arXiv subjects

Min Xu

Publications and source records attributed to Min Xu.

At least 199 records · Page 11Linked to original sources

arXiv2021

Cryo-shift: Reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization

Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared to real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms. In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with `warp' modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data.

q-bio.QM↗

arXiv2021

Towards Robust Partially Supervised Multi-Structure Medical Image Segmentation on Small-Scale Data

The data-driven nature of deep learning (DL) models for semantic segmentation requires a large number of pixel-level annotations. However, large-scale and fully labeled medical datasets are often unavailable for practical tasks. Recently, partially supervised methods have been proposed to utilize images with incomplete labels in the medical domain. To bridge the methodological gaps in partially supervised learning (PSL) under data scarcity, we propose Vicinal Labels Under Uncertainty (VLUU), a simple yet efficient framework utilizing the human structure similarity for partially supervised medical image segmentation. Motivated by multi-task learning and vicinal risk minimization, VLUU transforms the partially supervised problem into a fully supervised problem by generating vicinal labels. We systematically evaluate VLUU under the challenges of small-scale data, dataset shift, and class imbalance on two commonly used segmentation datasets for the tasks of chest organ segmentation and optic disc-and-cup segmentation. The experimental results show that VLUU can consistently outperform previous partially supervised models in these settings. Our research suggests a new research direction in label-efficient deep learning with partial supervision.

cs.CV↗

arXiv2021

Single-Target Real-Time Passive WiFi Tracking

Device-free human tracking is an essential ingredient for ubiquitous wireless sensing. Recent passive WiFi tracking systems face the challenges of inaccurate separation of dynamic human components and time-consuming estimation of multi-dimensional signal parameters. In this work, we present a scheme named WiFi Doppler Frequency Shift (WiDFS), which can achieve single-target real-time passive tracking using channel state information (CSI) collected from commercial-off-the-shelf (COTS) WiFi devices. We consider the typical system setup including a transmitter with a single antenna and a receiver with three antennas; while our scheme can be readily extended to another setup. To remove the impact of transceiver asynchronization, we first apply CSI cross-correlation between each RX antenna pair. We then combine them to estimate a Doppler frequency shift (DFS) in a short-time window. After that, we leverage the DFS estimate to separate dynamic human components from CSI self-correlation terms of each antenna, thereby separately calculating angle-of-arrival (AoA) and human reflection distance for tracking. In addition, a hardware calibration algorithm is presented to refine the spacing between RX antennas and eliminate the hardware-related phase differences between them. A prototype demonstrates that WiDFS can achieve real-time tracking with a median position error of 72.32 cm in multipath-rich environments.

cs.NI↗

arXiv2021

Task-wise Split Gradient Boosting Trees for Multi-center Diabetes Prediction

Diabetes prediction is an important data science application in the social healthcare domain. There exist two main challenges in the diabetes prediction task: data heterogeneity since demographic and metabolic data are of different types, data insufficiency since the number of diabetes cases in a single medical center is usually limited. To tackle the above challenges, we employ gradient boosting decision trees (GBDT) to handle data heterogeneity and introduce multi-task learning (MTL) to solve data insufficiency. To this end, Task-wise Split Gradient Boosting Trees (TSGB) is proposed for the multi-center diabetes prediction task. Specifically, we firstly introduce task gain to evaluate each task separately during tree construction, with a theoretical analysis of GBDT's learning objective. Secondly, we reveal a problem when directly applying GBDT in MTL, i.e., the negative task gain problem. Finally, we propose a novel split method for GBDT in MTL based on the task gain statistics, named task-wise split, as an alternative to standard feature-wise split to overcome the mentioned negative task gain problem. Extensive experiments on a large-scale real-world diabetes dataset and a commonly used benchmark dataset demonstrate TSGB achieves superior performance against several state-of-the-art methods. Detailed case studies further support our analysis of negative task gain problems and provide insightful findings. The proposed TSGB method has been deployed as an online diabetes risk assessment software for early diagnosis.

