arXiv subjects

Yue Zhao

Publications and source records attributed to Yue Zhao.

At least 253 records · Page 14Linked to original sources

arXiv2024

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive software solution designed to handle the entire pipeline of omics data processing. GenoCraft offers a unified platform featuring advanced bioinformatics tools, covering all aspects of omics data analysis. It encompasses a range of functionalities, such as normalization, quality control, differential analysis, network analysis, pathway analysis, and diverse visualization techniques. This software makes state-of-the-art omics data analysis more accessible to a wider range of users. With GenoCraft, researchers and data scientists have access to an array of cutting-edge bioinformatics tools under a user-friendly interface, making it a valuable resource for managing and analyzing large-scale omics data. The API with an interactive web interface is publicly available at https://genocraft.stanford. edu/. We also release all the codes in https://github.com/futianfan/GenoCraft.

q-bio.GN↗

arXiv2024

DPU: Dynamic Prototype Updating for Multimodal Out-of-Distribution Detection

Out-of-distribution (OOD) detection is essential for ensuring the robustness of machine learning models by identifying samples that deviate from the training distribution. While traditional OOD detection has primarily focused on single-modality inputs, such as images, recent advances in multimodal models have demonstrated the potential of leveraging multiple modalities (e.g., video, optical flow, audio) to enhance detection performance. However, existing methods often overlook intra-class variability within in-distribution (ID) data, assuming that samples of the same class are perfectly cohesive and consistent. This assumption can lead to performance degradation, especially when prediction discrepancies are uniformly amplified across all samples. To address this issue, we propose Dynamic Prototype Updating (DPU), a novel plug-and-play framework for multimodal OOD detection that accounts for intra-class variations. Our method dynamically updates class center representations for each class by measuring the variance of similar samples within each batch, enabling adaptive adjustments. This approach allows us to amplify prediction discrepancies based on the updated class centers, thereby improving the model's robustness and generalization across different modalities. Extensive experiments on two tasks, five datasets, and nine base OOD algorithms demonstrate that DPU significantly improves OOD detection performance, setting a new state-of-the-art in multimodal OOD detection, with improvements of up to 80 percent in Far-OOD detection. To facilitate accessibility and reproducibility, our code is publicly available on GitHub.

cs.CV↗

arXiv2024

Variance-reduced random batch Langevin dynamics

The random batch method is advantageous in accelerating force calculations in particle simulations, but it poses a challenge of removing the artificial heating effect in application to the Langevin dynamics. We develop an approach to solve this issue by estimating the force variance, resulting in a variance-reduced random batch Langevin dynamics. Theoretical analysis shows the high-order local truncation error of the time step in the numerical discretization scheme, in consistent with the fluctuation-dissipation theorem. Numerical results indicate that the method can achieve a significant variance reduction since a smaller batch size provides accurate approximation, demonstrating the attractive feature of the variance-reduced random batch method for Langevin dynamics.

physics.comp-ph↗

arXiv2024

Meta-Learning for Speeding Up Large Model Inference in Decentralized Environments

The deployment of large-scale models, such as large language models (LLMs) and sophisticated image generation systems, incurs substantial costs due to their computational demands. To mitigate these costs and address challenges related to scalability and data security, there is a growing shift towards decentralized systems for deploying such models. In these decentralized environments, efficient inference acceleration becomes crucial to manage computational resources effectively and enhance system responsiveness. In this work, we address the challenge of selecting optimal acceleration methods in decentralized systems by introducing a meta-learning-based framework. This framework automates the selection process by learning from historical performance data of various acceleration techniques across different tasks. Unlike traditional methods that rely on random selection or expert intuition, our approach systematically identifies the best acceleration strategies based on the specific characteristics of each task. We demonstrate that our meta-learning framework not only streamlines the decision-making process but also consistently outperforms conventional methods in terms of efficiency and performance. Our results highlight the potential of meta-learning to revolutionize inference acceleration in decentralized AI systems, offering a path towards more democratic and economically feasible artificial intelligence solutions.

cs.LG↗

arXiv2024

MultiOOD: Scaling Out-of-Distribution Detection for Multiple Modalities

Detecting out-of-distribution (OOD) samples is important for deploying machine learning models in safety-critical applications such as autonomous driving and robot-assisted surgery. Existing research has mainly focused on unimodal scenarios on image data. However, real-world applications are inherently multimodal, which makes it essential to leverage information from multiple modalities to enhance the efficacy of OOD detection. To establish a foundation for more realistic Multimodal OOD Detection, we introduce the first-of-its-kind benchmark, MultiOOD, characterized by diverse dataset sizes and varying modality combinations. We first evaluate existing unimodal OOD detection algorithms on MultiOOD, observing that the mere inclusion of additional modalities yields substantial improvements. This underscores the importance of utilizing multiple modalities for OOD detection. Based on the observation of Modality Prediction Discrepancy between in-distribution (ID) and OOD data, and its strong correlation with OOD performance, we propose the Agree-to-Disagree (A2D) algorithm to encourage such discrepancy during training. Moreover, we introduce a novel outlier synthesis method, NP-Mix, which explores broader feature spaces by leveraging the information from nearest neighbor classes and complements A2D to strengthen OOD detection performance. Extensive experiments on MultiOOD demonstrate that training with A2D and NP-Mix improves existing OOD detection algorithms by a large margin. Our source code and MultiOOD benchmark are available at https://github.com/donghao51/MultiOOD.

