arXiv subjects

Ji Cao

Publications and source records attributed to Ji Cao.

8 recordsLinked to original sources

arXiv2026

Quantum tunnelling-integrated optoplasmonic nanotrap enables conductance visualisation of individual proteins

Biological electron transfer (ET) relies on quantum mechanical tunnelling through a dynamically folded protein. Yet, the spatiotemporal coupling between structural fluctuations and electron flux remains poorly understood, largely due to limitations in existing experimental techniques, such as ensemble averaging and non-physiological operating conditions. Here, we introduce a quantum tunnelling-integrated optoplasmonic nanotrap (QTOP-trap), an optoelectronic platform that combines plasmonic optical trapping with real-time quantum tunnelling measurements. This label-free approach enables single-molecule resolution of protein conductance in physiological electrolytes, achieving sub-3 nm spatial precision and 10-{\mu}s temporal resolution. By synchronising optoelectronic measurements, QTOP-trap resolves protein-specific conductance signatures and directly correlates tertiary structure dynamics with conductance using a "protein switch" strategy. This methodology establishes a universal framework for dissecting non-equilibrium ET mechanisms in individual conformational-active proteins, with broad implications for bioenergetics research and biomimetic quantum device design.

physics.bio-ph↗

arXiv2025

Learning Multi-Modal Mobility Dynamics for Generalized Next Location Recommendation

The precise prediction of human mobility has produced significant socioeconomic impacts, such as location recommendations and evacuation suggestions. However, existing methods suffer from limited generalization capability: unimodal approaches are constrained by data sparsity and inherent biases, while multi-modal methods struggle to effectively capture mobility dynamics caused by the semantic gap between static multi-modal representation and spatial-temporal dynamics. Therefore, we leverage multi-modal spatial-temporal knowledge to characterize mobility dynamics for the location recommendation task, dubbed as \textbf{M}ulti-\textbf{M}odal \textbf{Mob}ility (\textbf{M}$^3$\textbf{ob}). First, we construct a unified spatial-temporal relational graph (STRG) for multi-modal representation, by leveraging the functional semantics and spatial-temporal knowledge captured by the large language models (LLMs)-enhanced spatial-temporal knowledge graph (STKG). Second, we design a gating mechanism to fuse spatial-temporal graph representations of different modalities, and propose an STKG-guided cross-modal alignment to inject spatial-temporal dynamic knowledge into the static image modality. Extensive experiments on six public datasets show that our proposed method not only achieves consistent improvements in normal scenarios but also exhibits significant generalization ability in abnormal scenarios.

cs.AI↗

arXiv2025

Dual-branch Spatial-Temporal Self-supervised Representation for Enhanced Road Network Learning

Road network representation learning (RNRL) has attracted increasing attention from both researchers and practitioners as various spatiotemporal tasks are emerging. Recent advanced methods leverage Graph Neural Networks (GNNs) and contrastive learning to characterize the spatial structure of road segments in a self-supervised paradigm. However, spatial heterogeneity and temporal dynamics of road networks raise severe challenges to the neighborhood smoothing mechanism of self-supervised GNNs. To address these issues, we propose a $\textbf{D}$ual-branch $\textbf{S}$patial-$\textbf{T}$emporal self-supervised representation framework for enhanced road representations, termed as DST. On one hand, DST designs a mix-hop transition matrix for graph convolution to incorporate dynamic relations of roads from trajectories. Besides, DST contrasts road representations of the vanilla road network against that of the hypergraph in a spatial self-supervised way. The hypergraph is newly built based on three types of hyperedges to capture long-range relations. On the other hand, DST performs next token prediction as the temporal self-supervised task on the sequences of traffic dynamics based on a causal Transformer, which is further regularized by differentiating traffic modes of weekdays from those of weekends. Extensive experiments against state-of-the-art methods verify the superiority of our proposed framework. Moreover, the comprehensive spatiotemporal modeling facilitates DST to excel in zero-shot learning scenarios.

cs.LG↗

arXiv2025

Capturing Context-Aware Route Choice Semantics for Trajectory Representation Learning

Trajectory representation learning (TRL) aims to encode raw trajectory data into low-dimensional embeddings for downstream tasks such as travel time estimation, mobility prediction, and trajectory similarity analysis. From a behavioral perspective, a trajectory reflects a sequence of route choices within an urban environment. However, most existing TRL methods ignore this underlying decision-making process and instead treat trajectories as static, passive spatiotemporal sequences, thereby limiting the semantic richness of the learned representations. To bridge this gap, we propose CORE, a TRL framework that integrates context-aware route choice semantics into trajectory embeddings. CORE first incorporates a multi-granular Environment Perception Module, which leverages large language models (LLMs) to distill environmental semantics from point of interest (POI) distributions, thereby constructing a context-enriched road network. Building upon this backbone, CORE employs a Route Choice Encoder with a mixture-of-experts (MoE) architecture, which captures route choice patterns by jointly leveraging the context-enriched road network and navigational factors. Finally, a Transformer encoder aggregates the route-choice-aware representations into a global trajectory embedding. Extensive experiments on 4 real-world datasets across 6 downstream tasks demonstrate that CORE consistently outperforms 15 state-of-the-art TRL methods, achieving an average improvement of 9.20\% over the best-performing baseline. Our code is available at https://github.com/caoji2001/CORE.

