Add WaveSystemGraphParser v4.7 synthetic-supervised checkpoint

.gitattributes

@@ -33,3 +33,6 @@ 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
+WaveSystemGraphParser_v47_Combined_RealSynthetic/figures/v47_adaptive.png filter=lfs diff=lfs merge=lfs -text
+WaveSystemGraphParser_v47_Combined_RealSynthetic/figures/v47_polar_samples.png filter=lfs diff=lfs merge=lfs -text
+WaveSystemGraphParser_v47_Combined_RealSynthetic/figures/v47_samples.png filter=lfs diff=lfs merge=lfs -text

WaveSystemGraphParser_v47_Combined_RealSynthetic/README.md

@@ -0,0 +1,34 @@
+# WaveSystemGraphParser v4.7 Synthetic-Supervised
+
+This checkpoint was trained with synthetic standard wave-spectrum strong supervision.
+
+Metrics:
+```json
+{
+  "stage": "synthetic",
+  "init_source": null,
+  "synthetic": {
+    "setDice": 0.7724944864000592,
+    "priorDice": 0.7703823858783359,
+    "bgHi": 0.2648096231241075,
+    "tv": 0.00892037698732955,
+    "count": 1.7669813547432422,
+    "std": 0.6376663809265427,
+    "count_mae": 0.07145379206538201,
+    "corr": 0.9800416584889784
+  },
+  "real": {
+    "setDice": 0.24845916628837586,
+    "priorDice": 0.24536485075950623,
+    "bgHi": 0.1085686294361949,
+    "tv": 0.017705129506066442,
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+    "std": 0.42235949895653924,
+    "count_mae": 1.3912431369535625,
+    "corr": 0.627906670567532
+  },
+  "score": 0.6207128147590648
+}
+```
+
+Main checkpoint: `best.pt`.

WaveSystemGraphParser_v47_Combined_RealSynthetic/checkpoints/best.pt

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WaveSystemGraphParser_v47_Combined_RealSynthetic/checkpoints/last.pt

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WaveSystemGraphParser_v47_Combined_RealSynthetic/logs/best_metrics.json

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+{
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+    "corr": 0.627906670567532
+  },
+  "score": 0.6207128147590648
+}

WaveSystemGraphParser_v47_Combined_RealSynthetic/logs/history.json

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WaveSystemGraphParser_v47_Combined_RealSynthetic/wave_system_graph_parser_v47_combined.py

