arXiv subjects

Xingyu Li

Publications and source records attributed to Xingyu Li.

At least 127 records · Page 7Linked to original sources

arXiv2023

DPSeq: A Novel and Efficient Digital Pathology Classifier for Predicting Cancer Biomarkers using Sequencer Architecture

In digital pathology tasks, transformers have achieved state-of-the-art results, surpassing convolutional neural networks (CNNs). However, transformers are usually complex and resource intensive. In this study, we developed a novel and efficient digital pathology classifier called DPSeq, to predict cancer biomarkers through fine-tuning a sequencer architecture integrating horizon and vertical bidirectional long short-term memory (BiLSTM) networks. Using hematoxylin and eosin (H&E)-stained histopathological images of colorectal cancer (CRC) from two international datasets: The Cancer Genome Atlas (TCGA) and Molecular and Cellular Oncology (MCO), the predictive performance of DPSeq was evaluated in series of experiments. DPSeq demonstrated exceptional performance for predicting key biomarkers in CRC (MSI status, Hypermutation, CIMP status, BRAF mutation, TP53 mutation and chromosomal instability [CING]), outperforming most published state-of-the-art classifiers in a within-cohort internal validation and a cross-cohort external validation. Additionally, under the same experimental conditions using the same set of training and testing datasets, DPSeq surpassed 4 CNN (ResNet18, ResNet50, MobileNetV2, and EfficientNet) and 2 transformer (ViT and Swin-T) models, achieving the highest AUROC and AUPRC values in predicting MSI status, BRAF mutation, and CIMP status. Furthermore, DPSeq required less time for both training and prediction due to its simple architecture. Therefore, DPSeq appears to be the preferred choice over transformer and CNN models for predicting cancer biomarkers.

eess.IV↗

arXiv2023

Whole-slide-imaging Cancer Metastases Detection and Localization with Limited Tumorous Data

Recently, various deep learning methods have shown significant successes in medical image analysis, especially in the detection of cancer metastases in hematoxylin and eosin (H&E) stained whole-slide images (WSIs). However, in order to obtain good performance, these research achievements rely on hundreds of well-annotated WSIs. In this study, we tackle the tumor localization and detection problem under the setting of few labeled whole slide images and introduce a patch-based analysis pipeline based on the latest reverse knowledge distillation architecture. To address the extremely unbalanced normal and tumorous samples in training sample collection, we applied the focal loss formula to the representation similarity metric for model optimization. Compared with prior arts, our method achieves similar performance by less than ten percent of training samples on the public Camelyon16 dataset. In addition, this is the first work that show the great potential of the knowledge distillation models in computational histopathology.

eess.IV↗

arXiv2023

Denoised Internal Models: a Brain-Inspired Autoencoder against Adversarial Attacks

Despite its great success, deep learning severely suffers from robustness; that is, deep neural networks are very vulnerable to adversarial attacks, even the simplest ones. Inspired by recent advances in brain science, we propose the Denoised Internal Models (DIM), a novel generative autoencoder-based model to tackle this challenge. Simulating the pipeline in the human brain for visual signal processing, DIM adopts a two-stage approach. In the first stage, DIM uses a denoiser to reduce the noise and the dimensions of inputs, reflecting the information pre-processing in the thalamus. Inspired from the sparse coding of memory-related traces in the primary visual cortex, the second stage produces a set of internal models, one for each category. We evaluate DIM over 42 adversarial attacks, showing that DIM effectively defenses against all the attacks and outperforms the SOTA on the overall robustness.

cs.CV↗

arXiv2023

Time to Embrace Natural Language Processing (NLP)-based Digital Pathology: Benchmarking NLP- and Convolutional Neural Network-based Deep Learning Pipelines

NLP-based computer vision models, particularly vision transformers, have been shown to outperform CNN models in many imaging tasks. However, most digital pathology artificial-intelligence models are based on CNN architectures, probably owing to a lack of data regarding NLP models for pathology images. In this study, we developed digital pathology pipelines to benchmark the five most recently proposed NLP models (vision transformer (ViT), Swin Transformer, MobileViT, CMT, and Sequencer2D) and four popular CNN models (ResNet18, ResNet50, MobileNetV2, and EfficientNet) to predict biomarkers in colorectal cancer (microsatellite instability, CpG island methylator phenotype, and BRAF mutation). Hematoxylin and eosin-stained whole-slide images from Molecular and Cellular Oncology and The Cancer Genome Atlas were used as training and external validation datasets, respectively. Cross-study external validations revealed that the NLP-based models significantly outperformed the CNN-based models in biomarker prediction tasks, improving the overall prediction and precision up to approximately 10% and 26%, respectively. Notably, compared with existing models in the current literature using large training datasets, our NLP models achieved state-of-the-art predictions for all three biomarkers using a relatively small training dataset, suggesting that large training datasets are not a prerequisite for NLP models or transformers, and NLP may be more suitable for clinical studies in which small training datasets are commonly collected. The superior performance of Sequencer2D suggests that further research and innovation on both transformer and bidirectional long short-term memory architectures are warranted in the field of digital pathology. NLP models can replace classic CNN architectures and become the new workhorse backbone in the field of digital pathology.