cs.CV↗

arXiv2024

Dark Photon Dark Matter and Low-Frequency Gravitational Wave Detection with Gaia-like Astrometry

Astrometric surveys offer us a method to search for elusive cosmic signatures, such as ultralight dark photon dark matter and gravitational waves, by observing the deflection to the apparent positions of the stars. The detection capabilities of such surveys rapidly decrease at low frequencies, because the signals become hardly distinguishable from the background motion of stars. In this work, we find that the background motion can be well described by a linear model over time, based on which we propose a linear background subtraction scheme. Compared to the conventional quadratic subtraction, the advantage of linear subtraction emerges within the frequency range below $6 \times 10^{-9}~{\rm Hz}$. Taking dark photons with purely gravitational interactions, dark photons with additional $U(1)_{B}$ or $U(1)_{B-L}$ gauge interactions, and low-frequency gravitational waves as examples, we illustrate that the linear subtraction scheme can result in an enhancement of more than one order of magnitude in the exclusion limits of Gaia-like experiments in the low-frequency range.

hep-ph↗

arXiv2024

BA-Net: Bridge Attention in Deep Neural Networks

Attention mechanisms, particularly channel attention, have become highly influential in numerous computer vision tasks. Despite their effectiveness, many existing methods primarily focus on optimizing performance through complex attention modules applied at individual convolutional layers, often overlooking the synergistic interactions that can occur across multiple layers. In response to this gap, we introduce bridge attention, a novel approach designed to facilitate more effective integration and information flow between different convolutional layers. Our work extends the original bridge attention model (BAv1) by introducing an adaptive selection operator, which reduces information redundancy and optimizes the overall information exchange. This enhancement results in the development of BAv2, which achieves substantial performance improvements in the ImageNet classification task, obtaining Top-1 accuracies of 80.49% and 81.75% when using ResNet50 and ResNet101 as backbone networks, respectively. These results surpass the retrained baselines by 1.61% and 0.77%, respectively. Furthermore, BAv2 outperforms other existing channel attention techniques, such as the classical SENet101, exceeding its retrained performance by 0.52% Additionally, integrating BAv2 into advanced convolutional networks and vision transformers has led to significant gains in performance across a wide range of computer vision tasks, underscoring its broad applicability.

cs.CV↗

arXiv2024

An Adaptive Reconstruction Method for Arbitrary High-Order Accuracy Using Discontinuity Feedback

This paper introduces an effcient class of adaptive stencil extension reconstruction methods based on a discontinuity feedback factor, addressing the challenges of weak robustness and high computational cost in high-order schemes, particularly those of 7th-order or above. Two key innovations are presented: The accuracy order adaptively increases from the lowest level based on local stencil smoothness, contrasting with conventional methods like Weighted Essentially Non-Oscillatory (WENO) and Monotonic Upstream-Centered Scheme for Conservation Laws (MUSCL)limiters, which typically reduce order from the highest level. The Discontinuity Feedback Factor (DF) serves a dual purpose: detecting sub-cell discontinuity strength and explicitly incorporating into the reconstruction process as a local smoothness measure. This approach eliminates the need for computationally expensive smoothness indicators often required in very high-order schemes, such as 9th-order schemes, and can be easily generalized to arbitrary high-order schemes. Rigorous test cases, including a Mach 20000 jet, demonstrate the exceptional robustness of this approach.

math.NA↗

arXiv2024

TrustLLM: Trustworthiness in Large Language Models

Large language models (LLMs), exemplified by ChatGPT, have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. Therefore, ensuring the trustworthiness of LLMs emerges as an important topic. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and utility (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Finally, we emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. Knowing the specific trustworthy technologies that have been employed is crucial for analyzing their effectiveness.

cs.CL↗

arXiv2024

Hidden in Plain Sight: Exploring Chat History Tampering in Interactive Language Models

