arXiv subjects

Xingyu Li

Publications and source records attributed to Xingyu Li.

At least 145 records · Page 8Linked to original sources

arXiv2022

Optimize Deep Learning Models for Prediction of Gene Mutations Using Unsupervised Clustering

Deep learning has become the mainstream methodological choice for analyzing and interpreting whole-slide digital pathology images (WSIs). It is commonly assumed that tumor regions carry most predictive information. In this paper, we proposed an unsupervised clustering-based multiple-instance learning, and apply our method to develop deep-learning models for prediction of gene mutations using WSIs from three cancer types in The Cancer Genome Atlas (TCGA) studies (CRC, LUAD, and HNSCC). We showed that unsupervised clustering of image patches could help identify predictive patches, exclude patches lack of predictive information, and therefore improve prediction on gene mutations in all three different cancer types, compared with the WSI based method without selection of image patches and models based on only tumor regions. Additionally, our proposed algorithm outperformed two recently published baseline algorithms leveraging unsupervised clustering to assist model prediction. The unsupervised-clustering-based approach for mutation prediction allows identification of the spatial regions related to mutation of a specific gene via the resolved probability scores, highlighting the heterogeneity of a predicted genotype in the tumor microenvironment. Finally, our study also demonstrated that selection of tumor regions of WSIs is not always the best way to identify patches for prediction of gene mutations, and other tissue types in the tumor micro-environment may provide better prediction ability for gene mutations than tumor tissues.

q-bio.QM↗

arXiv2022

FedLGA: Towards System-Heterogeneity of Federated Learning via Local Gradient Approximation

Federated Learning (FL) is a decentralized machine learning architecture, which leverages a large number of remote devices to learn a joint model with distributed training data. However, the system-heterogeneity is one major challenge in a FL network to achieve robust distributed learning performance, which comes from two aspects: i) device-heterogeneity due to the diverse computational capacity among devices; ii) data-heterogeneity due to the non-identically distributed data across the network. Prior studies addressing the heterogeneous FL issue, e.g., FedProx, lack formalization and it remains an open problem. This work first formalizes the system-heterogeneous FL problem and proposes a new algorithm, called FedLGA, to address this problem by bridging the divergence of local model updates via gradient approximation. To achieve this, FedLGA provides an alternated Hessian estimation method, which only requires extra linear complexity on the aggregator. Theoretically, we show that with a device-heterogeneous ratio $ρ$, FedLGA achieves convergence rates on non-i.i.d. distributed FL training data for the non-convex optimization problems with $\mathcal{O} \left( \frac{(1+ρ)}{\sqrt{ENT}} + \frac{1}{T} \right)$ and $\mathcal{O} \left( \frac{(1+ρ)\sqrt{E}}{\sqrt{TK}} + \frac{1}{T} \right)$ for full and partial device participation respectively, where $E$ is the number of local learning epoch, $T$ is the number of total communication round, $N$ is the total device number and $K$ is the number of selected device in one communication round under partially participation scheme. The results of comprehensive experiments on multiple datasets show that FedLGA outperforms current FL methods against the system-heterogeneity.

cs.LG↗

arXiv2022

Anomaly Detection via Reverse Distillation from One-Class Embedding

Knowledge distillation (KD) achieves promising results on the challenging problem of unsupervised anomaly detection (AD).The representation discrepancy of anomalies in the teacher-student (T-S) model provides essential evidence for AD. However, using similar or identical architectures to build the teacher and student models in previous studies hinders the diversity of anomalous representations. To tackle this problem, we propose a novel T-S model consisting of a teacher encoder and a student decoder and introduce a simple yet effective "reverse distillation" paradigm accordingly. Instead of receiving raw images directly, the student network takes teacher model's one-class embedding as input and targets to restore the teacher's multiscale representations. Inherently, knowledge distillation in this study starts from abstract, high-level presentations to low-level features. In addition, we introduce a trainable one-class bottleneck embedding (OCBE) module in our T-S model. The obtained compact embedding effectively preserves essential information on normal patterns, but abandons anomaly perturbations. Extensive experimentation on AD and one-class novelty detection benchmarks shows that our method surpasses SOTA performance, demonstrating our proposed approach's effectiveness and generalizability.

