benchmark_sources_{stress}.csv") def auc_ci(y, x, paired_idx=None): y, x = np.asarray(y), np.asarray(x) a = roc_auc_score(y, x) boot = [] for _ in range(N_BOOT): if paired_idx is None: i = rng.integers(0, len(y), len(y)) if len(set(y[i])) < 2: continue else: k = rng.integers(0, len(paired_idx), len(paired_idx)) i = paired_idx[k].ravel() boot.append(roc_auc_score(y[i], x[i])) lo, hi = np.percentile(boot, [2.5, 97.5]) return a, lo, hi def smd(x1, x0): return (x1.mean() - x0.mean()) / np.sqrt((x1.var() + x0.var()) / 2) summary, terc, val, roc_rows = [], [], [], [] for stratum, ex in STRATA.items(): for stress in ("oxidative", "osmotic"): lab = sgd_labels(stress, exptypes=ex) lab = lab[lab.index.isin(Z.index)] y = (lab == -1).astype(int).values e = E[stress].loc[lab.index] conc = (np.sign(e) == -lab).astype(int) k, n = int(conc.sum()), len(conc) row = {"stratum": stratum, "stress": stress, "genes": n, "decreased": int(y.sum()), "increased": int((1 - y).sum()), "concordant": k, "concordance": k / n, "p_binomial": stats.binomtest(k, n, 0.5, alternative="greater").pvalue, "smd_slow_growth": smd(b.loc[lab.index][y == 1], b.loc[lab.index][y == 0]), "p_slow_growth_bias": stats.mannwhitneyu(b.loc[lab.index][y == 1], b.loc[lab.index][y == 0], alternative="greater").pvalue} for name, sc in (("baseline_adjusted", e), ("naive", N[stress].loc[lab.index]), ("slow_growth", b.loc[lab.index])): a, lo, hi = auc_ci(y, sc.values) row.update({f"auroc_{name}": a, f"auroc_{name}_lo": lo, f"auroc_{name}_hi": hi}) summary.append(row) if stratum == "all annotations": val.append(pd.DataFrame({"stress": stress, "gene": lab.index, "effect": e.values, "sgd_dir": lab.values, "concordant": conc.values, "slow_growth": b.loc[lab.index].values})) fpr, tpr, _ = roc_curve(y, e.values) roc_rows.append(pd.DataFrame({"stress": stress, "fpr": fpr, "tpr": tpr})) order = np.argsort(-e.abs().values) for bname, idx in zip(("large", "medium", "small"), np.array_split(order, 3)): cb = conc.values[idx] lo, hi = stats.binomtest(int(cb.sum()), len(cb)).proportion_ci() terc.append((stress, bname, len(idx), cb.mean(), lo, hi, float(np.median(e.abs().values[idx])))) S = pd.DataFrame(summary) S.to_csv(RES / "benchmark_summary.csv", index=False) pd.concat(val).to_csv(RES / "validation.csv", index=False) pd.concat(roc_rows).round(4).to_csv(RES / "roc.csv", index=False) T = pd.DataFrame(terc, columns=["stress", "tercile", "genes", "concordance", "ci_low", "ci_high", "median_abs_effect"]) T.to_csv(RES / "benchmark_terciles.csv", index=False) x = pd.concat(val) trend = [] for stress in ("oxidative", "osmotic"): v = x[x.stress == stress] m = sm.Logit(v.concordant.values, sm.add_constant(np.column_stack([np.abs(v.effect.values), v.slow_growth.values]))).fit(disp=0) trend.append((stress, m.params[1], m.pvalues[1], m.params[2], m.pvalues[2], len(v))) pd.DataFrame(trend, columns=["stress", "coef_abs_effect", "p_abs_effect", "coef_slow_growth", "p_slow_growth", "genes"]).to_csv( RES / "benchmark_concordance_trend.csv", index=False) def greedy(dec, inc, s, cal, order): pool = set(inc) pairs = [] for g in order: if not pool: break p = sorted(pool) d = np.abs(s.loc[p].values - s[g]) j = int(np.argmin(d)) if d[j] <= cal: pairs.append((g, p[j])) pool.remove(p[j]) return pairs def optimal(dec, inc, s, cal): C = np.abs(s.loc[dec].values[:, None] - s.loc[inc].values[None, :]) r, c = linear_sum_assignment(C) return [(dec[i], inc[j]) for i, j in zip(r, c) if C[i, j] <= cal] def evaluate(pairs, stress, method, cal): g = [p for pr in pairs for p in pr] y = np.array([1, 0] * len(pairs)) idx = np.arange(2 * len(pairs)).reshape(-1, 2) d, i = b.loc[[p[0] for p in pairs]], b.loc[[p[1] for p in pairs]] out = {"stress": stress, "method": method, "caliper_sd": cal, "pairs": len(pairs), "smd_after": smd(d, i), "variance_ratio": d.var() / i.var(), "ks_after": stats.ks_2samp(d, i).statistic} for name, sc in (("baseline_adjusted", E[stress]), ("naive", N[stress]), ("slow_growth", b)): a, lo, hi = auc_ci(y, sc.loc[g].values, idx) out.update({f"auroc_{name}": a, f"auroc_{name}_lo": lo, f"auroc_{name}_hi": hi}) return out match = [] for stress in ("oxidative", "osmotic"): lab = sgd_labels(stress) lab = lab[lab.index.isin(Z.index)] dec, inc = list(lab.index[lab == -1]), list(lab.index[lab == 1]) sd = b.loc[lab.index].std() for cal in CALIPERS: match.append(evaluate(greedy(dec, inc, b, cal * sd, dec), stress, "greedy nearest neighbour", cal)) match.append(evaluate(optimal(dec, inc, b, cal * sd), stress, "optimal 1:1", cal)) orders = [] for _ in range(N_ORDERS): pr = greedy(dec, inc, b, PRIMARY_CALIPER * sd, list(rng.permutation(dec))) g = [p for q in pr for p in q] yy = np.array([1, 0] * len(pr)) orders.append((len(pr), roc_auc_score(yy, E[stress].loc[g]), roc_auc_score(yy, b.loc[g]))) O = np.array(orders) match.append({"stress": stress, "method": f"greedy, {N_ORDERS} random orders (median; 2.5-97.5%)", "caliper_sd": PRIMARY_CALIPER, "pairs": float(np.median(O[:, 0])), "auroc_baseline_adjusted": float(np.median(O[:, 1])), "auroc_baseline_adjusted_lo": float(np.percentile(O[:, 1], 2.5)), "auroc_baseline_adjusted_hi": float(np.percentile(O[:, 1], 97.5)), "auroc_slow_growth": float(np.median(O[:, 2]))}) q = pd.qcut(b.loc[lab.index], 5, labels=False) w, aucs = [], [] for k in range(5): ii = lab.index[q == k] yy = (lab[ii] == -1).astype(int) if yy.nunique() == 2: aucs.append(roc_auc_score(yy, E[stress].loc[ii])) w.append(len(ii)) match.append({"stress": stress, "method": "stratified (slow-growth quintiles), weighted mean", "caliper_sd": np.nan, "pairs": np.nan, "auroc_baseline_adjusted": float(np.average(aucs, weights=w))}) y = (lab == -1).astype(int).values Xr = sm.add_constant(np.column_stack([stats.zscore(E[stress].loc[lab.index].values), stats.zscore(b.loc[lab.index].values)])) m = sm.Logit(y, Xr).fit(disp=0) ci = m.conf_int()[1] match.append({"stress": stress, "method": "logistic regression adjusting for slow growth (odds ratio per SD)", "caliper_sd": np.nan, "pairs": np.nan, "odds_ratio": float(np.exp(m.params[1])), "odds_ratio_lo": float(np.exp(ci[0])), "odds_ratio_hi": float(np.exp(ci[1])), "p": float(m.pvalues[1])}) M = pd.DataFrame(match) M.to_csv(RES / "benchmark_matching.csv", index=False) rng_d = np.random.default_rng(SEED + 1) def auc_difference(y, x1, x2, paired_idx=None): y, x1, x2 = np.asarray(y), np.asarray(x1), np.asarray(x2) obs = roc_auc_score(y, x1) - roc_auc_score(y, x2) boot = [] for _ in range(N_BOOT): if paired_idx is None: i = rng_d.integers(0, len(y), len(y)) if len(set(y[i])) < 2: continue else: i = paired_idx[rng_d.integers(0, len(paired_idx), len(paired_idx))].ravel() boot.append(roc_auc_score(y[i], x1[i]) - roc_auc_score(y[i], x2[i])) boot = np.array(boot) lo, hi = np.percentile(boot, [2.5, 97.5]) return obs, lo, hi, min(1.0, 2 * min((boot <= 0).mean(), (boot >= 0).mean())) diff = [] for stress in ("oxidative", "osmotic"): lab = sgd_labels(stress) lab = lab[lab.index.isin(Z.index)] y = (lab == -1).astype(int).values for name, x2 in (("naive", N[stress]), ("slow_growth", b)): d, lo, hi, p = auc_difference(y, E[stress].loc[lab.index].values, x2.loc[lab.index].values) diff.append((stress, "all annotations", f"baseline_adjusted - {name}", len(lab), d, lo, hi, p)) dec, inc = list(lab.index[lab == -1]), list(lab.index[lab == 1]) pairs = greedy(dec, inc, b, PRIMARY_CALIPER * b.loc[lab.index].std(), dec) g = [q for pr in pairs for q in pr] yy = np.array([1, 0] * len(pairs)) idx = np.arange(2 * len(pairs)).reshape(-1, 2) for name, x2 in (("naive", N[stress]), ("slow_growth", b)): d, lo, hi, p = auc_difference(yy, E[stress].loc[g].values, x2.loc[g].values, idx) diff.append((stress, f"growth-matched (greedy, caliper {PRIMARY_CALIPER} SD)", f"baseline_adjusted - {name}", len(pairs), d, lo, hi, p)) pd.DataFrame(diff, columns=["stress", "benchmark", "comparison", "n", "auroc_difference", "ci_low", "ci_high", "p_two_sided"]).to_csv(RES / "benchmark_auroc_differences.csv", index=False) pd.set_option("display.width", 250) pd.set_option("display.max_columns", 30)