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Xiaoyin Chen

Xiaoyin Chen contributes to research discovery and scholarly infrastructure.

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Published work

2 published item(s)

preprint2026arXiv

A Measure-Theoretic Analysis of Reasoning: Structural Generalization and Approximation Limits

While empirical scaling laws for LLM reasoning are well-documented, the theoretical mechanisms governing out-of-distribution (OOD) generalization remain elusive. We formalize reasoning via optimal transport, projecting discrete trajectories into a continuous metric space to quantify domain shifts using the Wasserstein-1 distance. Invoking Kantorovich duality, we bound OOD generalization via architectural Lipschitz continuity and functional approximation limits. This exposes two primary constraints. First, position-dependent attention (e.g., Absolute Positional Encoding) fails to preserve shift invariance, yielding an $Ω(1)$ Lipschitz constant and expected risk, whereas shift-invariant mechanisms (e.g., Rotary Embeddings) preserve equivariance and bound the error. Second, by mapping sequential backtracking to a Dyck-$k$ language, we establish a strict circuit depth lower bound for $\text{TC}^0$ Transformers. Scaling physical layer depth is necessary to avert representation collapse -- a constraint that scaling representation width cannot bypass due to irreducible approximation bounds in Barron spaces. Evaluations across 54 Transformer configurations on combinatorial search corroborate these bounds, demonstrating that generalization risk degrades monotonically with the Wasserstein domain shift.

preprint2022arXiv

On the current failure -- but bright future -- of topology-driven biological network alignment

The function of a protein is defined by its interaction partners. Thus, topology-driven network alignment of the protein-protein interaction (PPI) networks of two species should uncover similar interaction patterns and allow identification of functionally similar proteins. Howver, few of the fifty or more algorithms for PPI network alignment have demonstrated a significant link between network topology and functional similarity, and none have recovered orthologs using network topology alone. We find that the major contributing factors to this failure are: (i) edge densities in current PPI networks are too low to expect topological network alignment to succeed; (ii) when edge densities are high enough, some measures of topological similarity easily uncover functionally similar proteins while others do not; and (iii) most network alignment algorithms fail to optimize their own topological objective functions, hampering their ability to use topology effectively. We demonstrate that SANA-the Simulated Annealing Network Aligner-significantly outperforms existing aligners at optimizing their own objective functions, even achieving near-optimal solutions when optimal solution is known. We offer the first demonstration of global network alignments based on topology alone that align functionally similar proteins with p-values in some cases below 1e-300. We predict that topological network alignment has a bright future as edge densities increase towards the value where good alignments become possible. We demonstrate that when enough common topology is present at high enough edge densities-for example in the recent, partly synthetic networks of the Integrated Interaction Database-topological network alignment easily recovers most orthologs, paving the way towards high-throughput functional prediction based on topology-driven network alignment.