cs.LG↗

arXiv2021

Free Lunch for Few-shot Learning: Distribution Calibration

Learning from a limited number of samples is challenging since the learned model can easily become overfitted based on the biased distribution formed by only a few training examples. In this paper, we calibrate the distribution of these few-sample classes by transferring statistics from the classes with sufficient examples, then an adequate number of examples can be sampled from the calibrated distribution to expand the inputs to the classifier. We assume every dimension in the feature representation follows a Gaussian distribution so that the mean and the variance of the distribution can borrow from that of similar classes whose statistics are better estimated with an adequate number of samples. Our method can be built on top of off-the-shelf pretrained feature extractors and classification models without extra parameters. We show that a simple logistic regression classifier trained using the features sampled from our calibrated distribution can outperform the state-of-the-art accuracy on two datasets (~5% improvement on miniImageNet compared to the next best). The visualization of these generated features demonstrates that our calibrated distribution is an accurate estimation.

cs.LG↗

arXiv2021

A Hybrid Vehicle Platoon for Connected and Automated Vehicles: Formulation, Stability Analysis, and Applications

Vehicle platooning has the potential to significantly improve traffic throughput and reduce fuel consumption and emissions and thus has attracted extensive attention recently. In this study, we propose a hybrid vehicle platoon system for the connected and automated vehicles (CAVs). First, a hybrid spacing policy combining the constant time gap (CTG) and constant spacing (CS) is formulated for the proposed platoon system, where the leader adopts the CTG and the followers use the CS policy. Based on the h2-norm string stability criteria, the notions of exogenous-head-to-tail string stability and hybrid string stability are newly introduced, and the sufficient conditions of the hybrid string stability in the frequency domain are derived using the Laplace transform. Numerical experiments are conducted to validate the hybrid string stability. Moreover, two typical scenarios and several measurements of effectiveness (MOE) are adopted to verify the effectiveness of the proposed hybrid platoon system in various aspects. The results show that the hybrid platoon system performs better than the CS-based platoon system. It also indicates that the hybrid platoon system has obvious advantages over the CTG-based platoon system under the periodical fluctuation scenario and it is also comparable to the CTG-based platoon system under the large deceleration and acceleration scenario. The findings have demonstrated the merits of the combined implementation of CTG and CS policy in enhancing the performance and applicability of the platoon system for CAVs.

eess.SY↗

arXiv2021

Active Learning to Classify Macromolecular Structures in situ for Less Supervision in Cryo-Electron Tomography

Motivation: Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning based subtomogram classification have played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset. Results: To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labelling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources.

q-bio.QM↗

arXiv2021

Disentangling semantic features of macromolecules in Cryo-Electron Tomography

Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the systemic study of shape, abundance, and distribution of macromolecular structures in single cells in near-atomic resolution. However, the systematic and efficient $\textit{de novo}$ recognition and recovery of macromolecular structures captured by Cryo-ET are very challenging due to the structural complexity and imaging limits. Even macromolecules with identical structures have various appearances due to different orientations and imaging limits, such as noise and the missing wedge effect. Explicitly disentangling the semantic features of macromolecules is crucial for performing several downstream analyses on the macromolecules. This paper has addressed the problem by proposing a 3D Spatial Variational Autoencoder that explicitly disentangle the structure, orientation, and shift of macromolecules. Extensive experiments on both synthesized and real cryo-ET datasets and cross-domain evaluations demonstrate the efficacy of our method.

q-bio.BM↗

arXiv2021

SiamSNN: Siamese Spiking Neural Networks for Energy-Efficient Object Tracking

Recently spiking neural networks (SNNs), the third-generation of neural networks has shown remarkable capabilities of energy-efficient computing, which is a promising alternative for deep neural networks (DNNs) with high energy consumption. SNNs have reached competitive results compared to DNNs in relatively simple tasks and small datasets such as image classification and MNIST/CIFAR, while few studies on more challenging vision tasks on complex datasets. In this paper, we focus on extending deep SNNs to object tracking, a more advanced vision task with embedded applications and energy-saving requirements, and present a spike-based Siamese network called SiamSNN. Specifically, we propose an optimized hybrid similarity estimation method to exploit temporal information in the SNNs, and introduce a novel two-status coding scheme to optimize the temporal distribution of output spike trains for further improvements. SiamSNN is the first deep SNN tracker that achieves short latency and low precision loss on the visual object tracking benchmarks OTB2013/2015, VOT2016/2018, and GOT-10k. Moreover, SiamSNN achieves notably low energy consumption and real-time on Neuromorphic chip TrueNorth.

cs.CV↗

arXiv2021

SSFG: Stochastically Scaling Features and Gradients for Regularizing Graph Convolutional Networks

