"""Post-hoc analysis: aggregation tables, figures, and micro->macro sensitivity. Everything here is CPU-only and reads ``results/runs//`` produced by ``pimamba.train``. Used to generate the tables and figures of the report. """ from __future__ import annotations import json import os from pathlib import Path from typing import Dict, Iterable, List, Optional import numpy as np import pandas as pd ROOT = Path(os.environ.get("PIMAMBA_ROOT") or Path(__file__).resolve().parents[2]) RUNS = ROOT / "results" / "runs" FIGS = ROOT / "results" / "figures" TABLES = ROOT / "results" / "tables" MODEL_LABEL = { "mlp": "MLP", "gru": "GRU", "lstm": "LSTM", "transformer": "Transformer", "mamba": "Mamba (S6)", "mamba2": "Mamba-2", "pimamba": "PI-Mamba", "pimamba_nocouple": "PI-Mamba w/o coupling", "pimamba_phys": "PI-Mamba + physics loss", "pimamba_nogeom": "PI-Mamba w/o geometry", "pimamba_noflags": "PI-Mamba w/o shape flags", "pimamba_noensemble": "PI-Mamba w/o ensemble", "pimamba_noinit": "PI-Mamba w/o initial state", "pimamba_nonorm": "PI-Mamba w/o normalisation", "pimamba_phys005": "PI-Mamba + physics loss (0.05)", # ---- next generation (2024-2026) ---- "llama": "LLaMA-style Transformer", "xlstm": "xLSTM (mLSTM)", "gdn": "Gated DeltaNet", "hymba": "Mamba+Attention hybrid", "koopman": "Deep Koopman", "node": "Neural ODE", "rssm": "RSSM world model", "flow": "Flow matching (generative)", "pimamba2": "PI-Mamba v2 (Taylor)", } PRIMARY_COLS = ["sigma_r2", "sigma_shape_r2", "macro_r2_primary", "rho_total_r2", "twin_r2", "xi_FCC_r2", "peak_rel_err"] def load_summary() -> pd.DataFrame: df = pd.read_csv(ROOT / "results" / "summary.csv") return df def agg(df: pd.DataFrame, by: str, cols: Optional[Iterable[str]] = None) -> pd.DataFrame: cols = list(cols or PRIMARY_COLS) g = df.groupby(by) mean = g[cols].mean() sd = g[cols].std() n = g.size().rename("n") out = mean.copy() for c in cols: out[c + "_sd"] = sd[c] out[c] = out[c].map(lambda v: round(float(v), 3)) out[c + "_sd"] = out[c + "_sd"].map(lambda v: round(float(v), 3)) return out.join(n).reset_index() def markdown_table(df: pd.DataFrame, cols: List[str], rename: Dict[str, str] = None) -> str: rename = rename or {} head = "| " + " | ".join(rename.get(c, c) for c in cols) + " |" sep = "|" + "|".join(["---"] * len(cols)) + "|" lines = [head, sep] for _, r in df.iterrows(): cells = [] for c in cols: v = r[c] if isinstance(v, float): cells.append("nan" if not np.isfinite(v) else f"{v:.3f}") else: cells.append(str(v)) lines.append("| " + " | ".join(cells) + " |") return "\n".join(lines) def fmt_pm(mean: float, sd: float, nd: int = 3) -> str: if not np.isfinite(mean): return "n/a" if not np.isfinite(sd): return f"{mean:.{nd}f}" return f"{mean:.{nd}f} ± {sd:.{nd}f}" # --------------------------------------------------------------------------- # figures # --------------------------------------------------------------------------- def _plt(): import matplotlib matplotlib.use("Agg") import matplotlib.pyplot as plt plt.rcParams.update({"figure.dpi": 150, "font.size": 8, "axes.spines.top": False, "axes.spines.right": False}) return plt def fig_model_comparison(df: pd.DataFrame, fname="fig1_model_comparison.png"): plt = _plt() sub = df[df.suite == "main"] order = ["mlp", "gru", "lstm", "transformer", "mamba", "mamba2", "pimamba"] metrics = [("sigma_r2", "Stress $R^2$"), ("sigma_shape_r2", "Curve-shape $R^2$"), ("rho_total_r2", "Dislocation $R^2$"), ("peak_rel_err", "Peak-stress rel. err. (lower better)")] fig, axes = plt.subplots(1, 4, figsize=(10, 2.6), sharey=False) for ax, (col, title) in zip(axes, metrics): m = [sub[sub.model == k][col].mean() for k in order] s = [sub[sub.model == k][col].std() for k in order] colr = ["#b0b0b0"] * 6 + ["#c0392b"] ax.bar(range(len(order)), m, yerr=s, color=colr, capsize=2, error_kw={"lw": 