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Researcher profile

Mahito Sugiyama

Mahito Sugiyama contributes to research discovery and scholarly infrastructure.

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Machine LearningMethodologyQuantitative Methods

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Published work

10 published item(s)

preprint2026arXiv

When Graph Language Models Go Beyond Memorization

It remains unclear whether graph language models learn structural regularities or merely memorize training graphs; this cannot be resolved by current aggregate fidelity metrics alone. We develop a calibrated diagnostic protocol that combines frequent subgraph mining, a graph-level bootstrap baseline, and three-level frequency stratification to disentangle memorization from structural alignment. Using this framework, we show that graph language models can acquire structural regularities beyond memorization at scale, primarily in the high-frequency regime. This is supported by the following empirical evidence: On five TU benchmarks, LLaMA-style graph language models reach high subgraph-rank correlation, yet their alignment is matched or exceeded by the memorization bootstrap in most cases. At small scale, under our bootstrap diagnostic, fidelity is largely indistinguishable from verbatim recall. In contrast, at large scale with 3.75M graphs, verbatim memorization drops sharply while rank correlation remains near ceiling. Crucially, in a separate fixed-subsample analysis, frequent subgraph mining restricted to the novel-only subset closely tracks the corresponding all-generation Spearman correlation, providing evidence that the alignment is not driven solely by verbatim recall. Across all scales, high-frequency patterns are well reproduced, while rare patterns remain poorly covered, and this deficit narrows only marginally as capacity increases. We observe the same scale-dependent crossover under two distinct graph serializations (canonical DFS code and action sequences), providing evidence of robustness in our analysis.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Neural Tangent Kernel Perspective of Infinite Tree Ensembles

In practical situations, the tree ensemble is one of the most popular models along with neural networks. A soft tree is a variant of a decision tree. Instead of using a greedy method for searching splitting rules, the soft tree is trained using a gradient method in which the entire splitting operation is formulated in a differentiable form. Although ensembles of such soft trees have been used increasingly in recent years, little theoretical work has been done to understand their behavior. By considering an ensemble of infinite soft trees, this paper introduces and studies the Tree Neural Tangent Kernel (TNTK), which provides new insights into the behavior of the infinite ensemble of soft trees. Using the TNTK, we theoretically identify several non-trivial properties, such as global convergence of the training, the equivalence of the oblivious tree structure, and the degeneracy of the TNTK induced by the deepening of the trees.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Fast Rank-1 NMF for Missing Data with KL Divergence

We propose a fast non-gradient-based method of rank-1 non-negative matrix factorization (NMF) for missing data, called A1GM, that minimizes the KL divergence from an input matrix to the reconstructed rank-1 matrix. Our method is based on our new finding of an analytical closed-formula of the best rank-1 non-negative multiple matrix factorization (NMMF), a variety of NMF. NMMF is known to exactly solve NMF for missing data if positions of missing values satisfy a certain condition, and A1GM transforms a given matrix so that the analytical solution to NMMF can be applied. We empirically show that A1GM is more efficient than a gradient method with competitive reconstruction errors.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Fast Rank Reduction for Non-negative Matrices via Mean Field Theory

We propose an efficient matrix rank reduction method for non-negative matrices, whose time complexity is quadratic in the number of rows or columns of a matrix. Our key insight is to formulate rank reduction as a mean-field approximation by modeling matrices via a log-linear model on structured sample space, which allows us to solve the rank reduction as convex optimization. The highlight of this formulation is that the optimal solution that minimizes the KL divergence from a given matrix can be analytically computed in a closed form. We empirically show that our rank reduction method is faster than NMF and its popular variant, lraNMF, while achieving competitive low rank approximation error on synthetic and real-world datasets.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Additive Poisson Process: Learning Intensity of Higher-Order Interaction in Stochastic Processes

We present the Additive Poisson Process (APP), a novel framework that can model the higher-order interaction effects of the intensity functions in stochastic processes using lower dimensional projections. Our model combines the techniques in information geometry to model higher-order interactions on a statistical manifold and in generalized additive models to use lower-dimensional projections to overcome the effects from the curse of dimensionality. Our approach solves a convex optimization problem by minimizing the KL divergence from a sample distribution in lower dimensional projections to the distribution modeled by an intensity function in the stochastic process. Our empirical results show that our model is able to use samples observed in the lower dimensional space to estimate the higher-order intensity function with extremely sparse observations.

