arXiv subjects

Yue Yu

Publications and source records attributed to Yue Yu.

At least 325 records · Page 18Linked to original sources

arXiv2022

EDoG: Adversarial Edge Detection For Graph Neural Networks

Graph Neural Networks (GNNs) have been widely applied to different tasks such as bioinformatics, drug design, and social networks. However, recent studies have shown that GNNs are vulnerable to adversarial attacks which aim to mislead the node or subgraph classification prediction by adding subtle perturbations. Detecting these attacks is challenging due to the small magnitude of perturbation and the discrete nature of graph data. In this paper, we propose a general adversarial edge detection pipeline EDoG without requiring knowledge of the attack strategies based on graph generation. Specifically, we propose a novel graph generation approach combined with link prediction to detect suspicious adversarial edges. To effectively train the graph generative model, we sample several sub-graphs from the given graph data. We show that since the number of adversarial edges is usually low in practice, with low probability the sampled sub-graphs will contain adversarial edges based on the union bound. In addition, considering the strong attacks which perturb a large number of edges, we propose a set of novel features to perform outlier detection as the preprocessing for our detection. Extensive experimental results on three real-world graph datasets including a private transaction rule dataset from a major company and two types of synthetic graphs with controlled properties show that EDoG can achieve above 0.8 AUC against four state-of-the-art unseen attack strategies without requiring any knowledge about the attack type; and around 0.85 with knowledge of the attack type. EDoG significantly outperforms traditional malicious edge detection baselines. We also show that an adaptive attack with full knowledge of our detection pipeline is difficult to bypass it.

cs.LG↗

arXiv2022

Multi-task Joint Strategies of Self-supervised Representation Learning on Biomedical Networks for Drug Discovery

Self-supervised representation learning (SSL) on biomedical networks provides new opportunities for drug discovery. However, how to effectively combine multiple SSL models is still challenging and has been rarely explored. Therefore, we propose multi-task joint strategies of self-supervised representation learning on biomedical networks for drug discovery, named MSSL2drug. We design six basic SSL tasks inspired by various modality features including structures, semantics, and attributes in heterogeneous biomedical networks. Importantly, fifteen combinations of multiple tasks are evaluated by a graph attention-based multi-task adversarial learning framework in two drug discovery scenarios. The results suggest two important findings. (1) Combinations of multimodal tasks achieve the best performance compared to other multi-task joint models. (2) The local-global combination models yield higher performance than random two-task combinations when there are the same size of modalities. Therefore, we conjecture that the multimodal and local-global combination strategies can be treated as the guideline of multi-task SSL for drug discovery.

cs.LG↗

arXiv2022

Unified Implementation of Finite Element Methods involving Jumps and Averages in Matlab

We provide unified implementations of the finite element methods involving jumps and averages in Maltab by combing the use of the software package varFEM, including the adaptive finite element methods for the Poisson equation and the $C^0$ interior penalty methods for the biharmonic equation. The design ideas can be extended to other Galerkin-based methods, for example, the discontinuous Galerkin methods and the virtual element methods.

math.NA↗

arXiv2022

Polynomial Distributions and Transformations

Polynomials are common algebraic structures, which are often used to approximate functions including probability distributions. This paper proposes to directly define polynomial distributions in order to describe stochastic properties of systems rather than to assume polynomials for only approximating known or empirically estimated distributions. Polynomial distributions offer a great modeling flexibility, and often, also mathematical tractability. However, unlike canonical distributions, polynomial functions may have non-negative values in the interval of support for some parameter values, the number of their parameters is usually much larger than for canonical distributions, and the interval of support must be finite. In particular, polynomial distributions are defined here assuming three forms of polynomial function. The transformation of polynomial distributions and fitting a histogram to a polynomial distribution are considered. The key properties of polynomial distributions are derived in closed-form. A piecewise polynomial distribution construction is devised to ensure that it is non-negative over the support interval. Finally, the problems of estimating parameters of polynomial distributions and generating polynomially distributed samples are also studied.

cs.IT↗

arXiv2022

OBMeshfree: An optimization-based meshfree solver for nonlocal diffusion and peridynamics models