0.8}) ax.set_xticks(range(len(order))) ax.set_xticklabels([MODEL_LABEL[k].replace(" ", "\n") for k in order], rotation=90, fontsize=6) ax.set_title(title, fontsize=8) ax.axhline(0, color="k", lw=0.5) fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname def fig_curves(tag: str, fname=None, max_samples=6): """Predicted vs reference stress-strain and microstructural evolution.""" plt = _plt() d = np.load(RUNS / tag / "predictions.npz", allow_pickle=True) pred, true, mask, sids = d["pred"], d["true"], d["mask"], d["sids"] m = json.loads((RUNS / tag / "metrics.json").read_text()) from .data import TARGET_KEYS js = TARGET_KEYS.index("sigma") n = min(max_samples, len(sids)) sel = np.argsort([-np.nanmax(np.abs(true[i, :, js])) for i in range(len(sids))])[:n] fig, axes = plt.subplots(1, 3, figsize=(9, 2.6)) eps = np.linspace(0, 0.2, true.shape[1]) for i in sel: mm = mask[i, :, js] > 0 axes[0].plot(eps[mm], true[i, mm, js], color="k", lw=0.8, alpha=0.55) axes[0].plot(eps[mm], pred[i, mm, js], color="#c0392b", lw=0.8, ls="--", alpha=0.75) axes[0].set_xlabel("true strain"); axes[0].set_ylabel("stress (GPa)") axes[0].set_title("stress-strain", fontsize=7) from matplotlib.lines import Line2D axes[0].legend(handles=[Line2D([], [], color="k", lw=0.9, label="MD reference"), Line2D([], [], color="#c0392b", lw=0.9, ls="--", label="PI-Mamba")], fontsize=6, frameon=False) for j, lab, col in ((TARGET_KEYS.index("rho_total"), "dislocation density", "#2c7fb8"), (TARGET_KEYS.index("twin"), "twin density", "#31a354")): for i in sel: mm = mask[i, :, j] > 0 if mm.sum() < 2: continue axes[1 if j == TARGET_KEYS.index("rho_total") else 2].plot( eps[mm], true[i, mm, j], color="k", lw=0.7, alpha=0.45) axes[1 if j == TARGET_KEYS.index("rho_total") else 2].plot( eps[mm], pred[i, mm, j], color=col, lw=0.7, ls="--", alpha=0.8) axes[1].set_xlabel("true strain"); axes[1].set_ylabel(r"$\rho$ ($10^{19}$ m$^{-2}$)") axes[1].set_title("total dislocation density", fontsize=7) axes[2].set_xlabel("true strain"); axes[2].set_ylabel(r"$\rho_{twin}$ (nm$^{-1}$)") axes[2].set_title("twin density", fontsize=7) fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fname = fname or f"fig_curves_{tag}.png" fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname# --------------------------------------------------------------------------- # micro -> macro coupling analysis (step 2, question 2) # --------------------------------------------------------------------------- def _load_model(tag: str, device="cpu"): """Rebuild a trained model from ``results/runs/``.""" import torch from .data import TARGETS from .models import build_model d = RUNS / tag ck = torch.load(d / "model.pt", map_location=device, weights_only=False) cfg = ck["cfg"] m = build_model(cfg["model"], n_static=int(np.sum(ck["keep_mask"])), n_out=len(TARGETS), d_model=cfg["d_model"], n_layers=cfg["n_layers"], d_state=cfg["d_state"], dropout=cfg["dropout"], coupling=cfg["coupling"]).to(device) m.load_state_dict(ck["state"]) m.eval() meta = json.loads((d / "metrics.json").read_text()) return m, cfg, meta, ck def coupling_sensitivity(tag: str, channel: str = "rho_total", delta: float = 0.05, device="cpu") -> Dict[str, float]: """Finite-difference counterfactual on the micro -> macro coupling path. The stress head sees ``[h, W * micro]``; we perturb one micro channel by ``delta`` (in its normalised units) and measure the relative change of the predicted flow stress, averaged over all evaluated trajectories and strains. """ import torch from .data import PROC m, cfg, meta, ck = _load_model(tag, device) if m.micro_proj is None: return {"error": "model has no coupling path"} # micro vector layout = [4 phase fractions, 7 dislocation types, twin] # i.e. the