cs.CL↗

arXiv2023

Fuzzy Expert Systems for Prediction of ICU Admission in Patients with COVID-19

The pandemic COVID-19 disease has had a dramatic impact on almost all countries around the world so that many hospitals have been overwhelmed with Covid-19 cases. As medical resources are limited, deciding on the proper allocation of these resources is a very crucial issue. Besides, uncertainty is a major factor that can affect decisions, especially in medical fields. To cope with this issue, we use fuzzy logic (FL) as one of the most suitable methods in modeling systems with high uncertainty and complexity. We intend to make use of the advantages of FL in decisions on cases that need to treat in ICU. In this study, an interval type-2 fuzzy expert system is proposed for prediction of ICU admission in COVID-19 patients. For this prediction task, we also developed an adaptive neuro-fuzzy inference system (ANFIS). Finally, the results of these fuzzy systems are compared to some well-known classification methods such as Naive Bayes (NB), Case-Based Reasoning (CBR), Decision Tree (DT), and K Nearest Neighbor (KNN). The results show that the type-2 fuzzy expert system and ANFIS models perform competitively in terms of accuracy and F-measure compared to the other system modeling techniques.

cs.LG↗

arXiv2022

RMove: Recommending Move Method Refactoring Opportunities using Structural and Semantic Representations of Code

Incorrect placement of methods within classes is a typical code smell called Feature Envy, which causes additional maintenance and cost during evolution. To remove this design flaw, several Move Method refactoring tools have been proposed. To the best of our knowledge, state-of-the-art related techniques can be broadly divided into two categories: the first line is non-machine-learning-based approaches built on software measurement, while the selection and thresholds of software metrics heavily rely on expert knowledge. The second line is machine learning-based approaches, which suggest Move Method refactoring by learning to extract features from code information. However, most approaches in this line treat different forms of code information identically, disregarding their significant variation on data analysis. In this paper, we propose an approach to recommend Move Method refactoring named RMove by automatically learning structural and semantic representation from code fragment respectively. We concatenate these representations together and further train the machine learning classifiers to guide the movement of method to suitable classes. We evaluate our approach on two publicly available datasets. The results show that our approach outperforms three state-of-the-art refactoring tools including PathMove, JDeodorant, and JMove in effectiveness and usefulness. The results also unveil useful findings and provide new insights that benefit other types of feature envy refactoring techniques.

cs.SE↗

arXiv2022

Improving Adversarial Robustness with Self-Paced Hard-Class Pair Reweighting

Deep Neural Networks are vulnerable to adversarial attacks. Among many defense strategies, adversarial training with untargeted attacks is one of the most effective methods. Theoretically, adversarial perturbation in untargeted attacks can be added along arbitrary directions and the predicted labels of untargeted attacks should be unpredictable. However, we find that the naturally imbalanced inter-class semantic similarity makes those hard-class pairs become virtual targets of each other. This study investigates the impact of such closely-coupled classes on adversarial attacks and develops a self-paced reweighting strategy in adversarial training accordingly. Specifically, we propose to upweight hard-class pair losses in model optimization, which prompts learning discriminative features from hard classes. We further incorporate a term to quantify hard-class pair consistency in adversarial training, which greatly boosts model robustness. Extensive experiments show that the proposed adversarial training method achieves superior robustness performance over state-of-the-art defenses against a wide range of adversarial attacks.