We present OBMeshfree, an Optimization-Based Meshfree solver for compactly supported nonlocal integro-differential equations (IDEs) that can describe material heterogeneity and brittle fractures. OBMeshfree is developed based on a quadrature rule calculated via an equality constrained least square problem to reproduce exact integrals for polynomials. As such, a meshfree discretization method is obtained, whose solution possesses the asymptotically compatible convergence to the corresponding local solution. Moreover, when fracture occurs, this meshfree formulation automatically provides a sharp representation of the fracture surface by breaking bonds, avoiding the loss of mass. As numerical examples, we consider the problem of modeling both homogeneous and heterogeneous materials with nonlocal diffusion and peridynamics models. Convergences to the analytical nonlocal solution and to the local theory are demonstrated. Finally, we verify the applicability of the approach to realistic problems by reproducing high-velocity impact results from the Kalthoff-Winkler experiments. Discussions on possible immediate extensions of the code to other nonlocal diffusion and peridynamics problems are provided. OBMeshfree is freely available on GitHub.

math.NA↗

arXiv2022

COCO-DR: Combating Distribution Shifts in Zero-Shot Dense Retrieval with Contrastive and Distributionally Robust Learning

We present a new zero-shot dense retrieval (ZeroDR) method, COCO-DR, to improve the generalization ability of dense retrieval by combating the distribution shifts between source training tasks and target scenarios. To mitigate the impact of document differences, COCO-DR continues pretraining the language model on the target corpora to adapt the model to target distributions via COtinuous COtrastive learning. To prepare for unseen target queries, COCO-DR leverages implicit Distributionally Robust Optimization (iDRO) to reweight samples from different source query clusters for improving model robustness over rare queries during fine-tuning. COCO-DR achieves superior average performance on BEIR, the zero-shot retrieval benchmark. At BERT Base scale, COCO-DR Base outperforms other ZeroDR models with 60x larger size. At BERT Large scale, COCO-DR Large outperforms the giant GPT-3 embedding model which has 500x more parameters. Our analysis show the correlation between COCO-DR's effectiveness in combating distribution shifts and improving zero-shot accuracy. Our code and model can be found at \url{https://github.com/OpenMatch/COCO-DR}.

cs.CL↗

arXiv2022

Online Poisoning Attacks Against Data-Driven Predictive Control

Data-driven predictive control (DPC) is a feedback control method for systems with unknown dynamics. It repeatedly optimizes a system's future trajectories based on past input-output data. We develop a numerical method that computes poisoning attacks that inject additive perturbations to the online output data to change the trajectories optimized by DPC. This method is based on implicitly differentiating the solution map of the trajectory optimization in DPC. We demonstrate that the resulting attacks can cause an output tracking error one order of magnitude higher than random perturbations in numerical experiments.

eess.SY↗

arXiv2022

Excitement Surfeited Turns to Errors: Deep Learning Testing Framework Based on Excitable Neurons

Despite impressive capabilities and outstanding performance, deep neural networks (DNNs) have captured increasing public concern about their security problems, due to their frequently occurred erroneous behaviors. Therefore, it is necessary to conduct a systematical testing for DNNs before they are deployed to real-world applications. Existing testing methods have provided fine-grained metrics based on neuron coverage and proposed various approaches to improve such metrics. However, it has been gradually realized that a higher neuron coverage does \textit{not} necessarily represent better capabilities in identifying defects that lead to errors. Besides, coverage-guided methods cannot hunt errors due to faulty training procedure. So the robustness improvement of DNNs via retraining by these testing examples are unsatisfactory. To address this challenge, we introduce the concept of excitable neurons based on Shapley value and design a novel white-box testing framework for DNNs, namely DeepSensor. It is motivated by our observation that neurons with larger responsibility towards model loss changes due to small perturbations are more likely related to incorrect corner cases due to potential defects. By maximizing the number of excitable neurons concerning various wrong behaviors of models, DeepSensor can generate testing examples that effectively trigger more errors due to adversarial inputs, polluted data and incomplete training. Extensive experiments implemented on both image classification models and speaker recognition models have demonstrated the superiority of DeepSensor.

cs.LG↗

arXiv2022

Simulating Hamiltonian dynamics in a programmable photonic quantum processor using linear combinations of unitary operations