Large Language Models (LLMs) such as ChatGPT and Llama have become prevalent in real-world applications, exhibiting impressive text generation performance. LLMs are fundamentally developed from a scenario where the input data remains static and unstructured. To behave interactively, LLM-based chat systems must integrate prior chat history as context into their inputs, following a pre-defined structure. However, LLMs cannot separate user inputs from context, enabling chat history tampering. This paper introduces a systematic methodology to inject user-supplied history into LLM conversations without any prior knowledge of the target model. The key is to utilize prompt templates that can well organize the messages to be injected, leading the target LLM to interpret them as genuine chat history. To automatically search for effective templates in a WebUI black-box setting, we propose the LLM-Guided Genetic Algorithm (LLMGA) that leverages an LLM to generate and iteratively optimize the templates. We apply the proposed method to popular real-world LLMs including ChatGPT and Llama-2/3. The results show that chat history tampering can enhance the malleability of the model's behavior over time and greatly influence the model output. For example, it can improve the success rate of disallowed response elicitation up to 97% on ChatGPT. Our findings provide insights into the challenges associated with the real-world deployment of interactive LLMs.

cs.AI↗

arXiv2024

Blowing in the Dark Matter Wind

Interactions between dark matter and ordinary matter will transfer momentum, and therefore give rise to a force on ordinary matter due to the dark matter `wind.' We show that this force can be maximal in a realistic model of dark matter, meaning that an order-1 fraction of the dark matter momentum incident on a target of ordinary matter is reflected. The model consists of light ($m_ϕ\lsim \text{eV}$) scalar dark matter with an effective interaction $ϕ^2 \barψψ$, where $ψ$ is an electron or nucleon field. If the coupling is repulsive and sufficiently strong, the field $ϕ$ is excluded from ordinary matter, analogous to the Meissner effect for photons in a superconductor. We show that there is a large region of parameter space that is compatible with existing constraints, where the force is large enough to be detected by existing force probes, such as satellite tests of the equivalence principle and torsion balance experiments. However, shielding of the dark matter by ordinary matter prevents existing experiments from being sensitive to the dark matter force. We show that precise measurements of spacecraft trajectories proposed to test long distance modifications of gravity are sensitive to this force for a wide range of parameters.

hep-ph↗

arXiv2024

Fast Unsupervised Deep Outlier Model Selection with Hypernetworks

Outlier detection (OD) finds many applications with a rich literature of numerous techniques. Deep neural network based OD (DOD) has seen a recent surge of attention thanks to the many advances in deep learning. In this paper, we consider a critical-yet-understudied challenge with unsupervised DOD, that is, effective hyperparameter (HP) tuning/model selection. While several prior work report the sensitivity of OD models to HPs, it becomes ever so critical for the modern DOD models that exhibit a long list of HPs. We introduce HYPER for tuning DOD models, tackling two fundamental challenges: (1) validation without supervision (due to lack of labeled anomalies), and (2) efficient search of the HP/model space (due to exponential growth in the number of HPs). A key idea is to design and train a novel hypernetwork (HN) that maps HPs onto optimal weights of the main DOD model. In turn, HYPER capitalizes on a single HN that can dynamically generate weights for many DOD models (corresponding to varying HPs), which offers significant speed-up. In addition, it employs meta-learning on historical OD tasks with labels to train a proxy validation function, likewise trained with our proposed HN efficiently. Extensive experiments on 35 OD tasks show that HYPER achieves high performance against 8 baselines with significant efficiency gains.

cs.LG↗

arXiv2024

Conditional nonparametric variable screening by neural factor regression

High-dimensional covariates often admit linear factor structure. To effectively screen correlated covariates in high-dimension, we propose a conditional variable screening test based on non-parametric regression using neural networks due to their representation power. We ask the question whether individual covariates have additional contributions given the latent factors or more generally a set of variables. Our test statistics are based on the estimated partial derivative of the regression function of the candidate variable for screening and a observable proxy for the latent factors. Hence, our test reveals how much predictors contribute additionally to the non-parametric regression after accounting for the latent factors. Our derivative estimator is the convolution of a deep neural network regression estimator and a smoothing kernel. We demonstrate that when the neural network size diverges with the sample size, unlike estimating the regression function itself, it is necessary to smooth the partial derivative of the neural network estimator to recover the desired convergence rate for the derivative. Moreover, our screening test achieves asymptotic normality under the null after finely centering our test statistics that makes the biases negligible, as well as consistency for local alternatives under mild conditions. We demonstrate the performance of our test in a simulation study and two real world applications.

econ.EM↗

arXiv2024

Exploring the Hidden Valley at MATHUSLA

Hidden valley models naturally predict numerous long-lived particles, the distinctive signatures of which would be compelling evidence for a hidden valley scenario. As these are typically low energy particles, they pose a challenge in terms of passing energy triggers in traditional searches at the Large Hadron Collider. The MATHUSLA experiment is specifically designed for the purpose of detecting long-lived particles. It also has the capability of detecting lower energy particles relative to ATLAS and CMS. In this paper, we assess MATHUSLA's potential for effectively probing hidden valley models. As a benchmark, we assume the hidden valley sector communicates with Standard Model sectors via a heavy vector propagator that couples to Standard Model quarks as well as hidden valley quarks. We model the showering and hadronization in the hidden valley sector using PYTHIA, and study the detector acceptance as a function of the hidden valley meson's lifetime. We find that MATHUSLA possesses significant capabilities to explore previously uncharted parameter space within hidden valley models.

