Quantum Laboratory, Fujitsu Research, Fujitsu Limited, 4-1-1 Kawasaki, Kanagawa 211-8588, Japan (Dated: September 18, 2025) Machine learning (ML) holds great promise for extracting insights from complex quantum many-body data obtained in quantum experiments. This approach can efficiently solve certain quantum problems that are classically intractable, suggesting potential advantages of harnessing quantum data. However, addressing large-scale problems still requires significant amounts of data beyond the limited computational resources of near-term quantum devices. We propose a scalable ML framework called Geometrically Local Quantum Kernel (GLQK), designed to efficiently learn quantum many-body experimental data by leveraging the exponential decay of correlations, a phenomenon prevalent in noncritical systems. In the task of learning an unknown polynomial of quantum expectation values, we rigorously prove that GLQK substantially improves polynomial sample complexity in the number of qubits n, compared to the existing shadow kernel, by constructing a feature space from local quantum information at the correlation length scale. This improvement is particularly notable when each term of the target polynomial involves few local subsystems. Remarkably, for translationally symmetric data, GLQK achieves constant sample complexity, independent of n. We numerically demonstrate its high scalability in two learning tasks on quantum many-body phenomena. These results establish new avenues for utilizing experimental data to advance the understanding of quantum many-body physics. Understanding complex quantum many-body phenomena is a pivotal challenge across various fields, including physics, chemistry, and biology. Classical computational approaches often struggle to capture the intricate interplay of interactions in these systems due to the exponential dimensionality of the Hilbert space. Recent advances in experimental control over quantum systems offer a promising avenue for probing these phenomena.

We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions ofgenes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks.These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier builtfrom such a kernel not only recognizes a given class of promoter regions,but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection ofaligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.

We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions of genes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks. These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier built from such a kernel not only recognizes a given class of promoter regions, but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection of aligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.

We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions of genes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks. These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier built from such a kernel not only recognizes a given class of promoter regions, but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection of aligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.