@@ -0,0 +1,342 @@
+"""
+WaveSystemGraphParser v4.7 combined real+synthetic core-locked: core-attached support topology graph parser for ICWDS
+===================================================================
+Purpose
+-------
+This model is the next-stage frontend after WaveSystemParser v3.x.
+It does not ask a CNN to draw wave-system masks from scratch. Instead:
+
+    E(f,theta)
+      -> physical peak/basin proposals generated outside the model
+      -> node/edge graph reasoning over proposals
+      -> learned merge / keep / slot assembly
+      -> light CNN boundary refinement
+
+This treats watershed-like basins as over-segmentation proposals, not labels.
+The learnable part decides which candidates are physical wave systems, which
+should be merged, and which should be sent to the downstream self-pruning VAE.
+
+v4.5 is designed for a double-layer physical teacher: peak-core proposals define
+system identity/count, while valley-constrained support proposals recover the full
+energetic wave-system footprint. Stripe-like bands can be attached as tails but
+are not allowed to become independent systems without a peak core.
+
+All operations are lightweight and Colab-friendly. No Transformer blocks.
+"""
+import math
+from dataclasses import dataclass, asdict
+from typing import Optional, Dict
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+
+@dataclass
+class GraphParserV47Config:
+    n_freqs: int = 47
+    n_dirs: int = 72
+    n_slots: int = 6
+    bg_index: int = 6
+    p_max: int = 18
+    prop_feat_dim: int = 22
+    width: int = 32
+    depth: int = 4
+    node_dim: int = 48
+    edge_dim: int = 64
+    pair_feat_dim: int = 8
+    use_coord: bool = True
+    use_physics: bool = True
+    rank_temp: float = 0.12
+    count_min: float = 1.0
+    count_max: float = 6.0
+    bg_prior_bias: float = 0.38
+    bg_energy_suppress: float = 14.5
+    bg_energy_gamma: float = 0.70
+    proposal_logit_gain: float = 5.25
+
+    def to_dict(self):
+        return asdict(self)
+
+
+class DepthwiseSeparable(nn.Module):
+    def __init__(self, ci: int, co: int):
+        super().__init__()
+        self.dw = nn.Conv2d(ci, ci, 3, padding=1, groups=ci, bias=False)
+        self.pw = nn.Conv2d(ci, co, 1, bias=False)
+        self.norm = nn.GroupNorm(min(8, co), co)
+        self.act = nn.GELU()
+
+    def forward(self, x):
+        return self.act(self.norm(self.pw(self.dw(x))))
+
+
+class PhysicsAwareModule(nn.Module):
+    def __init__(self, ch: int, n_dirs: int):
+        super().__init__()
+        self.n_dirs = n_dirs
+        dirs = torch.linspace(0, 2 * math.pi, n_dirs + 1)[:n_dirs]
+        self.register_buffer("cos_d", torch.cos(dirs).view(1, 1, 1, n_dirs))
+        self.register_buffer("sin_d", torch.sin(dirs).view(1, 1, 1, n_dirs))
+        self.fuse = nn.Conv2d(ch + 3, ch, 1, bias=False)
+        self.norm = nn.GroupNorm(min(8, ch), ch)
+        self.act = nn.GELU()
+
+    def _phys_features(self, E):
+        eps = 1e-8
+        En = torch.nan_to_num(E, nan=0.0, posinf=1.0, neginf=0.0).clamp_min(0)
+        En = En / (En.amax(dim=(2, 3), keepdim=True) + eps)
+        nf = En.shape[2]
+        rev_cumsum = torch.flip(torch.cumsum(torch.flip(En, dims=[2]), dim=2), dims=[2])
+        col_sum = En.sum(dim=2, keepdim=True) + eps
+        hf_tail = rev_cumsum / col_sum
+        cx = (En * self.cos_d).sum(dim=3, keepdim=True)
+        cy = (En * self.sin_d).sum(dim=3, keepdim=True)
+        row_sum = En.sum(dim=3, keepdim=True) + eps