cs.CV↗

arXiv2022

Confidence Intervals of Treatment Effects in Panel Data Models with Interactive Fixed Effects

We consider the construction of confidence intervals for treatment effects estimated using panel models with interactive fixed effects. We first use the factor-based matrix completion technique proposed by Bai and Ng (2021) to estimate the treatment effects, and then use bootstrap method to construct confidence intervals of the treatment effects for treated units at each post-treatment period. Our construction of confidence intervals requires neither specific distributional assumptions on the error terms nor large number of post-treatment periods. We also establish the validity of the proposed bootstrap procedure that these confidence intervals have asymptotically correct coverage probabilities. Simulation studies show that these confidence intervals have satisfactory finite sample performances, and empirical applications using classical datasets yield treatment effect estimates of similar magnitudes and reliable confidence intervals.

econ.EM↗

arXiv2022

LoMar: A Local Defense Against Poisoning Attack on Federated Learning

Federated learning (FL) provides a high efficient decentralized machine learning framework, where the training data remains distributed at remote clients in a network. Though FL enables a privacy-preserving mobile edge computing framework using IoT devices, recent studies have shown that this approach is susceptible to poisoning attacks from the side of remote clients. To address the poisoning attacks on FL, we provide a \textit{two-phase} defense algorithm called {Lo}cal {Ma}licious Facto{r} (LoMar). In phase I, LoMar scores model updates from each remote client by measuring the relative distribution over their neighbors using a kernel density estimation method. In phase II, an optimal threshold is approximated to distinguish malicious and clean updates from a statistical perspective. Comprehensive experiments on four real-world datasets have been conducted, and the experimental results show that our defense strategy can effectively protect the FL system. {Specifically, the defense performance on Amazon dataset under a label-flipping attack indicates that, compared with FG+Krum, LoMar increases the target label testing accuracy from $96.0\%$ to $98.8\%$, and the overall averaged testing accuracy from $90.1\%$ to $97.0\%$.

cs.LG↗

arXiv2022

Improving Feature Extraction from Histopathological Images Through A Fine-tuning ImageNet Model

Due to lack of annotated pathological images, transfer learning has been the predominant approach in the field of digital pathology.Pre-trained neural networks based on ImageNet database are often used to extract "off the shelf" features, achieving great success in predicting tissue types, molecular features, and clinical outcomes, etc. We hypothesize that fine-tuning the pre-trained models using histopathological images could further improve feature extraction, and downstream prediction performance.We used 100,000 annotated HE image patches for colorectal cancer (CRC) to finetune a pretrained Xception model via a twostep approach.The features extracted from finetuned Xception (FTX2048) model and Imagepretrained (IMGNET2048) model were compared through: (1) tissue classification for HE images from CRC, same image type that was used for finetuning; (2) prediction of immunerelated gene expression and (3) gene mutations for lung adenocarcinoma (LUAD).Fivefold cross validation was used for model performance evaluation. The extracted features from the finetuned FTX2048 exhibited significantly higher accuracy for predicting tisue types of CRC compared to the off the shelf feature directly from Xception based on ImageNet database. Particularly, FTX2048 markedly improved the accuracy for stroma from 87% to 94%. Similarly, features from FTX2048 boosted the prediction of transcriptomic expression of immunerelated genesin LUAD. For the genes that had signigicant relationships with image fetures, the features fgrom the finetuned model imprroved the prediction for the majority of the genes. Inaddition, fetures from FTX2048 improved prediction of mutation for 5 out of 9 most frequently mutated genes in LUAD.

eess.IV↗

arXiv2021

A Retrospective Analysis using Deep-Learning Models for Prediction of Survival Outcome and Benefit of Adjuvant Chemotherapy in Stage II/III Colorectal Cancer

