arXiv subjects

Danyu Li

Publications and source records attributed to Danyu Li.

7 recordsLinked to original sources

arXiv2026

EGRL: Edge generation-guided relation-aware learning for RNA-protein interaction prediction

RNA-Protein Interactions (RPIs) are critical for regulating cellular functions. While traditional wet-lab experiments for RPI detection are costly and time-consuming, Deep Learning (DL) methods provide an efficient computational alternative for RPI Prediction (RPIP). In particular, Graph Neural Networks (GNNs) are promising, as they naturally model RPI networks. However, existing GNN-based methods often rely on homogeneous graphs or predefined meta-paths, which limit their ability to handle data sparsity and to generalize to cold-start scenarios involving unknown molecules. To address these limitations, we propose Edge Generation-guided Relation-aware Learning (EGRL), a novel framework with several key components: implicit meta-path learning to capture relational semantics without handcrafted paths; a multi-relation-aware attention mechanism for adaptive fusion of interaction patterns; a graph generator that predicts potential ("soft") edges to support cold-start nodes; and a multi-feature fusion predictor for final interaction scoring. EGRL is jointly trained with a primary task loss and an auxiliary generator loss. Comprehensive evaluations on four benchmark datasets demonstrate that EGRL achieves competitive overall performance. More importantly, it exhibits superior generalization in cold-start settings, achieving an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.867 and an Area Under the Precision-Recall curve (AUPR) of 0.861 on unknown molecules, corresponding to improvements of 8.6% in AUROC and 5.0% in AUPR over prior state-of-the-art methods. The code will be released soon.

cs.LG↗

arXiv2026

ATGBuilder: Feature-Assisted Graph Learning for Activity Transition Graph Construction with Seed Supervision

Android applications are organized around activities that provide visual Graphical User Interface (GUI) containers that host the UI and handle user interaction events. Activity Transition Graphs (ATGs) have been widely used to model apps' GUI navigation. However, the construction of high-quality ATGs is challenging: ATGs based on static analysis may miss acceptable transitions and may extract infeasible ones; while dynamically explored ATGs can yield incomplete transitions. Recent learning-based approaches can treat ATG construction as a seed-supervised link-prediction task. However, the use of activity-layout and widget-trigger information for ATG construction remains limited. We propose ATGBuilder, a feature-assisted graph-learning approach for seed-supervised ATG construction. ATGBuilder uses a Large Language Model (LLM) to summarize UI activity metadata from layouts into compact textual functionality summaries. ATGBuilder explicitly models widget-trigger information into the edge attribute: It then uses an auxiliary widget-attribute reconstruction objective on this information during model training. ATGBuilder's performance was evaluated across a series of ablations on the frontmatter corpus, and an experiment on benchmark using manually-checked ground-truth ATGs. Experiments on multiple benchmarks show that ATGBuilder significantly outperforms state-of-the-art methods. We further demonstrate its effectiveness by improving automated GUI exploration tools through better navigation guidance.

cs.SE↗

arXiv2024

Ribonucleic-Acid Protein Interaction Prediction Based on Deep Learning: A Comprehensive Survey

The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), governs biological processes, including gene regulation and disease pathogenesis. This comprehensive survey examines Artificial Intelligence (AI) applications in Deep Learning-based RPI Prediction (DL-based RPIP) through eight Research Questions (RQs), analyzing 179 studies (2014--2023). The key findings include: sustained technical evolution through embryonic (2014--2017), accelerated (2018--2022), and expansion phases (2023) (RQ1); hybrid models integrating Graph Neural Networks (GNNs) (for topological interface modeling) and Transformers (for long-range dependencies) achieve state-of-the-art performance (RQ4); pretrained language models enhance small-sample learning, but the cross-species generalization declines sharply with evolutionary distance (RQ5). Critical challenges persist, including data heterogeneity across databases, the scarcity of standardized benchmarks (RQ2), and balancing the trade-off between feature encoding and information preservation (RQ3). Future advancements require biologically informed DL architectures, multi-feature fusion, and rigorous cross-validation to bridge the generalization-interpretability gap (RQ8): This would accelerate the clinical translation of predictive tools (RQ6/RQ7). As the first comprehensive analysis spanning feature encoding, modeling, evaluation, applications, and tools, this work fills a critical gap in the DL-based RPIP literature.