+        dir_conc = torch.sqrt(cx ** 2 + cy ** 2) / row_sum
+        dir_conc = dir_conc.expand(-1, -1, -1, self.n_dirs)
+        fcoord = torch.linspace(0, 1, nf, device=E.device, dtype=E.dtype).view(1, 1, nf, 1)
+        fc = (En * fcoord).sum(dim=2, keepdim=True) / col_sum
+        spread = torch.sqrt(((En * (fcoord - fc) ** 2).sum(dim=2, keepdim=True)) / col_sum)
+        spread = spread.expand(-1, -1, nf, -1)
+        return torch.cat([hf_tail, dir_conc, spread], dim=1)
+
+    def forward(self, h, E):
+        return self.act(self.norm(self.fuse(torch.cat([h, self._phys_features(E)], dim=1))))
+
+
+class WaveSystemGraphParserV47(nn.Module):
+    """Proposal graph parser.
+
+    forward inputs
+    --------------
+    x:            [B,1,47,72], normalized to [-1,1]
+    prop_masks:   [B,P,47,72], binary/soft physical basin proposals
+    prop_feats:   [B,P,F], proposal features produced by the training script
+    prop_valid:   [B,P], 1 if proposal exists
+
+    outputs include final probability masks, node slot assignments, edge logits,
+    count prediction, and diagnostics.
+    """
+    def __init__(self, cfg: Optional[GraphParserV47Config] = None):
+        super().__init__()
+        self.cfg = cfg or GraphParserV47Config()
+        c = self.cfg
+        in_ch = 1 + (3 if c.use_coord else 0)
+        self.stem = nn.Conv2d(in_ch, c.width, 3, padding=1)
+        self.stem_norm = nn.GroupNorm(min(8, c.width), c.width)
+        self.physics = PhysicsAwareModule(c.width, c.n_dirs) if c.use_physics else None
+        self.blocks = nn.ModuleList([DepthwiseSeparable(c.width, c.width) for _ in range(c.depth)])
+        self.global_pool = nn.AdaptiveAvgPool2d(1)
+        self.residual_head = nn.Conv2d(c.width, c.n_slots + 1, 1)
+        nn.init.zeros_(self.residual_head.weight)
+        nn.init.zeros_(self.residual_head.bias)
+
+        self.node_mlp = nn.Sequential(
+            nn.Linear(c.width + c.prop_feat_dim, c.node_dim), nn.GELU(),
+            nn.Linear(c.node_dim, c.node_dim), nn.GELU(),
+        )
+        self.node_keep = nn.Linear(c.node_dim, 1)
+        self.node_slot = nn.Linear(c.node_dim, c.n_slots)
+        self.count_head = nn.Sequential(
+            nn.Linear(c.width + c.node_dim, c.width), nn.GELU(), nn.Linear(c.width, c.n_slots)
+        )
+        # Edge head uses node_i, node_j, absolute difference, product, plus handcrafted physical pair features.
+        self.edge_head = nn.Sequential(
+            nn.Linear(4 * c.node_dim + c.pair_feat_dim, c.edge_dim), nn.GELU(),
+            nn.Linear(c.edge_dim, c.edge_dim), nn.GELU(), nn.Linear(c.edge_dim, 1)
+        )
+        self._coord_cache = None
+
+
+    @staticmethod
+    def _clean_tensor(x, fill=0.0, lo=-30.0, hi=30.0):
+        return torch.nan_to_num(x, nan=fill, posinf=hi, neginf=lo).clamp(lo, hi)
+
+    @staticmethod
+    def _safe_softmax(logits, dim):
+        logits = torch.nan_to_num(logits, nan=0.0, posinf=30.0, neginf=-30.0).clamp(-30.0, 30.0)
+        logits = logits - logits.max(dim=dim, keepdim=True).values.detach()
+        p = torch.softmax(logits, dim=dim)
+        return torch.nan_to_num(p, nan=0.0, posinf=1.0, neginf=0.0)
+
+    def _coord_channels(self, B, device, dtype):
+        c = self.cfg
+        if self._coord_cache is None:
+            nf, nd = c.n_freqs, c.n_dirs
+            fcoord = torch.linspace(0, 1, nf).view(1, 1, nf, 1).expand(1, 1, nf, nd)
+            ang = torch.linspace(0, 2 * math.pi, nd + 1)[:nd].view(1, 1, 1, nd).expand(1, 1, nf, nd)
