refactor: 将子模块转为普通目录，移除外部 git 依赖

- 移除 JEPA/lejepa-identifiability 子模块 gitlink
- 移除 research/multiply/MultiPLY 子模块 gitlink
- 删除 .gitmodules（不再有外部 URL 依赖）
- 两个目录内容作为普通文件纳入主仓库追踪
- 删除各自内部 .git 目录，消除嵌套 git 仓库

JEPA/lejepa-identifiability/experiments/analysis/make_table_ablation.py

@@ -0,0 +1,98 @@
+"""
+Ablation table: 4 mixings × 3 source distributions × {SIGReg, Whitening}.
+Reports R²(h→z). The winner per (mixing, α) is bolded when the difference
+is statistically significant (Welch's t-test, p < 0.05).
+
+Usage:
+    python analysis/make_table_ablation.py --out figures/tab_ablation.tex
+"""
+import argparse, glob, json, os
+import numpy as np
+from scipy import stats
+from collections import defaultdict
+
+MIXINGS = [("spiral", "Spiral"), ("banana", "Banana"),
+           ("sinusoid", "Sinusoid"), ("nvp", "NVP")]
+ALPHAS = [
+    (None, r"Gaussian ($\alpha = 2$)"),
+    (0.25, r"Heavy tail / sparse ($\alpha = 1/4$)"),
+    (16.0, r"Light tail / uniform ($\alpha = 16$)"),
+]
+# METRIC = "r2_hz" # marginal
+METRIC = "r2_hz_grid" # grid
+P_THRESH = 0.05
+
+
+def alpha_key(r):
+    if r.get("source_dist") == "gennorm":
+        return r.get("source_alpha")
+    return None
+
+
+def fmt(vals, bold=False):
+    if not vals:
+        return r"$-$"
+    s = f"{np.mean(vals):.3f} \\pm {np.std(vals):.3f}"
+    return rf"$\mathbf{{{s}}}$" if bold else f"${s}$"
+
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument("--dirs", nargs="+",
+                   default=["results/2d",
+                            "results/ablation_alpha_0.25",
+                            "results/ablation_alpha_16"])
+    p.add_argument("--out", default="figures/tab_ablation.tex")
+    args = p.parse_args()
+
+    groups = defaultdict(list)
+    for d in args.dirs:
+        for path in sorted(glob.glob(os.path.join(d, "*.json"))):
+            with open(path) as f:
+                r = json.load(f)
+            if METRIC not in r:
+                continue
+            key = (r["mixing"], alpha_key(r), r["mode"])
+            groups[key].append(r[METRIC])
+
+    col_spec = "l" + " cc" * len(ALPHAS)
+    multicol = " & ".join(rf"\multicolumn{{2}}{{c}}{{{lab}}}" for _, lab in ALPHAS)
+    cmidrules = "".join(rf"\cmidrule(lr){{{2*i+2}-{2*i+3}}}" for i in range(len(ALPHAS)))
+    method_hdr = " & ".join(["SIGReg & Whitening"] * len(ALPHAS))
+
+    lines = [
+        rf"\begin{{tabular}}{{{col_spec}}}",
+        r"\toprule",
+        rf" & {multicol} \\",
+        cmidrules,
+        rf"Mixing & {method_hdr} \\",
+        r"\midrule",
+    ]
+    for mix_key, mix_name in MIXINGS:
+        row = [mix_name]
+        for alpha_k, _ in ALPHAS:
+            v_lej = groups.get((mix_key, alpha_k, "lejepa"), [])
+            v_wht = groups.get((mix_key, alpha_k, "whiten"), [])
+            bold_lej = bold_wht = False
+            if len(v_lej) >= 2 and len(v_wht) >= 2:
+                _, pval = stats.ttest_ind(v_lej, v_wht, equal_var=False)
+                if pval < P_THRESH:
+                    if np.mean(v_lej) > np.mean(v_wht):
+                        bold_lej = True
+                    else:
+                        bold_wht = True
+            row.append(fmt(v_lej, bold=bold_lej))
+            row.append(fmt(v_wht, bold=bold_wht))
+        lines.append(" & ".join(row) + r" \\")
+    lines += [r"\bottomrule", r"\end{tabular}"]
+
+    out = "\n".join(lines)
+    print(out)
+    os.makedirs(os.path.dirname(args.out) or ".", exist_ok=True)
+    with open(args.out, "w") as f:
+        f.write(out + "\n")
+    print(f"\nSaved {args.out}")
+
+
+if __name__ == "__main__":
+    main()