q-bio.QM↗

arXiv2020

Experimental Realization of Universal Time-optimal non-Abelian Geometric Gates

Based on the geometrical nature of quantum phases, non-adiabatic holonomic quantum control (NHQC) has become a standard technique for enhancing robustness in constructing quantum gates. However, the conventional approach of NHQC is sensitive to control instability, as it requires the driving pulses to cover a fixed pulse area. Furthermore, even for small-angle rotations, all operations need to be completed with the same duration of time. Here we experimentally demonstrate a time-optimal and unconventional approach of NHQC (called TOUNHQC), which can optimize the operation time of any holonomic gate. Compared with the conventional approach, TOUNHQC provides an extra layer of robustness to decoherence and control errors. The experiment involves a scalable architecture of superconducting circuit, where we achieved a fidelity of 99.51% for a single qubit gate using interleaved randomized benchmarking. Moreover, a two-qubit holonomic control-phase gate has been implemented where the gate error can be reduced by as much as 18% compared with NHQC.

quant-ph↗

arXiv2019

Realization of Superadiabatic Two-qubit Gates Using Parametric Modulation in Superconducting Circuits

Fast robust two-qubit gate operation with low susceptibility to crosstalk are the key to scalable quantum information processing. Parametrically driven gate is inherently insensitive to crosstalk while superadiabatic control can speed up the gate without losing accuracy. We propose and experimentally implement superadiabatic two-qubit gates using parametric modulation on superconducting quantum circuits. Our results demonstrate the preservation of adiabaticity at a gate speed close to the quantum limit, in addition to robustness against control instability. We demonstrate a CZ gate with error rate of 5.8$\%$, limited largely by qubit decoherence, promising future improvement and scalable implementation.

quant-ph↗

arXiv2019

Experimental Measurement of the Quantum Metric Tensor and Related Topological Phase Transition with a Superconducting Qubit

Berry curvature is an imaginary component of the quantum geometric tensor (QGT) and is well studied in many branches of modern physics; however, the quantum metric as a real component of the QGT is less explored. Here, by using tunable superconducting circuits, we experimentally demonstrate two methods to directly measure the quantum metric tensor for characterizing the geometry and topology of underlying quantum states in parameter space. The first method is to probe the transition probability after a sudden quench, and the second one is to detect the excitation rate under weak periodic driving. Furthermore, based on quantum-metric and Berry-curvature measurements, we explore a topological phase transition in a simulated time-reversal-symmetric system, which is characterized by the Euler characteristic number instead of the Chern number. The work opens up a unique approach to explore the topology of quantum states with the QGT.

quant-ph↗

arXiv2018

Demonstration of Hopf-link semimetal bands with superconducting circuits

Hopf-link semimetals exhibit exotic gapless band structures with fascinating topological properties, which have never been observed in nature. Here we demonstrate nodal lines with topological form of Hopf-link chains in artificial semimetal-bands. Driving superconducting quantum circuits with elaborately designed microwave fields, we mapped the momentum space of a lattice to a parameter space of the Hamiltonian for a Hopf-link semimetal. By measuring the energy spectrum, we directly imaged nodal lines in cubic lattices. By tuning the driving fields, we adjusted various parameters of Hamiltonian. Important topological features, such as link-unlink topological transitions and the robustness of the Hopf-link chain structure were investigated. Moreover, we extracted the linking number by detecting the Berry phase associated with different loops encircling nodal lines. This topological invariant clearly reveals the nontrivial topology of the Hopf-link semimetal. Our results provide knowledge for developing new materials and quantum devices.

quant-ph↗