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matter-embryogenesis
developmental-fabrication
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passive-networks
| """Gauge-aware passive fabrication; all quantities have declared finite scope. | |
| The graph estimator is classical relative-measurement least squares. Its | |
| effective-resistance covariance is prior art. The reserve feasibility, | |
| robust construction, and manufacturing interpretation are derived in the report. | |
| No electrical calibration algorithm certifies its own unmodeled bias. | |
| """ | |
| import itertools | |
| import numpy as np | |
| from scipy.linalg import cho_factor, cho_solve | |
| from scipy.sparse import coo_matrix | |
| from scipy.sparse.csgraph import connected_components, shortest_path | |
| def incidence(nodes, edges): | |
| edges = np.asarray(edges, int).reshape(-1, 2) | |
| m = len(edges) | |
| return coo_matrix((np.tile([-1., 1.], m), | |
| (np.repeat(np.arange(m), 2), edges.ravel())), | |
| shape=(m, nodes)).tocsr() | |
| def grid_edges(n, dim): | |
| shape = (n,) * dim | |
| coords = np.array(list(np.ndindex(shape)), dtype=int) | |
| index = {tuple(x): i for i, x in enumerate(coords)} | |
| edges = [] | |
| for i, x in enumerate(coords): | |
| for axis in range(dim): | |
| if x[axis] + 1 < n: | |
| y = x.copy(); y[axis] += 1 | |
| edges.append((i, index[tuple(y)])) | |
| return coords, np.asarray(edges, int) | |
| def comparison_line_graph(functional_edges): | |
| """Module comparisons at shared junctions; one extra stable witness. | |
| The witness is uncalibrated in absolute units. Its numerical coordinate is | |
| fixed, and its physical response must stay stable throughout an epoch. | |
| """ | |
| touches = {} | |
| for i, pair in enumerate(functional_edges): | |
| for node in pair: | |
| touches.setdefault(int(node), []).append(i) | |
| edges = set() | |
| for neighbours in touches.values(): | |
| edges.update(itertools.combinations(sorted(neighbours), 2)) | |
| count = len(functional_edges) | |
| edges.add((0, count)) | |
| return count + 1, np.array(sorted(edges), dtype=int) | |
| def edge_colors(nodes, edges): | |
| """Greedy matching schedule: no module is probed twice in one slot.""" | |
| used = [set() for _ in range(nodes)] | |
| colors = [] | |
| for a, b in edges: | |
| color = 0 | |
| while color in used[a] or color in used[b]: | |
| color += 1 | |
| used[a].add(color); used[b].add(color); colors.append(color) | |
| return np.asarray(colors, int) | |
| class RelativeEstimator: | |
| def __init__(self, nodes, edges, reference=None): | |
| self.nodes = int(nodes) | |
| self.edges = np.asarray(edges, int) | |
| self.reference = nodes - 1 if reference is None else int(reference) | |
| self.B = incidence(nodes, edges) | |
| self.L = self.B.T @ self.B | |
| graph = self.L.copy() | |
| graph.setdiag(0); graph.eliminate_zeros() | |
| graph.data[:] = 1. | |
| if connected_components(graph, directed=False, return_labels=False) != 1: | |
| raise ValueError("The comparison graph is disconnected") | |
| self.free = np.delete(np.arange(nodes), self.reference) | |
| self.Bg = self.B[:, self.free] | |
| self.Lg = (self.Bg.T @ self.Bg).tocsr() | |
| self.factor = cho_factor(self.Lg.toarray()) | |
| # This dense covariance is for finite numerical validation/compilation. | |
| self.covariance_unit = cho_solve(self.factor, np.eye(nodes-1)) | |
| self.rho = np.diag(self.covariance_unit).copy() | |
| self.rho_max = float(self.rho.max()) | |
| self.colors = edge_colors(nodes, edges) | |
| self.diameter = int(np.max(shortest_path(graph, directed=False, | |
| unweighted=True))) | |
| def estimate(self, y): | |
| y = np.asarray(y) | |
| z = np.zeros(self.nodes) | |
| rhs = np.asarray(self.Bg.T @ y) | |
| z[self.free] = cho_solve(self.factor, rhs) | |
| residual = rhs-self.Lg@z[self.free] | |
| # Unit-edge inverse entries are <= graph diameter by resistance and | |
| # Cauchy-Schwarz bounds, so the inverse infinity norm is <= R*diameter. | |
| # A conservative standard-roundoff allowance covers the sparse row sums | |
| # and residual evaluation (normal finite arithmetic, no under/overflow). | |
| degree = int(self.L.diagonal().max()) | |
| machine = np.finfo(float).eps | |
| gamma = (2*degree+8)*machine/(1-(2*degree+8)*machine) | |
| arithmetic = gamma*(degree*np.max(np.abs(y)) + | |
| 2*degree*np.max(np.abs(z))+1.) | |
| self.last_numerical_bound = float((self.nodes-1)*self.diameter * | |
| (np.max(np.abs(residual))+arithmetic)) | |
| return z | |
| def radius(self, sigma, samples, horizon, delta): | |
| return float(sigma * np.sqrt( | |
| 2*self.rho_max*np.log(2*(self.nodes-1)*horizon/delta)/samples)) | |
| def sample_budget(self, sigma, radius, horizon, delta): | |
| return max(1, int(np.ceil( | |
| 2*sigma*sigma*self.rho_max * | |
| np.log(2*(self.nodes-1)*horizon/delta)/(radius*radius)))) | |