full 13-dim output minus the leading stress channel from .data import TARGETS as _TG idx = {t.key: i - 1 for i, t in enumerate(_TG) if i > 0} ch = idx[channel] rec = [] def pre_hook(module, args): x = args[0].clone() x[..., ch] = x[..., ch] + delta rec.append(1) return (x,) d = np.load(RUNS / tag / "predictions.npz", allow_pickle=True) # re-run the model on the same test samples from .data import PackedDataset, Normalizer, build_static_frame, collate mtab = pd.read_csv(PROC / "samples_meta.csv") traj = pd.read_csv(PROC / "trajectories.csv") Xraw, names, kinds = build_static_frame(mtab) km = np.asarray(ck["keep_mask"], dtype=bool) keep = [n for n, k in zip(names, km) if k] norm = Normalizer.from_json(meta["normalizer"]) test_ids = [int(s) for s in meta["test_ids"]] ds = PackedDataset(test_ids, mtab, traj, norm, names, kinds, km) dl = torch.utils.data.DataLoader(ds, batch_size=8, shuffle=False, collate_fn=collate) base, pert = [], [] with torch.no_grad(): for st, x, Y, M, _ in dl: base.append(m(st, x)["pred"][..., 0].numpy()) h = m.micro_proj.register_forward_pre_hook(pre_hook) pert.append(m(st, x)["pred"][..., 0].numpy()) h.remove() b = np.concatenate(base, 0) p = np.concatenate(pert, 0) # stress is z-scored (no asinh), so the inverse is a plain affine map rb = b * norm.tgt_sd[0] + norm.tgt_mu[0] rp = p * norm.tgt_sd[0] + norm.tgt_mu[0] rel = (rp - rb) / np.maximum(np.abs(rb), 1e-6) return { "tag": tag, "channel": channel, "delta_norm": delta, "mean_rel_change": float(np.mean(rel)), "median_abs_rel_change": float(np.median(np.abs(rel))), "p95_abs_rel_change": float(np.percentile(np.abs(rel), 95)), "sign_consistency": float(np.mean(np.sign(rel) == np.sign(np.mean(rel)))), } def autograd_sensitivity(tag: str, device="cpu") -> pd.DataFrame: """d sigma / d (normalised micro channel) via autograd, per strain point.""" import torch from .data import PROC, PackedDataset, Normalizer, build_static_frame, collate m, cfg, meta, ck = _load_model(tag, device) if m.micro_proj is None: return pd.DataFrame() mtab = pd.read_csv(PROC / "samples_meta.csv") traj = pd.read_csv(PROC / "trajectories.csv") Xraw, names, kinds = build_static_frame(mtab) km = np.asarray(ck["keep_mask"], dtype=bool) norm = Normalizer.from_json(meta["normalizer"]) test_ids = [int(s) for s in meta["test_ids"]] ds = PackedDataset(test_ids, mtab, traj, norm, names, kinds, km) dl = torch.utils.data.DataLoader(ds, batch_size=1, shuffle=False, collate_fn=collate) labels = ["xi_BCC", "xi_FCC", "xi_HCP", "xi_other"] + \ [f"rho_{i}" for i in range(7)] + ["twin"] rows = [] for st, x, Y, M, sid in dl: m.zero_grad(set_to_none=True) # capture the micro vector by hooking micro_proj input cache = {} def pre(module, args): a = args[0].clone().requires_grad_(True) cache["micro"] = a return (a,) h = m.micro_proj.register_forward_pre_hook(pre) out = m(st, x) h.remove() sig = out["pred"][..., 0] g = torch.autograd.grad(sig.sum(), cache["micro"])[0][0] # (T, n_micro) arr = g.detach().numpy() eps = np.linspace(0, 0.2, arr.shape[0]) for k, lab in enumerate(labels): rows.append(pd.DataFrame({"strain": eps, "channel": lab, "grad": arr[:, k], "sid": int(sid[0])})) return pd.concat(rows, ignore_index=True) def fig_sensitivity(df: pd.DataFrame, fname="fig_coupling_sensitivity.png"): plt = _plt() chans = ["xi_BCC", "xi_FCC", "xi_HCP", "rho_total", "twin"] fig, ax = plt.subplots(figsize=(4.2, 2.6)) for c in chans: if c not in set(df.channel): continue g = df[df.channel == c].groupby("strain").grad mu, sd = g.mean(), g.std() ax.plot(mu.index, mu.values, lw=1.0, label=c) ax.fill_between(mu.index, mu - sd, mu + sd, alpha=0.15, lw=0) ax.set_xlabel("true strain"); ax.set_ylabel(r"$\partial \sigma/\partial z_{micro}$") ax.set_title("micro -> macro coupling