Simulating the dynamic evolutions of physical and molecular systems in a quantum computer is of fundamental interest in many applications. Its implementation requires efficient quantum simulation algorithms. The Lie-Trotter-Suzuki approximation algorithm, also well known as the Trotterization, is a basic algorithm in quantum dynamic simulation. A multi-product algorithm that is a linear combination of multiple Trotterizations has been proposed to improve the approximation accuracy. Implementing such multi-product Trotterization in quantum computers however remains experimentally challenging and its success probability is limited. Here, we modify the multi-product Trotterization and combine it with the oblivious amplitude amplification to simultaneously reach a high simulation precision and high success probability. We experimentally implement the modified multi-product algorithm in an integrated-photonics programmable quantum simulator in silicon, which allows the initialization, manipulation and measurement of four-qubit states and a sequence of linearly combined controlled-unitary gates, to emulate the dynamics of a coupled electron and nuclear spins system. Theoretical and experimental results are in good agreement, and they both show the modified multi-product algorithm can simulate Hamiltonian dynamics with a higher precision than conventional Trotterizations and a nearly deterministic success probability. We certificate the multi-product algorithm in a small-scale quantum simulator based on linear combinations of operations, and this work promises the practical implementations of quantum dynamics simulations.

quant-ph↗

arXiv2022

Learning Task-Aware Effective Brain Connectivity for fMRI Analysis with Graph Neural Networks

Functional magnetic resonance imaging (fMRI) has become one of the most common imaging modalities for brain function analysis. Recently, graph neural networks (GNN) have been adopted for fMRI analysis with superior performance. Unfortunately, traditional functional brain networks are mainly constructed based on similarities among region of interests (ROI), which are noisy and agnostic to the downstream prediction tasks and can lead to inferior results for GNN-based models. To better adapt GNNs for fMRI analysis, we propose TBDS, an end-to-end framework based on \underline{T}ask-aware \underline{B}rain connectivity \underline{D}AG (short for Directed Acyclic Graph) \underline{S}tructure generation for fMRI analysis. The key component of TBDS is the brain network generator which adopts a DAG learning approach to transform the raw time-series into task-aware brain connectivities. Besides, we design an additional contrastive regularization to inject task-specific knowledge during the brain network generation process. Comprehensive experiments on two fMRI datasets, namely Adolescent Brain Cognitive Development (ABCD) and Philadelphia Neuroimaging Cohort (PNC) datasets demonstrate the efficacy of TBDS. In addition, the generated brain networks also highlight the prediction-related brain regions and thus provide unique interpretations of the prediction results. Our implementation will be published to https://github.com/yueyu1030/TBDS upon acceptance.

q-bio.NC↗

arXiv2022

Reduce Catastrophic Forgetting of Dense Retrieval Training with Teleportation Negatives

In this paper, we investigate the instability in the standard dense retrieval training, which iterates between model training and hard negative selection using the being-trained model. We show the catastrophic forgetting phenomena behind the training instability, where models learn and forget different negative groups during training iterations. We then propose ANCE-Tele, which accumulates momentum negatives from past iterations and approximates future iterations using lookahead negatives, as "teleportations" along the time axis to smooth the learning process. On web search and OpenQA, ANCE-Tele outperforms previous state-of-the-art systems of similar size, eliminates the dependency on sparse retrieval negatives, and is competitive among systems using significantly more (50x) parameters. Our analysis demonstrates that teleportation negatives reduce catastrophic forgetting and improve convergence speed for dense retrieval training. Our code is available at https://github.com/OpenMatch/ANCE-Tele.

cs.CL↗

arXiv2022

ReSel: N-ary Relation Extraction from Scientific Text and Tables by Learning to Retrieve and Select

We study the problem of extracting N-ary relation tuples from scientific articles. This task is challenging because the target knowledge tuples can reside in multiple parts and modalities of the document. Our proposed method ReSel decomposes this task into a two-stage procedure that first retrieves the most relevant paragraph/table and then selects the target entity from the retrieved component. For the high-level retrieval stage, ReSel designs a simple and effective feature set, which captures multi-level lexical and semantic similarities between the query and components. For the low-level selection stage, ReSel designs a cross-modal entity correlation graph along with a multi-view architecture, which models both semantic and document-structural relations between entities. Our experiments on three scientific information extraction datasets show that ReSel outperforms state-of-the-art baselines significantly.

cs.CL↗

arXiv2022

Inverse Matrix Games with Unique Quantal Response Equilibrium

In an inverse game problem, one needs to infer the cost function of the players in a game such that a desired joint strategy is a Nash equilibrium. We study the inverse game problem for a class of multiplayer matrix games, where the cost perceived by each player is corrupted by random noise. We provide sufficient conditions for the players' quantal response equilibrium -- a generalization of the Nash equilibrium to games with perception noise -- to be unique. We develop efficient optimization algorithms for inferring the cost matrix based on semidefinite programs and bilevel optimization. We demonstrate the application of these methods in encouraging collision avoidance and fair resource allocation.