Most early-stage colorectal cancer (CRC) patients can be cured by surgery alone, and only certain high-risk early-stage CRC patients benefit from adjuvant chemotherapies. However, very few validated biomarkers are available to accurately predict survival benefit from postoperative chemotherapy. We developed a novel deep-learning algorithm (CRCNet) using whole-slide images from Molecular and Cellular Oncology (MCO) to predict survival benefit of adjuvant chemotherapy in stage II/III CRC. We validated CRCNet both internally through cross-validation and externally using an independent cohort from The Cancer Genome Atlas (TCGA). We showed that CRCNet can accurately predict not only survival prognosis but also the treatment effect of adjuvant chemotherapy. The CRCNet identified high-risk subgroup benefits from adjuvant chemotherapy most and significant longer survival is observed among chemo-treated patients. Conversely, minimal chemotherapy benefit is observed in the CRCNet low- and medium-risk subgroups. Therefore, CRCNet can potentially be of great use in guiding treatments for Stage II/III CRC.

cs.LG↗

arXiv2021

CoverTheFace: face covering monitoring and demonstrating using deep learning and statistical shape analysis

Wearing a mask is a strong protection against the COVID-19 pandemic, even though the vaccine has been successfully developed and is widely available. However, many people wear them incorrectly. This observation prompts us to devise an automated approach to monitor the condition of people wearing masks. Unlike previous studies, our work goes beyond mask detection; it focuses on generating a personalized demonstration on proper mask-wearing, which helps people use masks better through visual demonstration rather than text explanation. The pipeline starts from the detection of face covering. For images where faces are improperly covered, our mask overlay module incorporates statistical shape analysis (SSA) and dense landmark alignment to approximate the geometry of a face and generates corresponding face-covering examples. Our results show that the proposed system successfully identifies images with faces covered properly. Our ablation study on mask overlay suggests that the SSA model helps to address variations in face shapes, orientations, and scales. The final face-covering examples, especially half profile face images, surpass previous arts by a noticeable margin.

cs.CV↗

arXiv2021

L2-Hypocoercivity and large time asymptotics of the linearized Vlasov-Poisson-Fokker-Planck system

This paper is devoted to the linearized Vlasov-Poisson-Fokker-Planck system in presence of an external potential of confinement. We investigate the large time behaviour of the solutions using hypocoercivity methods and a notion of scalar product adapted to the presence of a Poisson coupling. Our framework provides estimates which are uniform in the diffusion limit. As an application in a simple case, we study the one-dimensional case and prove the exponential convergence of the nonlinear Vlasov-Poisson-Fokker-Planck system without any small mass assumption.

math.AP↗

arXiv2021

On the limits of algorithmic prediction across the globe

The impact of predictive algorithms on people's lives and livelihoods has been noted in medicine, criminal justice, finance, hiring and admissions. Most of these algorithms are developed using data and human capital from highly developed nations. We tested how well predictive models of human behavior trained in a developed country generalize to people in less developed countries by modeling global variation in 200 predictors of academic achievement on nationally representative student data for 65 countries. Here we show that state-of-the-art machine learning models trained on data from the United States can predict achievement with high accuracy and generalize to other developed countries with comparable accuracy. However, accuracy drops linearly with national development due to global variation in the importance of different achievement predictors, providing a useful heuristic for policymakers. Training the same model on national data yields high accuracy in every country, which highlights the value of local data collection.

cs.LG↗

arXiv2021

Learning with Instance-Dependent Label Noise: A Sample Sieve Approach

Human-annotated labels are often prone to noise, and the presence of such noise will degrade the performance of the resulting deep neural network (DNN) models. Much of the literature (with several recent exceptions) of learning with noisy labels focuses on the case when the label noise is independent of features. Practically, annotations errors tend to be instance-dependent and often depend on the difficulty levels of recognizing a certain task. Applying existing results from instance-independent settings would require a significant amount of estimation of noise rates. Therefore, providing theoretically rigorous solutions for learning with instance-dependent label noise remains a challenge. In this paper, we propose CORES$^{2}$ (COnfidence REgularized Sample Sieve), which progressively sieves out corrupted examples. The implementation of CORES$^{2}$ does not require specifying noise rates and yet we are able to provide theoretical guarantees of CORES$^{2}$ in filtering out the corrupted examples. This high-quality sample sieve allows us to treat clean examples and the corrupted ones separately in training a DNN solution, and such a separation is shown to be advantageous in the instance-dependent noise setting. We demonstrate the performance of CORES$^{2}$ on CIFAR10 and CIFAR100 datasets with synthetic instance-dependent label noise and Clothing1M with real-world human noise. As of independent interests, our sample sieve provides a generic machinery for anatomizing noisy datasets and provides a flexible interface for various robust training techniques to further improve the performance. Code is available at https://github.com/UCSC-REAL/cores.