hep-ph↗

arXiv2024

Long-baseline quantum sensor network as dark matter haloscope

Ultralight dark photons constitute a well-motivated candidate for dark matter. A coherent electromagnetic wave is expected to be induced by dark photons when coupled with Standard-Model photons through kinetic mixing mechanism, and should be spatially correlated within the de Broglie wavelength of dark photons. Here we report the first search for correlated dark-photon signals using a long-baseline network of 15 atomic magnetometers, which are situated in two separated meter-scale shield rooms with a distance of about 1700 km. Both the network's multiple sensors and the shields large size significantly enhance the expected dark-photon electromagnetic signals, and long-baseline measurements confidently reduce many local noise sources. Using this network, we constrain the kinetic mixing coefficient of dark photon dark matter over the mass range 4.1 feV-2.1 peV, which represents the most stringent constraints derived from any terrestrial experiments operating over the aforementioned mass range. Our prospect indicates that future data releases may go beyond the astrophysical constraints from the cosmic microwave background and the plasma heating.

quant-ph↗

arXiv2024

Evidence chain for time-reversal symmetry-breaking kagome superconductivity

Superconductivity and magnetism are antagonistic quantum matter, while their intertwining has long been considered in frustrated-lattice systems1-3. In this work, we utilize scanning tunneling microscopy and muon spin resonance to discover time-reversal symmetry-breaking superconductivity in kagome metal Cs(V,Ta)3Sb5, where the Cooper pairing exhibits magnetism and is modulated by it. In the magnetic channel, we observe spontaneous internal magnetism in a full-gap superconducting state. Under perturbations of inverse magnetic fields, we detect a time-reversal asymmetrical interference of Bogoliubov quasi-particles at a circular vector. At this vector, the pairing gap spontaneously modulates, which is distinct from pair density waves occurring at a point vector and consistent with the theoretical proposal of unusual interference effect under time-reversal symmetry-breaking. The correlation between internal magnetism, Bogoliubov quasi-particles, and pairing modulation provides a chain of experimental clues for time-reversal symmetry-breaking kagome superconductivity.

cond-mat.supr-con↗

arXiv2024

Local excitation of kagome spin ice magnetism in HoAgGe seen by scanning tunneling microscopy

The kagome spin ice can host frustrated magnetic excitations by flipping its local spin. Under an inelastic tunneling condition, the tip in a scanning tunneling microscope can flip the local spin, and we apply this technique to kagome metal HoAgGe with a long-range ordered spin ice ground state. Away from defects, we discover a pair of pronounced dips in the local tunneling spectrum at symmetrical bias voltages with negative intensity values, serving as a striking inelastic tunneling signal. This signal disappears above the spin ice formation temperature and has a dependence on the magnetic fields, demonstrating its intimate relation with the spin ice magnetism. We provide a two-level spin-flip model to explain the tunneling dips considering the spin ice magnetism under spin-orbit coupling. Our results uncover a local emergent excitation of spin ice magnetism in a kagome metal, suggesting that local electrical field induced spin flip climbs over a barrier caused by spin-orbital locking.

cond-mat.str-el↗

arXiv2024

Crystal-symmetry-paired spin-valley locking in a layered room-temperature antiferromagnet

Recent theoretical efforts predicted a type of unconventional antiferromagnet characterized by the crystal symmetry C (rotation or mirror), which connects antiferromagnetic sublattices in real space and simultaneously couples spin and momentum in reciprocal space. This results in a unique C-paired spin-valley locking (SVL) and corresponding novel properties such as piezomagnetism and noncollinear spin current even without spin-orbit coupling. However, the unconventional antiferromagnets reported thus far are not layered materials, limiting their potential in spintronic applications. Additionally, they do not meet the necessary symmetry requirements for nonrelativistic spin current. Here, we report the realization of C-paired SVL in a layered room-temperature antiferromagnetic compound, Rb1-δV2Te2O. Spin resolved photoemission measurements directly demonstrate the opposite spin splitting between C-paired valleys. Quasi-particle interference patterns reveal the suppression of inter-valley scattering due to the spin selection rules, as a direct consequence of C-paired SVL. All these experiments are well consistent with the results obtained from first-principles calculations. Our observations represent the first realization of layered antiferromagnets with C-paired SVL, enabling both the advantages of layered materials and possible control through crystal symmetry manipulation. These results hold significant promise and broad implications for advancements in magnetism, electronics, and information technology.

cond-mat.str-el↗