cs.CV↗

arXiv2025

From GNNs to Trees: Multi-Granular Interpretability for Graph Neural Networks

Interpretable Graph Neural Networks (GNNs) aim to reveal the underlying reasoning behind model predictions, attributing their decisions to specific subgraphs that are informative. However, existing subgraph-based interpretable methods suffer from an overemphasis on local structure, potentially overlooking long-range dependencies within the entire graphs. Although recent efforts that rely on graph coarsening have proven beneficial for global interpretability, they inevitably reduce the graphs to a fixed granularity. Such an inflexible way can only capture graph connectivity at a specific level, whereas real-world graph tasks often exhibit relationships at varying granularities (e.g., relevant interactions in proteins span from functional groups, to amino acids, and up to protein domains). In this paper, we introduce a novel Tree-like Interpretable Framework (TIF) for graph classification, where plain GNNs are transformed into hierarchical trees, with each level featuring coarsened graphs of different granularity as tree nodes. Specifically, TIF iteratively adopts a graph coarsening module to compress original graphs (i.e., root nodes of trees) into increasingly coarser ones (i.e., child nodes of trees), while preserving diversity among tree nodes within different branches through a dedicated graph perturbation module. Finally, we propose an adaptive routing module to identify the most informative root-to-leaf paths, providing not only the final prediction but also the multi-granular interpretability for the decision-making process. Extensive experiments on the graph classification benchmarks with both synthetic and real-world datasets demonstrate the superiority of TIF in interpretability, while also delivering a competitive prediction performance akin to the state-of-the-art counterparts.

cs.LG↗

arXiv2025

Holistic Semantic Representation for Navigational Trajectory Generation

Trajectory generation has garnered significant attention from researchers in the field of spatio-temporal analysis, as it can generate substantial synthesized human mobility trajectories that enhance user privacy and alleviate data scarcity. However, existing trajectory generation methods often focus on improving trajectory generation quality from a singular perspective, lacking a comprehensive semantic understanding across various scales. Consequently, we are inspired to develop a HOlistic SEmantic Representation (HOSER) framework for navigational trajectory generation. Given an origin-and-destination (OD) pair and the starting time point of a latent trajectory, we first propose a Road Network Encoder to expand the receptive field of road- and zone-level semantics. Second, we design a Multi-Granularity Trajectory Encoder to integrate the spatio-temporal semantics of the generated trajectory at both the point and trajectory levels. Finally, we employ a Destination-Oriented Navigator to seamlessly integrate destination-oriented guidance. Extensive experiments on three real-world datasets demonstrate that HOSER outperforms state-of-the-art baselines by a significant margin. Moreover, the model's performance in few-shot learning and zero-shot learning scenarios further verifies the effectiveness of our holistic semantic representation.

cs.CV↗

arXiv2022

AGMI: Attention-Guided Multi-omics Integration for Drug Response Prediction with Graph Neural Networks

Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG) for each cell line, and then aggregates multi-omics features to predict drug response using a novel structure, called Graph edge-aware Network (GeNet). For the first time, our AGMI approach explores gene constraint based multi-omics integration for DRP with the whole-genome using GNNs. Empirical experiments on the CCLE and GDSC datasets show that our AGMI largely outperforms state-of-the-art DRP methods by 8.3%--34.2% on four metrics. Our data and code are available at https://github.com/yivan-WYYGDSG/AGMI.

q-bio.GN↗

arXiv2018

Spontaneous PT symmetry breaking in non-Hermitian coupled cavities array

We study the effects of the position of the passive and active cavities on the spontaneous parity-time (PT) symmetry breaking behavior in non-Hermitian coupled cavities array model. We analyze and discuss the energy eigenvalue spectrums and PT symmetry in the topologically trivial and nontrivial regimes under three different cases in detail, i.e., the passive and active cavities are located at, respectively, the two end positions, the second and penultimate positions, and each position in coupled cavities array. The odevity of the number of cavities is further considered to check the effects of the non-Hermitian terms applied on the PT symmetric and asymmetric systems. We find that the position of the passive and active cavities has remarkable impacts on the spontaneous PT symmetry breaking behavior, and in each case the system exhibits distinguishable and novel spontaneous PT symmetry breaking characteristic, respectively. The effects of the non-Hermitian terms on the $\mathcal{PT}$ symmetric and asymmetric systems due to the odevity are comparatively different in the first case while qualitatively same in the second case.

quant-ph↗