+            self._coord_cache = torch.cat([fcoord, torch.sin(ang), torch.cos(ang)], dim=1)
+        return self._coord_cache.to(device=device, dtype=dtype).expand(B, -1, -1, -1)
+
+    def _rank_prune_presence(self, slot_mass, count_soft):
+        c = self.cfg
+        B, K = slot_mass.shape
+        _, order = torch.sort(slot_mass, dim=1, descending=True)
+        rank_pos = torch.arange(1, K + 1, device=slot_mass.device, dtype=slot_mass.dtype).view(1, K)
+        cs = count_soft.clamp(c.count_min, c.count_max).view(B, 1)
+        gate_sorted = torch.sigmoid((cs + 0.5 - rank_pos) / c.rank_temp)
+        gate = torch.zeros_like(gate_sorted).scatter(1, order, gate_sorted)
+        return gate.clamp(0, 1)
+
+    def _node_pool(self, h, prop_masks, prop_valid):
+        # h: [B,C,H,W], prop_masks [B,P,H,W]
+        B, C, H, W = h.shape
+        P = prop_masks.shape[1]
+        denom = prop_masks.flatten(2).sum(dim=2).clamp_min(1.0)  # [B,P]
+        pooled = torch.einsum("bchw,bphw->bpc", h, prop_masks) / denom[:, :, None]
+        pooled = pooled * prop_valid[:, :, None]
+        return pooled
+
+    def _edge_logits(self, node, prop_feats, prop_valid):
+        B, P, D = node.shape
+        ni = node[:, :, None, :].expand(B, P, P, D)
+        nj = node[:, None, :, :].expand(B, P, P, D)
+        # Pair physical features from proposal features: distance in f/theta and mass contrast.
+        # feat layout is defined in training script: mass, peak, area, mu_f, sin_t, cos_t, ...
+        fi = prop_feats[:, :, 3][:, :, None]
+        fj = prop_feats[:, :, 3][:, None, :]
+        d_f = (fi - fj).abs()
+        si = prop_feats[:, :, 4][:, :, None]; ci = prop_feats[:, :, 5][:, :, None]
+        sj = prop_feats[:, :, 4][:, None, :]; cj = prop_feats[:, :, 5][:, None, :]
+        dot = (si * sj + ci * cj).clamp(-1.0 + 1e-5, 1.0 - 1e-5)
+        d_t = torch.acos(dot) / math.pi
+        mi = prop_feats[:, :, 0][:, :, None]
+        mj = prop_feats[:, :, 0][:, None, :]
+        d_m = (mi - mj).abs()
+        sf_i = prop_feats[:, :, 6][:, :, None]; sf_j = prop_feats[:, :, 6][:, None, :]
+        st_i = prop_feats[:, :, 7][:, :, None]; st_j = prop_feats[:, :, 7][:, None, :]
+        d_sf = (sf_i - sf_j).abs()
+        d_st = (st_i - st_j).abs()
+        prom_i = prop_feats[:, :, 12][:, :, None]; prom_j = prop_feats[:, :, 12][:, None, :]
+        prom_min = torch.minimum(prom_i, prom_j)
+        stripe_i = prop_feats[:, :, 13][:, :, None]; stripe_j = prop_feats[:, :, 13][:, None, :]
+        stripe_max = torch.maximum(stripe_i, stripe_j)
+        qual_i = prop_feats[:, :, 11][:, :, None]; qual_j = prop_feats[:, :, 11][:, None, :]
+        qual_min = torch.minimum(qual_i, qual_j)
+        pair_phys = torch.stack([d_f, d_t, d_m, d_sf, d_st, prom_min, stripe_max, qual_min], dim=-1)
+        inp = torch.cat([ni, nj, (ni - nj).abs(), ni * nj, pair_phys], dim=-1)
+        e = self.edge_head(inp).squeeze(-1)
+        valid_pair = (prop_valid[:, :, None] * prop_valid[:, None, :]).bool()
+        eye = torch.eye(P, device=node.device, dtype=torch.bool).view(1, P, P)
+        e = e.masked_fill(~valid_pair | eye, 0.0)
+        return e, valid_pair & (~eye)
+
+    def forward(self, x, prop_masks, prop_feats, prop_valid, prior_w=2.5, residual_w=0.0):
+        c = self.cfg
+        B, _, H, W = x.shape
+        prop_masks = torch.nan_to_num(prop_masks.float(), nan=0.0, posinf=0.0, neginf=0.0).clamp(0, 1)
+        prop_feats = torch.nan_to_num(prop_feats.float(), nan=0.0, posinf=5.0, neginf=-5.0).clamp(-5.0, 5.0)