cs.CV↗

arXiv2022

Common Corruption Robustness of Point Cloud Detectors: Benchmark and Enhancement

Object detection through LiDAR-based point cloud has recently been important in autonomous driving. Although achieving high accuracy on public benchmarks, the state-of-the-art detectors may still go wrong and cause a heavy loss due to the widespread corruptions in the real world like rain, snow, sensor noise, etc. Nevertheless, there is a lack of a large-scale dataset covering diverse scenes and realistic corruption types with different severities to develop practical and robust point cloud detectors, which is challenging due to the heavy collection costs. To alleviate the challenge and start the first step for robust point cloud detection, we propose the physical-aware simulation methods to generate degraded point clouds under different real-world common corruptions. Then, for the first attempt, we construct a benchmark based on the physical-aware common corruptions for point cloud detectors, which contains a total of 1,122,150 examples covering 7,481 scenes, 25 common corruption types, and 6 severities. With such a novel benchmark, we conduct extensive empirical studies on 8 state-of-the-art detectors that contain 6 different detection frameworks. Thus we get several insight observations revealing the vulnerabilities of the detectors and indicating the enhancement directions. Moreover, we further study the effectiveness of existing robustness enhancement methods based on data augmentation and data denoising. The benchmark can potentially be a new platform for evaluating point cloud detectors, opening a door for developing novel robustness enhancement methods.

cs.CV↗

arXiv2022

Prognostic Significance of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images in Colorectal Cancers

Purpose Tumor-infiltrating lymphocytes (TILs) have significant prognostic values in cancers. However, very few automated, deep-learning-based TIL scoring algorithms have been developed for colorectal cancers (CRC). Methods We developed an automated, multiscale LinkNet workflow for quantifying cellular-level TILs for CRC tumors using H&E-stained images. The predictive performance of the automatic TIL scores (TIL) for disease progression and overall survival was evaluate using two international datasets, including 554 CRC patients from The Cancer Genome Atlas (TCGA) and 1130 CRC patients from Molecular and Cellular Oncology (MCO). Results The LinkNet model provided an outstanding precision (0.9508), recall (0.9185), and overall F1 score (0.9347). Clear dose-response relationships were observed between TILs and risk of disease progression or death decreased in both TCGA and MCO cohorts. Both univariate and multivariate Cox regression analyses for the TCGA data demonstrated that patients with high TILs had significant (approx. 75%) reduction of risk for disease progression. In both MCO and TCGA studies, the TIL-high group was significantly associated with improved overall survival in univariate analysis (30% and 54% reduction in risk, respectively). However, potential confounding was observed in the MCO dataset. The favorable effects of high TILs were consistently observed in different subgroups according to know risk factors. Conclusion A deep-learning workflow for automatic TIL quantification based on LinkNet was successfully developed.

q-bio.QM↗

arXiv2022

Colorectal cancer survival prediction using deep distribution based multiple-instance learning

Several deep learning algorithms have been developed to predict survival of cancer patients using whole slide images (WSIs).However, identification of image phenotypes within the WSIs that are relevant to patient survival and disease progression is difficult for both clinicians, and deep learning algorithms. Most deep learning based Multiple Instance Learning (MIL) algorithms for survival prediction use either top instances (e.g., maxpooling) or top/bottom instances (e.g., MesoNet) to identify image phenotypes. In this study, we hypothesize that wholistic information of the distribution of the patch scores within a WSI can predict the cancer survival better. We developed a distribution based multiple-instance survival learning algorithm (DeepDisMISL) to validate this hypothesis. We designed and executed experiments using two large international colorectal cancer WSIs datasets - MCO CRC and TCGA COAD-READ. Our results suggest that the more information about the distribution of the patch scores for a WSI, the better is the prediction performance. Including multiple neighborhood instances around each selected distribution location (e.g., percentiles) could further improve the prediction. DeepDisMISL demonstrated superior predictive ability compared to other recently published, state-of-the-art algorithms. Furthermore, our algorithm is interpretable and could assist in understanding the relationship between cancer morphological phenotypes and patients cancer survival risk.

eess.IV↗

arXiv2022

Predicting microsatellite instability and key biomarkers in colorectal cancer from H&E-stained images: Achieving SOTA predictive performance with fewer data using Swin Transformer

Artificial intelligence (AI) models have been developed for predicting clinically relevant biomarkers, including microsatellite instability (MSI), for colorectal cancers (CRC). However, the current deep-learning networks are data-hungry and require large training datasets, which are often lacking in the medical domain. In this study, based on the latest Hierarchical Vision Transformer using Shifted Windows (Swin-T), we developed an efficient workflow for biomarkers in CRC (MSI, hypermutation, chromosomal instability, CpG island methylator phenotype, BRAF, and TP53 mutation) that only required relatively small datasets, but achieved the state-of-the-art (SOTA) predictive performance. Our Swin-T workflow not only substantially outperformed published models in an intra-study cross-validation experiment using TCGA-CRC-DX dataset (N = 462), but also showed excellent generalizability in cross-study external validation and delivered a SOTA AUROC of 0.90 for MSI using the MCO dataset for training (N = 1065) and the same TCGA-CRC-DX for testing. Similar performance (AUROC=0.91) was achieved by Echle and colleagues using approximately 8000 training samples (ResNet18) on the same testing dataset. Swin-T was extremely efficient using small training datasets and exhibits robust predictive performance with only 200-500 training samples. These data indicate that Swin-T may be 5-10 times more efficient than the current state-of-the-art algorithms for MSI based on ResNet18 and ShuffleNet. Furthermore, the Swin-T models showed promise as pre-screening tests for MSI status and BRAF mutation status, which could exclude and reduce the samples before the subsequent standard testing in a cascading diagnostic workflow to allow turnaround time reduction and cost saving.