sensitivity", fontsize=8) ax.legend(fontsize=6, frameon=False) ax.axhline(0, color="k", lw=0.4) fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname def fig_ablation(df: pd.DataFrame, fname="fig4_ablation.png"): plt = _plt() sub = df[df.suite == "ablation"] names = [n for n in sub.variant.unique()] names.sort(key=lambda n: -sub[sub.variant == n].sigma_r2.mean()) fig, ax = plt.subplots(figsize=(5.2, 2.4)) m = [sub[sub.variant == n]["sigma_r2"].mean() for n in names] s = [sub[sub.variant == n]["sigma_r2"].std() for n in names] s = [0.0 if not np.isfinite(v) else v for v in s] ax.bar(range(len(names)), m, yerr=s, color="#2c7fb8", capsize=2, error_kw={"lw": 0.8}) ax.set_xticks(range(len(names))) ax.set_xticklabels([MODEL_LABEL.get(n, n) for n in names], rotation=30, ha="right", fontsize=6) ax.set_ylabel("stress $R^2$") fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname def fig_dataeff(df: pd.DataFrame, fname="fig5_data_efficiency.png"): plt = _plt() sub = df[df.suite == "dataeff"].copy() if not len(sub): return None sub["frac"] = sub.variant.str.split("@").str[-1].astype(float) fig, ax = plt.subplots(figsize=(3.4, 2.4)) for mdl, g in sub.groupby("model"): a = g.groupby("frac").sigma_r2 ax.errorbar(a.mean().index, a.mean().values, yerr=a.std().values, marker="o", ms=3, lw=1, capsize=2, label=MODEL_LABEL.get(mdl, mdl)) ax.set_xlabel("fraction of training set"); ax.set_ylabel("stress $R^2$") ax.legend(fontsize=6, frameon=False) fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname def fig_selectivity(tag: str, fname="fig6_selectivity.png", device="cpu"): """Visualise the input-dependent step size Delta_t of the S6 blocks. Delta_t is what makes the SSM *selective*: small Delta -> long memory (elastic regime), large Delta -> fast forgetting (yielding / dislocation multiplication). """ import torch import torch.nn.functional as F from .data import PROC, PackedDataset, Normalizer, build_static_frame, collate plt = _plt() m, cfg, meta, ck = _load_model(tag, device) mtab = pd.read_csv(PROC / "samples_meta.csv") traj = pd.read_csv(PROC / "trajectories.csv") Xraw, names, kinds = build_static_frame(mtab) km = np.asarray(ck["keep_mask"], dtype=bool) norm = Normalizer.from_json(meta["normalizer"]) test_ids = [int(s) for s in meta["test_ids"]] ds = PackedDataset(test_ids, mtab, traj, norm, names, kinds, km) dl = torch.utils.data.DataLoader(ds, batch_size=1, shuffle=False, collate_fn=collate) blocks = list(getattr(m, "blocks", [])) if not blocks: return None caps: Dict[int, List[np.ndarray]] = {i: [] for i in range(len(blocks))} handles = [] for i, blk in enumerate(blocks): def mk(i): def hook(module, inp, out): caps[i].append(F.softplus(out).detach().mean(-1)[0].numpy()) return hook handles.append(blk.dt_proj.register_forward_hook(mk(i))) sig, eps = [], [] with torch.no_grad(): for st, x, Y, M, sid in dl: m(st, x) sig.append(Y[0, :, 0].numpy()) eps.append(x[0, :, 0].numpy() * 0.2) for h in handles: h.remove() fig, axes = plt.subplots(1, 2, figsize=(6.4, 2.3)) ax = axes[0] for i in range(len(blocks)): d = np.stack(caps[i]) # (N, T) ax.plot(eps[0], d.mean(0), lw=1.0, label=f"layer {i+1}") ax.fill_between(eps[0], d.mean(0) - d.std(0), d.mean(0) + d.std(0), alpha=0.15, lw=0) ax.set_xlabel("true strain"); ax.set_ylabel(r"$\bar\Delta_t$ (softplus)") ax.set_title(r"learned step size $\Delta_t$", fontsize=8) ax.legend(fontsize=6, frameon=False) ax = axes[1] D = np.stack(caps[0]) # (N, T) first-layer Delta_t S_ = np.stack(sig) # (N, T) reference stress d0 = D.mean(0) s = S_.mean(0) dsde = np.abs(np.gradient(s, eps[0])) ax.scatter(dsde, d0, s=3, alpha=0.4) ax.set_xlabel(r"$|d\sigma/d\varepsilon|$ (GPa)"); ax.set_ylabel(r"$\bar\Delta_t$") ax.set_title("selectivity vs. hardening rate", fontsize=8) r = float(np.corrcoef(dsde, d0)[0, 