"""Dataset B: typed knowledge graph for motif-topology retrieval. Replaces the phase-0 toy semantic world. The phase-0 world was a bag of attributes on a taxonomic PATH, which the topology program already falsified as "simple unlabeled paths are enough" -> Falsified (see ../topology/docs/research_program/claim_review_final.md). A path has no recurrence topology, which is why ordered==unordered==typed there. This dataset is a typed directed graph whose memory objects (rooted walks) have real recurrence: shared intermediates create diamonds. Example motif: K-001 <--SUPPORTS-- L-001 --USES_METHOD--> long_window_motifs ^ ^ |--WEAKENS--- L-002 --USES_METHOD----------+ Both records point at K-001 and share the method `long_window_motifs`, so a depth-2 walk from K-001 revisits the method node -> recurrence -> a canonical motif exists. Three claims built on the same typed diamond consolidate. Motif families (each >=2 symbolically-disjoint instances so they consolidate): contested_claim : SUPPORTS + WEAKENS records sharing a method (diamond) validated_claim : single SUPPORTS record (star; expected WEAK motif, like a path) superseded_claim : SUPPORTS + SUPERSEDED_BY another claim (chain recurrence) The validated_claim family is included ON PURPOSE as a predicted-weak control: per the topology falsification, a star has no recurrence and should NOT consolidate into a discriminative motif. If it does as well as the diamond, something is wrong. """ from __future__ import annotations from collections.abc import Iterable from dataclasses import dataclass, field # --------------------------------------------------------------------------- # graph model # --------------------------------------------------------------------------- # node "kind" is metadata, not part of the canonical signature (signature is # identity-free over node labels). It exists so humans can read the graph. NODES: dict[str, str] = { # claims "K-001": "claim", "K-002": "claim", "K-003": "claim", "K-004": "claim", "K-005": "claim", "K-006": "claim", "K-007": "claim", "K-008": "claim", "K-009": "claim", # learning records "L-001": "record", "L-002": "record", "L-003": "record", "L-004": "record", "L-005": "record", "L-006": "record", "L-007": "record", "L-008": "record", "L-009": "record", "L-010": "record", # shared intermediates (the source of recurrence) "long_window_motifs": "method", "short_window_motifs": "method", "structural_signature": "method", "degree_match_control": "method", "true_inclusion": "metric", "coverage": "metric", "candidate_reduction": "metric", "false_activation_rate": "metric", "topology_memory": "domain", "retrieval_specificity": "domain", # verdicts are leaves "passed": "verdict", "failed": "verdict", "inconclusive": "verdict", } # directed typed edges: (source, edge_type, target) EDGES: list[tuple[str, str, str]] = [ # --- family: contested_claim (SUPPORTS + WEAKENS sharing a method) ------- # K-001 contested on topology_memory; both records use long_window_motifs ("L-001", "SUPPORTS", "K-001"), ("L-001", "USES_METHOD", "long_window_motifs"), ("L-001", "MEASURES", "true_inclusion"), ("L-001", "IN_DOMAIN", "topology_memory"), ("L-001", "HAS_VERDICT", "passed"), ("L-002", "WEAKENS", "K-001"), ("L-002", "USES_METHOD", "long_window_motifs"), ("L-002", "MEASURES", "coverage"), ("L-002", "IN_DOMAIN", "topology_memory"), ("L-002", "HAS_VERDICT", "failed"), # K-002 contested on retrieval_specificity; both records use structural_signature ("L-003", "SUPPORTS", "K-002"), ("L-003", "USES_METHOD", "structural_signature"), ("L-003", "MEASURES", "candidate_reduction"), ("L-003", "IN_DOMAIN", "retrieval_specificity"), ("L-003", "HAS_VERDICT", "passed"), ("L-004", "WEAKENS", "K-002"), ("L-004", "USES_METHOD", "structural_signature"), ("L-004", "MEASURES", "coverage"), ("L-004", "IN_DOMAIN", "retrieval_specificity"), ("L-004", "HAS_VERDICT", "failed"), # K-003 contested on topology_memory; both records use short_window_motifs ("L-005", "SUPPORTS", "K-003"), ("L-005", "USES_METHOD", "short_window_motifs"), ("L-005", "MEASURES", "true_inclusion"), ("L-005", "IN_DOMAIN", "topology_memory"), ("L-005", "HAS_VERDICT", "inconclusive"), ("L-006", "WEAKENS", "K-003"), ("L-006", "USES_METHOD", "short_window_motifs"), ("L-006", "MEASURES", "coverage"), ("L-006", "IN_DOMAIN", "topology_memory"), ("L-006", "HAS_VERDICT", "failed"), # --- family: validated_claim (single SUPPORTS star; predicted-weak) ----- ("L-007", "SUPPORTS", "K-004"), ("L-007", "USES_METHOD", "degree_match_control"), ("L-007", "MEASURES", "false_activation_rate"), ("L-007", "IN_DOMAIN", "retrieval_specificity"), ("L-007", "HAS_VERDICT", "passed"), ("L-008", "SUPPORTS", "K-005"), ("L-008", "USES_METHOD", "degree_match_control"), ("L-008", "MEASURES", "false_activation_rate"), ("L-008", "IN_DOMAIN", "retrieval_specificity"), ("L-008", "HAS_VERDICT", "passed"), # --- family: superseded_claim (SUPPORTS + SUPERSEDED_BY chain) ---------- ("L-009", "SUPPORTS", "K-006"), ("L-009", "USES_METHOD", "long_window_motifs"), ("L-009", "MEASURES", "true_inclusion"), ("L-009", "IN_DOMAIN", "topology_memory"), ("L-009", "HAS_VERDICT", "passed"), ("K-006", "SUPERSEDED_BY", "K-007"), # NOTE: K-008 gets its OWN support record L-010 below (not a reuse of L-009). # Reusing L-009 for both K-006 and K-008 coupled the two claims through the # shared record and made their typed signatures differ (correct behavior, # but it broke the "family consolidates >=2" design). ] EDGES = [e for e in EDGES if not (e[0] == "L-007" and e[1] == "SUPPORTS" and e[2] == "K-008")] EDGES += [ ("L-010", "SUPPORTS", "K-008"), ("L-010", "USES_METHOD", "long_window_motifs"), ("L-010", "MEASURES", "true_inclusion"), ("L-010", "IN_DOMAIN", "topology_memory"), ("L-010", "HAS_VERDICT", "passed"), ("K-008", "SUPERSEDED_BY", "K-009"), ] # focal entities whose rooted walks are the "memory objects" / retrieval targets FOCAL_CLAIMS = ["K-001", "K-002", "K-003", "K-004", "K-005", "K-006", "K-008"] FOCAL_RECORDS = ["L-001", "L-003", "L-005", "L-007", "L-009"] # declared motif families for evaluation (focal claim -> expected family) FAMILY_OF_CLAIM = { "K-001": "contested_claim", "K-002": "contested_claim", "K-003": "contested_claim", "K-004": "validated_claim", "K-005": "validated_claim", "K-006": "superseded_claim", "K-008": "superseded_claim", } @dataclass class TypedGraph: nodes: dict[str, str] out_edges: dict[str, list[tuple[str, str]]] = field(default_factory=dict) in_edges: dict[str, list[tuple[str, str]]] = field(default_factory=dict) def neighbors(self, node: str) -> list[tuple[str, str, str]]: """All incident edges as (other_node, edge_type, direction). direction='out' means node->other via edge_type; direction='in' means other->node via edge_type (traversed backward). Reverse traversal is tagged so the typed signature can distinguish 'A supports B' (out) from 'A is-supported-by B' (in). """ out = [(tgt, et, "out") for (et, tgt) in self.out_edges.get(node, [])] inn = [(src, et, "in") for (et, src) in self.in_edges.get(node, [])] # deterministic order: by (edge_type, direction, other_node) return sorted(out + inn, key=lambda e: (e[1], e[2], e[0])) def build_graph() -> TypedGraph: g = TypedGraph(nodes=dict(NODES)) for src, et, tgt in EDGES: g.out_edges.setdefault(src, []).append((et, tgt)) g.in_edges.setdefault(tgt, []).append((et, src)) for d in (g.out_edges, g.in_edges): for k, v in d.items(): v.sort() return g def rooted_walk(g: TypedGraph, root: str, max_depth: int = 2) -> list[tuple]: """Deterministic DFS walk from `root`. Returns a list of steps. Step 0 is the root. Each subsequent step is (node, edge_type, direction) describing the edge traversed to reach `node` from the previous node in the walk. Direction in {'out','in'} (see neighbors). Visited-set is per-branch (we allow revisiting a node if it sits on a different incident edge, because recurrence is exactly what we want to capture); we cap depth and total steps to stay bounded. """ walk: list[tuple] = [(root, None, None)] # stack of (node, depth, path-set of canonical node ids on this branch) stack = [(root, 0, (root,))] # iterative DFS yielding in insertion order while stack: node, depth, branch_path = stack.pop(0) if depth >= max_depth: continue for other, et, direction in g.neighbors(node): step = (other, et, direction) walk.append(step) stack.append((other, depth + 1, branch_path + (other,))) return walk def walks_for(g: TypedGraph, focals: Iterable[str], max_depth: int = 2) -> dict[str, list[tuple]]: return {f: rooted_walk(g, f, max_depth=max_depth) for f in focals}