cs.LG↗

arXiv2021

Sample Elicitation

It is important to collect credible training samples $(x,y)$ for building data-intensive learning systems (e.g., a deep learning system). Asking people to report complex distribution $p(x)$, though theoretically viable, is challenging in practice. This is primarily due to the cognitive loads required for human agents to form the report of this highly complicated information. While classical elicitation mechanisms apply to eliciting a complex and generative (and continuous) distribution $p(x)$, we are interested in eliciting samples $x_i \sim p(x)$ from agents directly. We coin the above problem "sample elicitation". This paper introduces a deep learning aided method to incentivize credible sample contributions from self-interested and rational agents. We show that with an accurate estimation of a certain $f$-divergence function we can achieve approximate incentive compatibility in eliciting truthful samples. We then present an efficient estimator with theoretical guarantees via studying the variational forms of the $f$-divergence function. We also show a connection between this sample elicitation problem and $f$-GAN, and how this connection can help reconstruct an estimator of the distribution based on collected samples. Experiments on synthetic data, MNIST, and CIFAR-10 datasets demonstrate that our mechanism elicits truthful samples. Our implementation is available at https://github.com/weijiaheng/Credible-sample-elicitation.git.

cs.LG↗

arXiv2021

Stragglers Are Not Disaster: A Hybrid Federated Learning Algorithm with Delayed Gradients

Federated learning (FL) is a new machine learning framework which trains a joint model across a large amount of decentralized computing devices. Existing methods, e.g., Federated Averaging (FedAvg), are able to provide an optimization guarantee by synchronously training the joint model, but usually suffer from stragglers, i.e., IoT devices with low computing power or communication bandwidth, especially on heterogeneous optimization problems. To mitigate the influence of stragglers, this paper presents a novel FL algorithm, namely Hybrid Federated Learning (HFL), to achieve a learning balance in efficiency and effectiveness. It consists of two major components: synchronous kernel and asynchronous updater. Unlike traditional synchronous FL methods, our HFL introduces the asynchronous updater which actively pulls unsynchronized and delayed local weights from stragglers. An adaptive approximation method, Adaptive Delayed-SGD (AD-SGD), is proposed to merge the delayed local updates into the joint model. The theoretical analysis of HFL shows that the convergence rate of the proposed algorithm is $\mathcal{O}(\frac{1}{t+τ})$ for both convex and non-convex optimization problems.

cs.LG↗

arXiv2021

Blind stain separation using model-aware generative learning and its applications on fluorescence microscopy images

Multiple stains are usually used to highlight biological substances in biomedical image analysis. To decompose multiple stains for co-localization quantification, blind source separation is usually performed. Prior model-based stain separation methods usually rely on stains' spatial distributions over an image and may fail to solve the co-localization problem. With the advantage of machine learning, deep generative models are used for this purpose. Since prior knowledge of imaging models is ignored in purely data-driven solutions, these methods may be sub-optimal. In this study, a novel learning-based blind source separation framework is proposed, where the physical model of biomedical imaging is incorporated to regularize the learning process. The introduced model-relevant adversarial loss couples all generators in the framework and limits the capacities of the generative models. Further more, a training algorithm is innovated for the proposed framework to avoid inter-generator confusion during learning. This paper particularly takes fluorescence unmixing in fluorescence microscopy images as an application example of the proposed framework. Qualitative and quantitative experimentation on a public fluorescence microscopy image set demonstrates the superiority of the proposed method over both prior model-based approaches and learning-based methods.