+        prop_valid = prop_valid.float().clamp(0, 1)
+        h_in = torch.cat([x, self._coord_channels(B, x.device, x.dtype)], dim=1) if c.use_coord else x
+        h = self._clean_tensor(F.gelu(self.stem_norm(self.stem(h_in))), lo=-20.0, hi=20.0)
+        E01 = torch.nan_to_num((x + 1.0) * 0.5, nan=0.0, posinf=1.0, neginf=0.0).clamp(0, 1)
+        if self.physics is not None:
+            h = self._clean_tensor(h + self.physics(h, E01), lo=-20.0, hi=20.0)
+        for blk in self.blocks:
+            h = self._clean_tensor(h + blk(h), lo=-20.0, hi=20.0)
+        global_feat = self.global_pool(h).flatten(1)
+        node_pool = self._node_pool(h, prop_masks, prop_valid)
+        node_in = torch.cat([node_pool, prop_feats], dim=-1)
+        node = self._clean_tensor(self.node_mlp(node_in), lo=-20.0, hi=20.0) * prop_valid[:, :, None]
+        node_keep_logit = self._clean_tensor(self.node_keep(node).squeeze(-1), lo=-20.0, hi=20.0).masked_fill(prop_valid <= 0, -20.0)
+        node_keep = torch.sigmoid(node_keep_logit) * prop_valid
+        node_slot_logits = self._clean_tensor(self.node_slot(node), lo=-20.0, hi=20.0).masked_fill(prop_valid[:, :, None] <= 0, -20.0)
+        node_slot = self._safe_softmax(node_slot_logits, dim=-1) * prop_valid[:, :, None]
+        node_context = (node * node_keep[:, :, None]).sum(dim=1) / node_keep.sum(dim=1, keepdim=True).clamp_min(1.0)
+        count_logits = self._clean_tensor(self.count_head(torch.cat([global_feat, node_context], dim=-1)), lo=-20.0, hi=20.0)
+        count_probs = torch.sigmoid(count_logits)
+        count_soft = count_probs.sum(dim=1).clamp(c.count_min, c.count_max)
+
+        # Proposal graph edge logits.
+        edge_logits, edge_valid = self._edge_logits(node, prop_feats, prop_valid)
+        edge_logits = self._clean_tensor(edge_logits, lo=-20.0, hi=20.0)
+        # Slot priors from proposal assembly.
+        assign = node_slot * node_keep[:, :, None]
+        prior_signal = torch.einsum("bpk,bphw->bkhw", assign, prop_masks)
+        # Normalize each slot prior but preserve zero slots.
+        prior_signal = prior_signal / prior_signal.amax(dim=(2, 3), keepdim=True).clamp_min(1e-6)
+        prior_signal = torch.nan_to_num(prior_signal, nan=0.0, posinf=1.0, neginf=0.0).clamp(0.0, 1.0)
+        denom = E01.sum(dim=(2, 3)).clamp_min(1e-6)
+        slot_mass = (prior_signal * E01).sum(dim=(2, 3)) / denom
+        presence = self._rank_prune_presence(slot_mass, count_soft)
+        prior_signal = prior_signal * presence[:, :, None, None]
+
+        En = E01 / E01.amax(dim=(2, 3), keepdim=True).clamp_min(1e-6)
+        bg_prior_logit = c.bg_prior_bias - c.bg_energy_suppress * En.pow(c.bg_energy_gamma)
+        residual_logits = self.residual_head(h)
+        signal_logits = prior_w * (c.proposal_logit_gain * torch.log(prior_signal.clamp_min(1e-6))) + residual_w * residual_logits[:, :c.n_slots]
+        bg_logits = prior_w * bg_prior_logit + residual_w * residual_logits[:, c.n_slots:c.n_slots + 1]
+        logits = self._clean_tensor(torch.cat([signal_logits, bg_logits], dim=1), lo=-60.0, hi=60.0)
+        prob_raw = self._safe_softmax(logits, dim=1)
+        prob = prob_raw / prob_raw.sum(dim=1, keepdim=True).clamp_min(1e-6)
+
+        prior_logits = self._clean_tensor(torch.cat([c.proposal_logit_gain * torch.log(prior_signal.clamp_min(1e-6)), bg_prior_logit], dim=1), lo=-60.0, hi=60.0)
+        prior_prob = self._safe_softmax(prior_logits, dim=1)
+        return {