0 citations0 reviewsNo code linkedOpen access
preprint2018arXiv

Legendre Decomposition for Tensors

We present a novel nonnegative tensor decomposition method, called Legendre decomposition, which factorizes an input tensor into a multiplicative combination of parameters. Thanks to the well-developed theory of information geometry, the reconstructed tensor is unique and always minimizes the KL divergence from an input tensor. We empirically show that Legendre decomposition can more accurately reconstruct tensors than other nonnegative tensor decomposition methods.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing

We present a novel algorithm, Westfall-Young light, for detecting patterns, such as itemsets and subgraphs, which are statistically significantly enriched in one of two classes. Our method corrects rigorously for multiple hypothesis testing and correlations between patterns through the Westfall-Young permutation procedure, which empirically estimates the null distribution of pattern frequencies in each class via permutations. In our experiments, Westfall-Young light dramatically outperforms the current state-of-the-art approach in terms of both runtime and memory efficiency on popular real-world benchmark datasets for pattern mining. The key to this efficiency is that unlike all existing methods, our algorithm neither needs to solve the underlying frequent itemset mining problem anew for each permutation nor needs to store the occurrence list of all frequent patterns. Westfall-Young light opens the door to significant pattern mining on large datasets that previously led to prohibitive runtime or memory costs.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Significant Subgraph Mining with Multiple Testing Correction

The problem of finding itemsets that are statistically significantly enriched in a class of transactions is complicated by the need to correct for multiple hypothesis testing. Pruning untestable hypotheses was recently proposed as a strategy for this task of significant itemset mining. It was shown to lead to greater statistical power, the discovery of more truly significant itemsets, than the standard Bonferroni correction on real-world datasets. An open question, however, is whether this strategy of excluding untestable hypotheses also leads to greater statistical power in subgraph mining, in which the number of hypotheses is much larger than in itemset mining. Here we answer this question by an empirical investigation on eight popular graph benchmark datasets. We propose a new efficient search strategy, which always returns the same solution as the state-of-the-art approach and is approximately two orders of magnitude faster. Moreover, we exploit the dependence between subgraphs by considering the effective number of tests and thereby further increase the statistical power.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Identifying Higher-order Combinations of Binary Features

Finding statistically significant interactions between binary variables is computationally and statistically challenging in high-dimensional settings, due to the combinatorial explosion in the number of hypotheses. Terada et al. recently showed how to elegantly address this multiple testing problem by excluding non-testable hypotheses. Still, it remains unclear how their approach scales to large datasets. We here proposed strategies to speed up the approach by Terada et al. and evaluate them thoroughly in 11 real-world benchmark datasets. We observe that one approach, incremental search with early stopping, is orders of magnitude faster than the current state-of-the-art approach.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Efficient network-guided multi-locus association mapping with graph cuts

As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic loci. While several methods for multi-locus mapping have been proposed, it is often unclear how to relate the detected loci to the growing knowledge about gene pathways and networks. The few methods that take biological pathways or networks into account are either restricted to investigating a limited number of predetermined sets of loci, or do not scale to genome-wide settings. We present SConES, a new efficient method to discover sets of genetic loci that are maximally associated with a phenotype, while being connected in an underlying network. Our approach is based on a minimum cut reformulation of the problem of selecting features under sparsity and connectivity constraints that can be solved exactly and rapidly. SConES outperforms state-of-the-art competitors in terms of runtime, scales to hundreds of thousands of genetic loci, and exhibits higher power in detecting causal SNPs in simulation studies than existing methods. On flowering time phenotypes and genotypes from Arabidopsis thaliana, SConES detects loci that enable accurate phenotype prediction and that are supported by the literature. Matlab code for SConES is available at http://webdav.tuebingen.mpg.de/u/karsten/Forschung/scones/

0 citations0 reviewsNo code linkedOpen access