Sparse Network Inference under Imperfect Detection and its Application to Ecological Networks

Estimating the generative mechanism of large-scale networks is a fundamental challenge in statistical machine learning. It requires the identification of the latent connectivity structure, which is in general an NP-hard combinatorial problem due to the absence of canonical node labels. We address this challenge by allowing for probabilistic couplings, thereby relaxing the assignment problem. Our estimation framework can be formulated as a semi-relaxed Gromov-Wasserstein objective and provides a low-dimensional representation of the generative structure. We solve this via a block-coordinate conditional gradient algorithm. Despite the relaxation, the resulting solution is typically deterministic: in fact, we show that the optimality gap between the relaxed solution and the deterministic assignment vanishes at rate $O(1/n)$, where $n$ is the number of nodes. This allows for tractable recovery of the underlying model and enables rigorous statistical analysis: we establish consistency and minimax-optimal convergence rates for both stochastic block models and Holder-smooth graphons. Our implementation scales efficiently with $n$, as demonstrated on both synthetic and real-world datasets.

We study the symmetric multi-type orthogonal non-negative matrix tri-factorization problem, where several symmetric non-negative matrices are simultaneously approximated by factors of the form $GS_{i}G^{\top}$, with a shared non-negative and orthogonal factor $G$. This model is motivated by clustering and network analysis, where non-negativity improves interpretability and orthogonality gives a natural assignment-type structure to the latent factor. Since the resulting optimization problem is highly non-convex, we develop two heuristic algorithms for computing high-quality local solutions. The first one is a fixed point method derived from the Karush-Kuhn-Tucker conditions after adding a penalty term for the orthogonality constraint. The second one is a three-stage ADAM-based method that combines non-negativity-preserving optimization, orthogonalization, and restricted ADAM refinement on the feasible set. We evaluate both methods on synthetic data, including noisy instances, and on citation network benchmarks. The synthetic experiments show that both algorithms recover factorizations close to the optimum and remain stable under noise. On real networks, the learned embeddings are competitive with or better than standard baselines such as SVD, node2vec, and classical link prediction heuristics in link prediction, node clustering, and node classification tasks.

We introduce \textbf{Prism}, a framework for structural symmetry diagnosis in complex networks. Given a graph Laplacian $L$ and a duality operator $P$ (a symmetric involution), Prism computes the \emph{duality defect} $δ(L,P) = \|LP - PL\|_F / \|L\|_F$ -- a scalar measuring how far the network deviates from structural self-consistency. When $P$ encodes the network's true symmetry, $δ$ starts near zero and rises monotonically as structure degrades; an arbitrary $P$ gives noise. We prove that the optimal $L'$ satisfying $[L', P] = 0$ is given by a closed-form block-diagonal projection, and provide an unsupervised alternating optimization that learns $P$ from the graph's own Fiedler vector. Experiments on synthetic networks show the true-$P$ defect is $3.38\times$ more sensitive to structural degradation than an index-reversal baseline and more sensitive than modularity. On Zachary's Karate Club with edge noise, Prism achieves $94.5\%$ community detection accuracy at $5\%$ noise versus $76.6\%$ for the raw Laplacian baseline. Applied to live S&P~500 data (2026-05-17), Prism detects rising structural stress (defect $0.43 \to 0.73$ over 90 days) while surface correlations remain low -- a signal invisible to correlation-based methods. In a historical backtest spanning five major stress events (2011--2020), the duality defect exhibits a consistent pattern: it reaches elevated levels \emph{before} the correlation spike that accompanies each crisis, and sustains high readings during periods of structural fragility that conventional metrics classify as calm. The duality defect is a first-principles structural admissibility condition, requiring no training data and computable in milliseconds.