+            "logits": logits, "prob": prob, "prob_raw": prob_raw,
+            "prior_signal": prior_signal, "prior_logits": prior_logits, "prior_prob": prior_prob,
+            "residual_logits": residual_logits,
+            "node": node, "node_keep_logit": node_keep_logit, "node_keep": node_keep,
+            "node_slot_logits": node_slot_logits, "node_slot": node_slot,
+            "edge_logits": edge_logits, "edge_valid": edge_valid,
+            "count_logits": count_logits, "count_probs": count_probs, "count_soft": count_soft,
+            "slot_mass": slot_mass, "presence": presence,
+        }
+
+    @torch.no_grad()
+    def prior_foreground_metrics(self, out, E01, high_quantile=0.80):
+        E = E01[:, 0] if E01.dim() == 4 else E01
+        flat = E.flatten(1)
+        thr = torch.quantile(flat, high_quantile, dim=1).view(-1, 1, 1)
+        mask_hi = E >= thr
+        denom = mask_hi.float().sum().clamp_min(1.0)
+        prior_prob = out.get("prior_prob", torch.softmax(out["prior_logits"], dim=1))
+        fg_prior = prior_prob[:, :self.cfg.n_slots].sum(dim=1)
+        bg_prior = prior_prob[:, self.cfg.bg_index]
+        return {"prior_fg_hi": (fg_prior * mask_hi).sum() / denom,
+                "prior_bg_hi": (bg_prior * mask_hi).sum() / denom}
+
+    @torch.no_grad()
+    def dominance_metrics(self, out, E01, high_quantile=0.80):
+        final = out["prob"].argmax(dim=1)
+        prior = out["prior_logits"].argmax(dim=1)
+        resid = out["residual_logits"].argmax(dim=1)
+        E = E01[:, 0] if E01.dim() == 4 else E01
+        flat = E.flatten(1)
+        thr = torch.quantile(flat, high_quantile, dim=1).view(-1, 1, 1)
+        mask = E >= thr
+        denom = mask.float().sum().clamp_min(1.0)
+        return {"prior_agree": ((final == prior) & mask).float().sum() / denom,
+                "residual_agree": ((final == resid) & mask).float().sum() / denom}
+
+    def graph_regularizers(self, out, prop_masks, prop_valid, E01):
+        # Slot compactness and smoothness proxies for final masks.
+        c = self.cfg
+        prob = out["prob"][:, :c.n_slots]
+        E = E01[:, 0] if E01.dim() == 4 else E01
+        nf, nd = c.n_freqs, c.n_dirs
+        f = torch.linspace(0, 1, nf, device=E.device, dtype=E.dtype).view(1, 1, nf, 1)
+        theta = torch.linspace(0, 2 * math.pi, nd + 1, device=E.device, dtype=E.dtype)[:nd].view(1, 1, 1, nd)
+        w = prob * E[:, None]
+        mass = w.sum(dim=(2, 3)).clamp_min(1e-8)
+        mu_f = (w * f).sum(dim=(2, 3)) / mass
+        cx = (w * torch.cos(theta)).sum(dim=(2, 3)) / mass
+        cy = (w * torch.sin(theta)).sum(dim=(2, 3)) / mass
+        mu_t = torch.atan2(cy, cx)
+        df2 = (f - mu_f[:, :, None, None]) ** 2
+        dt = torch.atan2(torch.sin(theta - mu_t[:, :, None, None]), torch.cos(theta - mu_t[:, :, None, None])) / math.pi
+        radius = ((w * (df2 + dt ** 2)).sum(dim=(2, 3)) / mass).mean()
+        tv = (prob[:, :, 1:, :] - prob[:, :, :-1, :]).abs().mean() + (prob[:, :, :, 1:] - prob[:, :, :, :-1]).abs().mean()
+        # Encourage node slot assignments to be confident only for valid proposals.
+        ns = out["node_slot"].clamp_min(1e-8)
+        ent = -(ns * ns.log()).sum(dim=-1)
+        ent = (ent * prop_valid).sum() / prop_valid.sum().clamp_min(1.0)
+        return {"slot_radius": radius, "slot_tv": tv, "node_slot_entropy": ent}
+
+    def num_params(self):
+        return sum(p.numel() for p in self.parameters())
+
+
+# Backward-compatible alias
+WaveSystemGraphParserV4 = WaveSystemGraphParserV47