eess.IV↗

arXiv2021

Large Time Asymptotic Behaviors of Two Types of Fast Diffusion Equations

We consider two types of non linear fast diffusion equations in R^N:(1) External drift type equation with general external potential. It is a natural extension of the harmonic potential case, which has been studied in many papers. In this paper we can prove the large time asymptotic behavior to the stationary state by using entropy methods.(2) Mean-field type equation with the convolution term. The stationary solution is the minimizer of the free energy functional, which has direct relation with reverse Hardy-Littlewood-Sobolev inequalities. In this paper, we prove that for some special cases, it also exists large time asymptotic behavior to the stationary state.

math.AP↗

arXiv2020

Ultra-uniform Nanocrystalline Materials via Two-Step Sintering

Nanocrystalline metals and ceramics with <100 nm grain sizes and superior properties (e.g., mechanical strength, hardness, fracture toughness and stored dielectric energy) are of great interest. Much has been discussed about achieving nano grains, but little is known about maintaining grain-size uniformity that is critical for material reliability. An especially intriguing question is whether it is possible to achieve a size distribution narrower than what Hillert[1] theoretically predicted for normal grain growth, a possibility suggested, for growth with a higher growth exponent, by the generalized mean-field theory[2] of Lifshitz, Slyozov, Wagner (LSW)[3,4] and Hillert but never realized in practice. We demonstrate that this can be achieved in bulk materials with an appropriately designed two-step sintering route that (a) takes advantage of the large growth exponent in the intermediate sintering stage to form a most uniform microstructure despite porosity remaining, and (b) freezes the grain growth thereon while continuing densification to reach full density. The resultant dense bulk Al2O3 ceramic has an average grain size of 34 nm and a much narrower size distribution than Hillert's prediction. Bulk Al2O3 with a grain-size distribution narrower than the particle-size distribution of starting powders was also demonstrated using this strategy, as were highly uniform bulk engineering metals and ceramics of either high purity and high melting points (Mo and W-Re) or highly complex compositions (core-shell BaTiO3 and 0.87BaTiO3-0.13Bi(Zn2/3(Nb0.85Ta0.15)1/3)O3).

cond-mat.mtrl-sci↗

arXiv2020

Stain Style Transfer of Histopathology Images Via Structure-Preserved Generative Learning

Computational histopathology image diagnosis becomes increasingly popular and important, where images are segmented or classified for disease diagnosis by computers. While pathologists do not struggle with color variations in slides, computational solutions usually suffer from this critical issue. To address the issue of color variations in histopathology images, this study proposes two stain style transfer models, SSIM-GAN and DSCSI-GAN, based on the generative adversarial networks. By cooperating structural preservation metrics and feedback of an auxiliary diagnosis net in learning, medical-relevant information presented by image texture, structure, and chroma-contrast features is preserved in color-normalized images. Particularly, the smart treat of chromatic image content in our DSCSI-GAN model helps to achieve noticeable normalization improvement in image regions where stains mix due to histological substances co-localization. Extensive experimentation on public histopathology image sets indicates that our methods outperform prior arts in terms of generating more stain-consistent images, better preserving histological information in images, and obtaining significantly higher learning efficiency. Our python implementation is published on https://github.com/hanwen0529/DSCSI-GAN.

eess.IV↗

arXiv2020

How Much Off-The-Shelf Knowledge Is Transferable From Natural Images To Pathology Images?

Deep learning has achieved a great success in natural image classification. To overcome data-scarcity in computational pathology, recent studies exploit transfer learning to reuse knowledge gained from natural images in pathology image analysis, aiming to build effective pathology image diagnosis models. Since transferability of knowledge heavily depends on the similarity of the original and target tasks, significant differences in image content and statistics between pathology images and natural images raise the questions: how much knowledge is transferable? Is the transferred information equally contributed by pre-trained layers? To answer these questions, this paper proposes a framework to quantify knowledge gain by a particular layer, conducts an empirical investigation in pathology image centered transfer learning, and reports some interesting observations. Particularly, compared to the performance baseline obtained by random-weight model, though transferability of off-the-shelf representations from deep layers heavily depend on specific pathology image sets, the general representation generated by early layers does convey transferred knowledge in various image classification applications. The observation in this study encourages further investigation of specific metric and tools to quantify effectiveness and feasibility of transfer learning in future.

eess.IV↗