cs.GT↗

arXiv2022

Bayesian Nonlocal Operator Regression (BNOR): A Data-Driven Learning Framework of Nonlocal Models with Uncertainty Quantification

We consider the problem of modeling heterogeneous materials where micro-scale dynamics and interactions affect global behavior. In the presence of heterogeneities in material microstructure it is often impractical, if not impossible, to provide quantitative characterization of material response. The goal of this work is to develop a Bayesian framework for uncertainty quantification (UQ) in material response prediction when using nonlocal models. Our approach combines the nonlocal operator regression (NOR) technique and Bayesian inference. Specifically, we use a Markov chain Monte Carlo (MCMC) method to sample the posterior probability distribution on parameters involved in the nonlocal constitutive law, and associated modeling discrepancies relative to higher fidelity computations. As an application, we consider the propagation of stress waves through a one-dimensional heterogeneous bar with randomly generated microstructure. Several numerical tests illustrate the construction, enabling UQ in nonlocal model predictions. Although nonlocal models have become popular means for homogenization, their statistical calibration with respect to high-fidelity models has not been presented before. This work is a first step towards statistical characterization of nonlocal model discrepancy in the context of homogenization.

cond-mat.mtrl-sci↗

arXiv2022

Time complexity analysis of quantum difference methods for linear high dimensional and multiscale partial differential equations

We investigate time complexities of finite difference methods for solving the high-dimensional linear heat equation, the high-dimensional linear hyperbolic equation and the multiscale hyperbolic heat system with quantum algorithms (hence referred to as the "quantum difference methods"). For the heat and linear hyperbolic equations we study the impact of explicit and implicit time discretizations on quantum advantages over the classical difference method. For the multiscale problem, we find the time complexity of both the classical treatment and quantum treatment for the explicit scheme scales as $\mathcal{O}(1/\varepsilon)$, where $\varepsilon$ is the scaling parameter, while the scaling for the multiscale Asymptotic-Preserving (AP) schemes does not depend on $\varepsilon$. This indicates that it is still of great importance to develop AP schemes for multiscale problems in quantum computing.

math.NA↗

arXiv2022

Surface acoustic microwave photonic filters on etchless lithium niobate integrated platform

Lithium niobate on insulator emerges as a promising platform for integrated microwave photonics because of its capability of ultralow-loss guidance and high-efficiency modulation of light. Chip-level integration of microwave filters is important for signal processing in the 5G/6G wireless communication. Here, we employed the principle of bound states in the continuum for low-loss waveguiding on an etchless lithium niobate integrated platform, and realized high-performance microwave photonic filters thereon. These microwave photonic filters consist of a high-quality photonic microcavity modulated by piezoelectrically excited surface acoustic waves. Acoustic time delays from 21 to 106 ns and passbands with bandwidth as narrow as 0.89 MHz were achieved in the fabricated filters operating at gigahertz frequencies. Our demonstration may open up new applications on the lithium niobate integrated platform, such as optical communication, signal processing, and beam steering.

physics.optics↗

arXiv2022

OpenMedIA: Open-Source Medical Image Analysis Toolbox and Benchmark under Heterogeneous AI Computing Platforms

In this paper, we present OpenMedIA, an open-source toolbox library containing a rich set of deep learning methods for medical image analysis under heterogeneous Artificial Intelligence (AI) computing platforms. Various medical image analysis methods, including 2D/3D medical image classification, segmentation, localisation, and detection, have been included in the toolbox with PyTorch and/or MindSpore implementations under heterogeneous NVIDIA and Huawei Ascend computing systems. To our best knowledge, OpenMedIA is the first open-source algorithm library providing compared PyTorch and MindSpore implementations and results on several benchmark datasets. The source codes and models are available at https://git.openi.org.cn/OpenMedIA.

eess.IV↗

arXiv2022

Hybrid mixed discontinuous Galerkin finite element method for incompressible miscible displacement problem

A new hybrid mixed discontinuous Galerkin finite element (HMDGFE) method is constructed for incompressible miscible displacement problem. In this method, the hybrid mixed finite element (HMFE) procedure is considered to solve pressure and velocity equations, and a new hybrid mixed discontinuous Galerkin procedure is constructed to solve the concentration equation with upwind technique. Compared with other traditional discontinuous Galerkin methods, the new method can reach global systems with less unknowns and sparser stencils. The consistency and conservation of the method are analyzed, the stability and optimal error estimates are also derived by the new technique.

math.NA↗