arXiv subjects

Chengkun Wu

Publications and source records attributed to Chengkun Wu.

6 recordsLinked to original sources

arXiv2026

Gene Ontology-Guided Hierarchical Spatial Gene Expression Prediction from Histopathology Images

Predicting spatial gene expression from histopathology images enables large-scale transcriptomic profiling without the cost of direct measurement. Existing methods decode the target gene set as a flat, unstructured vector, ignoring the inter-gene dependencies arising from shared biological pathways and regulatory programs. Without explicit structural guidance, models must infer these dependencies entirely from limited paired data, constraining prediction quality. We propose MSGR (Multi-Scale Gene Refiner), which bridges this gap by incorporating the Gene Ontology (GO), a curated functional hierarchy of genes, as an explicit structural prior. MSGR organizes target genes into a four-level GO tree. Its GO-guided decoder then progressively refines predictions from coarse functional domains to fine individual genes via residual corrections under scale-weighted supervision. Operating solely on the gene side, the GO-guided decoder serves as a seamless plug-in replacement that consistently improves existing architectures without requiring any image-side modifications. Extensive experiments on nine datasets from the HEST-1k benchmark provide empirical evidence for two central claims: GO-structured decoding consistently outperforms flat decoding, even against a state-of-the-art generative baseline, and the gain is attributable to biological ontology structure rather than hierarchical decomposition per se, as confirmed by a +0.027 margin over a structurally equivalent random hierarchy.

cs.AI↗

arXiv2025

LLM-based Multi-Agent Copilot for Quantum Sensor

Large language models (LLM) exhibit broad utility but face limitations in quantum sensor development, stemming from interdisciplinary knowledge barriers and involving complex optimization processes. Here we present QCopilot, an LLM-based multi-agent framework integrating external knowledge access, active learning, and uncertainty quantification for quantum sensor design and diagnosis. Comprising commercial LLMs with few-shot prompt engineering and vector knowledge base, QCopilot employs specialized agents to adaptively select optimization methods, automate modeling analysis, and independently perform problem diagnosis. Applying QCopilot to atom cooling experiments, we generated 10${}^{\rm{8}}$ sub-$\rm{\mu}$K atoms without any human intervention within a few hours, representing $\sim$100$\times$ speedup over manual experimentation. Notably, by continuously accumulating prior knowledge and enabling dynamic modeling, QCopilot can autonomously identify anomalous parameters in multi-parameter experimental settings. Our work reduces barriers to large-scale quantum sensor deployment and readily extends to other quantum information systems.

quant-ph↗

arXiv2025

LAMBench: A Benchmark for Large Atomistic Models

Large Atomistic Models (LAMs) have undergone remarkable progress recently, emerging as universal or fundamental representations of the potential energy surface defined by the first-principles calculations of atomistic systems. However, our understanding of the extent to which these models achieve true universality, as well as their comparative performance across different models, remains limited. This gap is largely due to the lack of comprehensive benchmarks capable of evaluating the effectiveness of LAMs as approximations to the universal potential energy surface. In this study, we introduce LAMBench, a benchmarking system designed to evaluate LAMs in terms of their generalizability, adaptability, and applicability. These attributes are crucial for deploying LAMs as ready-to-use tools across a diverse array of scientific discovery contexts. We benchmark ten state-of-the-art LAMs released prior to August 1, 2025, using LAMBench. Our findings reveal a significant gap between the current LAMs and the ideal universal potential energy surface. They also highlight the need for incorporating cross-domain training data, supporting multi-fidelity modeling, and ensuring the models' conservativeness and differentiability. As a dynamic and extensible platform, LAMBench is intended to continuously evolve, thereby facilitating the development of robust and generalizable LAMs capable of significantly advancing scientific research. The LAMBench code is open-sourced at https://github.com/deepmodeling/lambench, and an interactive leaderboard is available at https://www.aissquare.com/openlam?tab=Benchmark.

physics.comp-ph↗

arXiv2022

HFN: Heterogeneous Feature Network for Multivariate Time Series Anomaly Detection