q-bio.QM↗

arXiv2022

On the Convergence of Multi-Server Federated Learning with Overlapping Area

Multi-server Federated learning (FL) has been considered as a promising solution to address the limited communication resource problem of single-server FL. We consider a typical multi-server FL architecture, where the coverage areas of regional servers may overlap. The key point of this architecture is that the clients located in the overlapping areas update their local models based on the average model of all accessible regional models, which enables indirect model sharing among different regional servers. Due to the complicated network topology, the convergence analysis is much more challenging than single-server FL. In this paper, we firstly propose a novel MS-FedAvg algorithm for this multi-server FL architecture and analyze its convergence on non-iid datasets for general non-convex settings. Since the number of clients located in each regional server is much less than in single-server FL, the bandwidth of each client should be large enough to successfully communicate training models with the server, which indicates that full client participation can work in multi-server FL. Also, we provide the convergence analysis of the partial client participation scheme and develop a new biased partial participation strategy to further accelerate convergence. Our results indicate that the convergence results highly depend on the ratio of the number of clients in each area type to the total number of clients in all three strategies. The extensive experiments show remarkable performance and support our theoretical results.

cs.DC↗

arXiv2022

Object Wake-up: 3D Object Rigging from a Single Image

Given a single image of a general object such as a chair, could we also restore its articulated 3D shape similar to human modeling, so as to animate its plausible articulations and diverse motions? This is an interesting new question that may have numerous downstream augmented reality and virtual reality applications. Comparing with previous efforts on object manipulation, our work goes beyond 2D manipulation and rigid deformation, and involves articulated manipulation. To achieve this goal, we propose an automated approach to build such 3D generic objects from single images and embed articulated skeletons in them. Specifically, our framework starts by reconstructing the 3D object from an input image. Afterwards, to extract skeletons for generic 3D objects, we develop a novel skeleton prediction method with a multi-head structure for skeleton probability field estimation by utilizing the deep implicit functions. A dataset of generic 3D objects with ground-truth annotated skeletons is collected. Empirically our approach is demonstrated with satisfactory performance on public datasets as well as our in-house dataset; our results surpass those of the state-of-the-arts by a noticeable margin on both 3D reconstruction and skeleton prediction.

cs.CV↗

arXiv2022

Generalized Federated Learning via Sharpness Aware Minimization

Federated Learning (FL) is a promising framework for performing privacy-preserving, distributed learning with a set of clients. However, the data distribution among clients often exhibits non-IID, i.e., distribution shift, which makes efficient optimization difficult. To tackle this problem, many FL algorithms focus on mitigating the effects of data heterogeneity across clients by increasing the performance of the global model. However, almost all algorithms leverage Empirical Risk Minimization (ERM) to be the local optimizer, which is easy to make the global model fall into a sharp valley and increase a large deviation of parts of local clients. Therefore, in this paper, we revisit the solutions to the distribution shift problem in FL with a focus on local learning generality. To this end, we propose a general, effective algorithm, \texttt{FedSAM}, based on Sharpness Aware Minimization (SAM) local optimizer, and develop a momentum FL algorithm to bridge local and global models, \texttt{MoFedSAM}. Theoretically, we show the convergence analysis of these two algorithms and demonstrate the generalization bound of \texttt{FedSAM}. Empirically, our proposed algorithms substantially outperform existing FL studies and significantly decrease the learning deviation.

cs.LG↗

arXiv2022

A robust and lightweight deep attention multiple instance learning algorithm for predicting genetic alterations