Graph convolutional networks have been successfully applied in various graph-based tasks. In a typical graph convolutional layer, node features are updated by aggregating neighborhood information. Repeatedly applying graph convolutions can cause the oversmoothing issue, i.e., node features at deep layers converge to similar values. Previous studies have suggested that oversmoothing is one of the major issues that restrict the performance of graph convolutional networks. In this paper, we propose a stochastic regularization method to tackle the oversmoothing problem. In the proposed method, we stochastically scale features and gradients (SSFG) by a factor sampled from a probability distribution in the training procedure. By explicitly applying a scaling factor to break feature convergence, the oversmoothing issue is alleviated. We show that applying stochastic scaling at the gradient level is complementary to that applied at the feature level to improve the overall performance. Our method does not increase the number of trainable parameters. When used together with ReLU, our SSFG can be seen as a stochastic ReLU activation function. We experimentally validate our SSFG regularization method on three commonly used types of graph networks. Extensive experimental results on seven benchmark datasets for four graph-based tasks demonstrate that our SSFG regularization is effective in improving the overall performance of the baseline graph networks.

cs.LG↗

arXiv2021

Research on Hopf Bifurcation and Stability of Heterogeneous Lorenz System with Single Time Delay

Time-delay chaotic systems refer to the hyperchaotic systems with multiple positive Lyapunov exponents. It is characterized by more complex dynamics and a wider range of applications as compared to those non-time-delay chaotic systems. In a three-dimensional general Lorenz chaotic system, time delays can be applied at different positions to build multiple heterogeneous Lorenz systems with a single time delay. Despite the same equilibrium point for multiple heterogeneous Lorenz systems with single time delay, their stability and Hopf bifurcation conditions are different due to the difference in time delay position. In this paper, the theory of nonlinear dynamics is applied to investigate the stability of the heterogeneous single-time-delay Lorenz system at the zero equilibrium point and the conditions required for the occurrence of Hopf bifurcation. First of all, the equilibrium point of each heterogeneous Lorenz system is calculated, so as to determine the condition that only zero equilibrium point exists. Then, an analysis is conducted on the distribution of the corresponding characteristic equation roots at the zero equilibrium point of the system to obtain the critical point of time delay at which the system is asymptotically stable at the zero equilibrium point and the Hopf bifurcation. Finally, mathematical software is applied to carry out simulation verification. Heterogeneous Lorenz systems with time delay have potential applications in secure communication and other fields.

math.DS↗

arXiv2021

Self-supervised Pretraining of Visual Features in the Wild

Recently, self-supervised learning methods like MoCo, SimCLR, BYOL and SwAV have reduced the gap with supervised methods. These results have been achieved in a control environment, that is the highly curated ImageNet dataset. However, the premise of self-supervised learning is that it can learn from any random image and from any unbounded dataset. In this work, we explore if self-supervision lives to its expectation by training large models on random, uncurated images with no supervision. Our final SElf-supERvised (SEER) model, a RegNetY with 1.3B parameters trained on 1B random images with 512 GPUs achieves 84.2% top-1 accuracy, surpassing the best self-supervised pretrained model by 1% and confirming that self-supervised learning works in a real world setting. Interestingly, we also observe that self-supervised models are good few-shot learners achieving 77.9% top-1 with access to only 10% of ImageNet. Code: https://github.com/facebookresearch/vissl

cs.CV↗

arXiv2021

Single-View 3D Object Reconstruction from Shape Priors in Memory

Existing methods for single-view 3D object reconstruction directly learn to transform image features into 3D representations. However, these methods are vulnerable to images containing noisy backgrounds and heavy occlusions because the extracted image features do not contain enough information to reconstruct high-quality 3D shapes. Humans routinely use incomplete or noisy visual cues from an image to retrieve similar 3D shapes from their memory and reconstruct the 3D shape of an object. Inspired by this, we propose a novel method, named Mem3D, that explicitly constructs shape priors to supplement the missing information in the image. Specifically, the shape priors are in the forms of "image-voxel" pairs in the memory network, which is stored by a well-designed writing strategy during training. We also propose a voxel triplet loss function that helps to retrieve the precise 3D shapes that are highly related to the input image from shape priors. The LSTM-based shape encoder is introduced to extract information from the retrieved 3D shapes, which are useful in recovering the 3D shape of an object that is heavily occluded or in complex environments. Experimental results demonstrate that Mem3D significantly improves reconstruction quality and performs favorably against state-of-the-art methods on the ShapeNet and Pix3D datasets.