Network or physical attacks on industrial equipment or computer systems may cause massive losses. Therefore, a quick and accurate anomaly detection (AD) based on monitoring data, especially the multivariate time-series (MTS) data, is of great significance. As the key step of anomaly detection for MTS data, learning the relations among different variables has been explored by many approaches. However, most of the existing approaches do not consider the heterogeneity between variables, that is, different types of variables (continuous numerical variables, discrete categorical variables or hybrid variables) may have different and distinctive edge distributions. In this paper, we propose a novel semi-supervised anomaly detection framework based on a heterogeneous feature network (HFN) for MTS, learning heterogeneous structure information from a mass of unlabeled time-series data to improve the accuracy of anomaly detection, and using attention coefficient to provide an explanation for the detected anomalies. Specifically, we first combine the embedding similarity subgraph generated by sensor embedding and feature value similarity subgraph generated by sensor values to construct a time-series heterogeneous graph, which fully utilizes the rich heterogeneous mutual information among variables. Then, a prediction model containing nodes and channel attentions is jointly optimized to obtain better time-series representations. This approach fuses the state-of-the-art technologies of heterogeneous graph structure learning (HGSL) and representation learning. The experiments on four sensor datasets from real-world applications demonstrate that our approach detects the anomalies more accurately than those baseline approaches, thus providing a basis for the rapid positioning of anomalies.

cs.LG↗

arXiv2022

An Unsupervised Short- and Long-Term Mask Representation for Multivariate Time Series Anomaly Detection

Anomaly detection of multivariate time series is meaningful for system behavior monitoring. This paper proposes an anomaly detection method based on unsupervised Short- and Long-term Mask Representation learning (SLMR). The main idea is to extract short-term local dependency patterns and long-term global trend patterns of the multivariate time series by using multi-scale residual dilated convolution and Gated Recurrent Unit(GRU) respectively. Furthermore, our approach can comprehend temporal contexts and feature correlations by combining spatial-temporal masked self-supervised representation learning and sequence split. It considers the importance of features is different, and we introduce the attention mechanism to adjust the contribution of each feature. Finally, a forecasting-based model and a reconstruction-based model are integrated to focus on single timestamp prediction and latent representation of time series. Experiments show that the performance of our method outperforms other state-of-the-art models on three real-world datasets. Further analysis shows that our method is good at interpretability.

cs.LG↗

arXiv2022

Deep Anomaly Discovery From Unlabeled Videos via Normality Advantage and Self-Paced Refinement

While classic video anomaly detection (VAD) requires labeled normal videos for training, emerging unsupervised VAD (UVAD) aims to discover anomalies directly from fully unlabeled videos. However, existing UVAD methods still rely on shallow models to perform detection or initialization, and they are evidently inferior to classic VAD methods. This paper proposes a full deep neural network (DNN) based solution that can realize highly effective UVAD. First, we, for the first time, point out that deep reconstruction can be surprisingly effective for UVAD, which inspires us to unveil a property named "normality advantage", i.e., normal events will enjoy lower reconstruction loss when DNN learns to reconstruct unlabeled videos. With this property, we propose Localization based Reconstruction (LBR) as a strong UVAD baseline and a solid foundation of our solution. Second, we propose a novel self-paced refinement (SPR) scheme, which is synthesized into LBR to conduct UVAD. Unlike ordinary self-paced learning that injects more samples in an easy-to-hard manner, the proposed SPR scheme gradually drops samples so that suspicious anomalies can be removed from the learning process. In this way, SPR consolidates normality advantage and enables better UVAD in a more proactive way. Finally, we further design a variant solution that explicitly takes the motion cues into account. The solution evidently enhances the UVAD performance, and it sometimes even surpasses the best classic VAD methods. Experiments show that our solution not only significantly outperforms existing UVAD methods by a wide margin (5% to 9% AUROC), but also enables UVAD to catch up with the mainstream performance of classic VAD.

cs.CV↗