Deep-learning models based on whole-slide digital pathology images (WSIs) become increasingly popular for predicting molecular biomarkers. Instance-based models has been the mainstream strategy for predicting genetic alterations using WSIs although bag-based models along with self-attention mechanism-based algorithms have been proposed for other digital pathology applications. In this paper, we proposed a novel Attention-based Multiple Instance Mutation Learning (AMIML) model for predicting gene mutations. AMIML was comprised of successive 1-D convolutional layers, a decoder, and a residual weight connection to facilitate further integration of a lightweight attention mechanism to detect the most predictive image patches. Using data for 24 clinically relevant genes from four cancer cohorts in The Cancer Genome Atlas (TCGA) studies (UCEC, BRCA, GBM and KIRC), we compared AMIML with one popular instance-based model and four recently published bag-based models (e.g., CHOWDER, HE2RNA, etc.). AMIML demonstrated excellent robustness, not only outperforming all the five baseline algorithms in the vast majority of the tested genes (17 out of 24), but also providing near-best-performance for the other seven genes. Conversely, the performance of the baseline published algorithms varied across different cancers/genes. In addition, compared to the published models for genetic alterations, AMIML provided a significant improvement for predicting a wide range of genes (e.g., KMT2C, TP53, and SETD2 for KIRC; ERBB2, BRCA1, and BRCA2 for BRCA; JAK1, POLE, and MTOR for UCEC) as well as produced outstanding predictive models for other clinically relevant gene mutations, which have not been reported in the current literature. Furthermore, with the flexible and interpretable attention-based MIL pooling mechanism, AMIML could further zero-in and detect predictive image patches.

q-bio.QM↗

arXiv2022

DDDM: a Brain-Inspired Framework for Robust Classification

Despite their outstanding performance in a broad spectrum of real-world tasks, deep artificial neural networks are sensitive to input noises, particularly adversarial perturbations. On the contrary, human and animal brains are much less vulnerable. In contrast to the one-shot inference performed by most deep neural networks, the brain often solves decision-making with an evidence accumulation mechanism that may trade time for accuracy when facing noisy inputs. The mechanism is well described by the Drift-Diffusion Model (DDM). In the DDM, decision-making is modeled as a process in which noisy evidence is accumulated toward a threshold. Drawing inspiration from the DDM, we propose the Dropout-based Drift-Diffusion Model (DDDM) that combines test-phase dropout and the DDM for improving the robustness for arbitrary neural networks. The dropouts create temporally uncorrelated noises in the network that counter perturbations, while the evidence accumulation mechanism guarantees a reasonable decision accuracy. Neural networks enhanced with the DDDM tested in image, speech, and text classification tasks all significantly outperform their native counterparts, demonstrating the DDDM as a task-agnostic defense against adversarial attacks.

cs.NE↗

arXiv2022

SHAPE: An Unified Approach to Evaluate the Contribution and Cooperation of Individual Modalities

As deep learning advances, there is an ever-growing demand for models capable of synthesizing information from multi-modal resources to address the complex tasks raised from real-life applications. Recently, many large multi-modal datasets have been collected, on which researchers actively explore different methods of fusing multi-modal information. However, little attention has been paid to quantifying the contribution of different modalities within the proposed models. In this paper, we propose the {\bf SH}apley v{\bf A}lue-based {\bf PE}rceptual (SHAPE) scores that measure the marginal contribution of individual modalities and the degree of cooperation across modalities. Using these scores, we systematically evaluate different fusion methods on different multi-modal datasets for different tasks. Our experiments suggest that for some tasks where different modalities are complementary, the multi-modal models still tend to use the dominant modality alone and ignore the cooperation across modalities. On the other hand, models learn to exploit cross-modal cooperation when different modalities are indispensable for the task. In this case, the scores indicate it is better to fuse different modalities at relatively early stages. We hope our scores can help improve the understanding of how the present multi-modal models operate on different modalities and encourage more sophisticated methods of integrating multiple modalities.

cs.LG↗

arXiv2022

Adversarial Fine-tune with Dynamically Regulated Adversary

Adversarial training is an effective method to boost model robustness to malicious, adversarial attacks. However, such improvement in model robustness often leads to a significant sacrifice of standard performance on clean images. In many real-world applications such as health diagnosis and autonomous surgical robotics, the standard performance is more valued over model robustness against such extremely malicious attacks. This leads to the question: To what extent we can boost model robustness without sacrificing standard performance? This work tackles this problem and proposes a simple yet effective transfer learning-based adversarial training strategy that disentangles the negative effects of adversarial samples on model's standard performance. In addition, we introduce a training-friendly adversarial attack algorithm, which facilitates the boost of adversarial robustness without introducing significant training complexity. Extensive experimentation indicates that the proposed method outperforms previous adversarial training algorithms towards the target: to improve model robustness while preserving model's standard performance on clean data.

cs.LG↗