| def local_estimate(self, y, tolerance=1e-5, max_rounds=200000): | |
| """Synchronous nearest-neighbour gradient messages, not pinned diffusion. | |
| Iterates have zero mean. A final reference-value broadcast fixes the | |
| numerical gauge. The conservative residual bound needs only graph size | |
| and diameter, not a centrally computed eigenvector. | |
| A global max of residual magnitudes is implementable by tree reduction. | |
| The returned round count excludes that reduction/broadcast latency. | |
| """ | |
| rhs = np.asarray(self.B.T @ y) | |
| rhs -= rhs.mean() # eliminate floating point sum residue | |
| z = np.zeros(self.nodes) | |
| step = 1/(float(self.L.diagonal().max())+1) | |
| lower_gap = 2/((self.nodes-1)*self.diameter) | |
| multiplier = np.sqrt(2*self.nodes)/lower_gap | |
| for turn in range(max_rounds+1): | |
| residual = rhs - self.L @ z | |
| bound = multiplier*np.max(np.abs(residual)) | |
| if bound <= tolerance: | |
| return z-z[self.reference], { | |
| 'rounds': turn, 'certified_numerical_radius': float(bound), | |
| 'residual_max': float(np.max(np.abs(residual)))} | |
| z += step*residual | |
| # The sum is invariant mathematically; no global recentering | |
| # operation is used inside the local iteration. | |
| raise RuntimeError("Local estimator did not converge within its budget") | |
| def ratio_observation(x, target, edges, common_gain, noise, physical_scale=1., | |
| node_bias=None): | |
| """Paired log measurements through the SAME gain, after offset removal. | |
| Independent log-noise of each completed ratio is supplied explicitly. | |
| Differential node_bias is NOT canceled and is an assumption-violation test. | |
| """ | |
| u, v = np.asarray(edges).T | |
| g = physical_scale*np.asarray(target)*np.asarray(x) | |
| gain = np.broadcast_to(np.asarray(common_gain), len(edges)) | |
| measured_u = gain*g[u] | |
| measured_v = gain*g[v] | |
| y = np.log(measured_v/measured_u) - np.log(target[v]/target[u]) | |
| if node_bias is not None: | |
| bias = np.asarray(node_bias) | |
| y += bias[v]-bias[u] | |
| return y + noise | |
| def exact_feasibility(x, capacity, tau): | |
| x = np.asarray(x, float); c = np.broadcast_to(capacity, x.shape) | |
| if np.any(x <= 0) or np.any(c < 0) or tau < 0: | |
| raise ValueError("Positive conductances and nonnegative reserves required") | |
| lower = float(np.exp(-tau)*x.max()) | |
| upper = float(np.exp(tau)*np.min(x+c)) | |
| feasible = lower <= upper + 1e-14 | |
| final = np.maximum(x, np.exp(-tau)*lower) if feasible else None | |
| return lower, upper, final | |
| def robust_feasibility(lower_x, upper_x, capacity, tau, seal_log, error_log, | |
| increment_max): | |
| """Sufficient finite-noise/finite-increment certificate, G3.""" | |
| half_band = tau-seal_log-2*error_log | |
| if half_band <= 0: | |
| return {'feasible': False, 'reason': 'no_guard_band'} | |
| a, b = np.exp(-half_band), np.exp(half_band) | |
| lo = max(float(np.max(upper_x)/b), increment_max/(b-a)) | |
| hi = float(np.min(np.asarray(lower_x)+capacity-increment_max)/a) | |
| return {'feasible': bool(lo <= hi), 'scale_lower': lo, | |
| 'scale_upper': hi, 'a': float(a), 'b': float(b), | |
| 'reason': 'feasible' if lo <= hi else 'reserve_interval_empty'} | |
| def uniform_reserve_yield(modules, low, high, capacity, tau): | |
| """Exact G4 iid Uniform[low, high] feasibility probability. | |
| Stable evaluation of the closed form; no simulation/fitting used here. | |
| """ | |
| if modules < 1 or high <= low or low <= 0 or capacity < 0 or tau < 0: | |
| raise ValueError("Invalid finite reserve problem") | |
| width = high-low | |
| q = float(np.exp(2*tau)) | |
| critical = max(0., high/q-low) | |
| if capacity >= critical: | |
| return 1. | |
| if modules == 1: | |
| return 1. | |
| if abs(q-1) < 1e-12: | |
| r = capacity/width | |
| return float(modules*r**(modules-1)-(modules-1)*r**modules) | |
| s = ((1-1/q)*high+capacity)/width | |
| t = ((q-1)*low+q*capacity)/width | |
| log_first = np.log(q)+modules*np.log(s) | |
| # q*s^R - t^R is positive on the branch in use. | |
| correction = -np.expm1(modules*np.log(t)-log_first) if t > 0 else 1. | |
| return float(np.clip(np.exp(log_first)*correction/(q-1), 0, 1)) | |
| def projective_response_error(actual, target): | |
| from contracts import relative_spectrum | |
| eigenvalues = relative_spectrum(actual, target) | |
| if np.min(eigenvalues) <= 0: | |
| return float('inf') | |
| return float(.5*np.log(eigenvalues.max()/eigenvalues.min())) | |
| def closure_bridge_is_needed(nodes, edges, reference_edge): | |
| """An unfinished calibration dependency cannot lose its only connection.""" | |
| keep = np.ones(len(edges), bool); keep[reference_edge] = False | |
| B = incidence(nodes, np.asarray(edges)[keep]) | |
| L = B.T @ B; L.setdiag(0); L.eliminate_zeros() | |
| return connected_components(L, directed=False, return_labels=False) > 1 | |