cs.CV↗

arXiv2021

Data-Driven Characterization and Detection of COVID-19 Themed Malicious Websites

COVID-19 has hit hard on the global community, and organizations are working diligently to cope with the new norm of "work from home". However, the volume of remote work is unprecedented and creates opportunities for cyber attackers to penetrate home computers. Attackers have been leveraging websites with COVID-19 related names, dubbed COVID-19 themed malicious websites. These websites mostly contain false information, fake forms, fraudulent payments, scams, or malicious payloads to steal sensitive information or infect victims' computers. In this paper, we present a data-driven study on characterizing and detecting COVID-19 themed malicious websites. Our characterization study shows that attackers are agile and are deceptively crafty in designing geolocation targeted websites, often leveraging popular domain registrars and top-level domains. Our detection study shows that the Random Forest classifier can detect COVID-19 themed malicious websites based on the lexical and WHOIS features defined in this paper, achieving a 98% accuracy and 2.7% false-positive rate.

cs.CR↗

arXiv2021

Characterizing the Landscape of COVID-19 Themed Cyberattacks and Defenses

COVID-19 (Coronavirus) hit the global society and economy with a big surprise. In particular, work-from-home has become a new norm for employees. Despite the fact that COVID-19 can equally attack innocent people and cybercriminals, it is ironic to see surges in cyberattacks leveraging COVID-19 as a theme, dubbed COVID-19 themed cyberattacks or COVID-19 attacks for short, which represent a new phenomenon that has yet to be systematically understood. In this paper, we make the first step towards fully characterizing the landscape of these attacks, including their sophistication via the Cyber Kill Chain model. We also explore the solution space of defenses against these attacks.

cs.CR↗

arXiv2021

A Visual Analytics Approach to Facilitate the Proctoring of Online Exams

Online exams have become widely used to evaluate students' performance in mastering knowledge in recent years, especially during the pandemic of COVID-19. However, it is challenging to conduct proctoring for online exams due to the lack of face-to-face interaction. Also, prior research has shown that online exams are more vulnerable to various cheating behaviors, which can damage their credibility. This paper presents a novel visual analytics approach to facilitate the proctoring of online exams by analyzing the exam video records and mouse movement data of each student. Specifically, we detect and visualize suspected head and mouse movements of students in three levels of detail, which provides course instructors and teachers with convenient, efficient and reliable proctoring for online exams. Our extensive evaluations, including usage scenarios, a carefully-designed user study and expert interviews, demonstrate the effectiveness and usability of our approach.

cs.HC↗

arXiv2021

Inference on the History of a Randomly Growing Tree

The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains important information such as the source of the infection. We consider the problem of statistical inference on aspects of the latent history using only a single snapshot of the final tree. Our approach is to apply random labels to the observed unlabeled tree and analyze the resulting distribution of the growth process, conditional on the final outcome. We show that this conditional distribution is tractable under a shape-exchangeability condition, which we introduce here, and that this condition is satisfied for many popular models for randomly growing trees such as uniform attachment, linear preferential attachment and uniform attachment on a $D$-regular tree. For inference of the root under shape-exchangeability, we propose O(n log n) time algorithms for constructing confidence sets with valid frequentist coverage as well as bounds on the expected size of the confidence sets. We also provide efficient sampling algorithms that extend our methods to a wide class of inference problems.

math.PR↗

arXiv2020

AITom: Open-source AI platform for cryo-electron tomography data analysis

Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET contain heterogeneous structures representing the complex and dynamic subcellular environment. Since the structures are not purified or fluorescently labeled, the spatial organization and interaction between both the known and unknown structures can be studied in their native environment. The rapid advances of cryo-electron tomography (cryo-ET) have generated abundant 3D cellular imaging data. However, the systematic localization, identification, segmentation, and structural recovery of the subcellular components require efficient and accurate large-scale image analysis methods. We introduce AITom, an open-source artificial intelligence platform for cryo-ET researchers. AITom provides many public as well as in-house algorithms for performing cryo-ET data analysis through both the traditional template-based or template-free approach and the deep learning approach. AITom also supports remote interactive analysis. Comprehensive tutorials for each analysis module are provided to guide the user through. We welcome researchers and developers to join this collaborative open-source software development project. Availability: https://github.com/xulabs/aitom

q-bio.QM↗