1]) # per-sample detrending removes the shared strain trend, which would # otherwise create a spurious correlation between two decaying curves dw, sw = [], [] for i in range(D.shape[0]): di = np.gradient(S_[i], eps[0]) dw.append(D[i] - D[i].mean()) sw.append(np.abs(di) - np.abs(di).mean()) r_detr = float(np.corrcoef(np.concatenate(dw), np.concatenate(sw))[0, 1]) ax.text(0.05, 0.88, f"r={r:.2f} (within-sample r={r_detr:.2f})", transform=ax.transAxes, fontsize=6) fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname, {"r_pooled": float(r), "r_detrended": r_detr} # --------------------------------------------------------------------------- # CLI: python -m pimamba.analysis --coupling [--autograd ] [--selectivity ] # --------------------------------------------------------------------------- def main(argv=None): import argparse ap = argparse.ArgumentParser("pimamba.analysis") ap.add_argument("--coupling", metavar="TAG", help="counterfactual sensitivity on the micro->macro path") ap.add_argument("--autograd", metavar="TAG", help="d sigma / d z_micro per strain point (dumps sens.csv)") ap.add_argument("--selectivity", metavar="TAG", help="figure of the input-dependent step size Delta_t") ap.add_argument("--device", default="cpu") args = ap.parse_args(argv) if args.coupling: rows = [] for ch in ["rho_total", "twin", "xi_FCC", "xi_BCC", "xi_HCP"]: for dv in [0.05, 0.1, 0.2]: r = coupling_sensitivity(args.coupling, ch, dv, device=args.device) rows.append(r) print(r) df = pd.DataFrame(rows) TABLES.mkdir(parents=True, exist_ok=True) df.to_csv(TABLES / "coupling_elasticity.csv", index=False) print("wrote", TABLES / "coupling_elasticity.csv") if args.autograd: df = autograd_sensitivity(args.autograd, device=args.device) if len(df): TABLES.mkdir(parents=True, exist_ok=True) df.to_csv(TABLES / "sens.csv", index=False) print("wrote", TABLES / "sens.csv", "->", fig_sensitivity(df)) if args.selectivity: print("wrote", fig_selectivity(args.selectivity, device=args.device)) if __name__ == "__main__": main() def fig_next(df: pd.DataFrame, fname: str = "fig_next_comparison.png"): """Next-generation backbones vs the best of the first wave.""" plt = _plt() order = ["pimamba", "mamba", "transformer", "llama", "xlstm", "gdn", "hymba", "koopman", "node", "rssm", "flow", "pimamba2"] sub = df[df.suite.isin(["main", "next", "v2"])].copy() rows = [] for m in order: suite = "main" if m in ("pimamba", "mamba", "mamba2", "transformer") else None g = sub[(sub.model == m) & ((sub.suite == suite) if suite else True)] if m == "pimamba2" and "variant" in g: # the v2 suite shares the "pimamba2" backbone between three variants # (plain / peak-loss / no-coupling) -- plot only the plain one. g = g[g.variant == "pimamba2"] if not len(g): continue rows.append({"model": m, "mu": g.sigma_r2.mean(), "sd": g.sigma_r2.std(), "shape": g.sigma_shape_r2.mean(), "params": g.n_params.mean()}) if not rows: return None t = pd.DataFrame(rows).sort_values("mu") fig, ax = plt.subplots(figsize=(4.6, 3.4)) colors = ["C1" if m in ("pimamba", "pimamba2") else ("C2" if m in ("mamba", "mamba2", "transformer") else "C0") for m in t.model] ax.barh(np.arange(len(t)), t.mu, xerr=t.sd, color=colors, alpha=0.85, error_kw=dict(lw=0.8, capsize=2)) ax.scatter(t["shape"], np.arange(len(t)), marker="|", color="k", s=40, label="shape $R^2$") ax.set_yticks(np.arange(len(t))) ax.set_yticklabels([MODEL_LABEL.get(m, m) for m in t.model], fontsize=7) ax.axvline(0, color="k", lw=0.6) ax.set_xlabel(r"stress $R^2$ (mean over runs)") ax.legend(fontsize=6, frameon=False, loc="lower right") ax.set_title("next-generation backbones", fontsize=8) fig.tight_layout() FIGS.mkdir(parents=True, exist_ok=True) fig.savefig(FIGS / fname, bbox_inches="tight") plt.close(fig) return FIGS / fname