arXiv subjects

Xiaofeng Zhu

Publications and source records attributed to Xiaofeng Zhu.

At least 73 records · Page 4Linked to original sources

arXiv2024

Estimation of the genetic Gaussian network using GWAS summary data

Genetic Gaussian network of multiple phenotypes constructed through the genetic correlation matrix is informative for understanding their biological dependencies. However, its interpretation may be challenging because the estimated genetic correlations are biased due to estimation errors and horizontal pleiotropy inherent in GWAS summary statistics. Here we introduce a novel approach called Estimation of Genetic Graph (EGG), which eliminates the estimation error bias and horizontal pleiotropy bias with the same techniques used in multivariable Mendelian randomization. The genetic network estimated by EGG can be interpreted as representing shared common biological contributions between phenotypes, conditional on others, and even as indicating the causal contributions. We use both simulations and real data to demonstrate the superior efficacy of our novel method in comparison with the traditional network estimators. R package EGG is available on https://github.com/harryyiheyang/EGG.

stat.ME↗

arXiv2023

Adaptive Multi-Modality Prompt Learning

Although current prompt learning methods have successfully been designed to effectively reuse the large pre-trained models without fine-tuning their large number of parameters, they still have limitations to be addressed, i.e., without considering the adverse impact of meaningless patches in every image and without simultaneously considering in-sample generalization and out-of-sample generalization. In this paper, we propose an adaptive multi-modality prompt learning to address the above issues. To do this, we employ previous text prompt learning and propose a new image prompt learning. The image prompt learning achieves in-sample and out-of-sample generalization, by first masking meaningless patches and then padding them with the learnable parameters and the information from texts. Moreover, each of the prompts provides auxiliary information to each other, further strengthening these two kinds of generalization. Experimental results on real datasets demonstrate that our method outperforms SOTA methods, in terms of different downstream tasks.

cs.LG↗

arXiv2023

An Efficient Membership Inference Attack for the Diffusion Model by Proximal Initialization

Recently, diffusion models have achieved remarkable success in generating tasks, including image and audio generation. However, like other generative models, diffusion models are prone to privacy issues. In this paper, we propose an efficient query-based membership inference attack (MIA), namely Proximal Initialization Attack (PIA), which utilizes groundtruth trajectory obtained by $ε$ initialized in $t=0$ and predicted point to infer memberships. Experimental results indicate that the proposed method can achieve competitive performance with only two queries on both discrete-time and continuous-time diffusion models. Moreover, previous works on the privacy of diffusion models have focused on vision tasks without considering audio tasks. Therefore, we also explore the robustness of diffusion models to MIA in the text-to-speech (TTS) task, which is an audio generation task. To the best of our knowledge, this work is the first to study the robustness of diffusion models to MIA in the TTS task. Experimental results indicate that models with mel-spectrogram (image-like) output are vulnerable to MIA, while models with audio output are relatively robust to MIA. {Code is available at \url{https://github.com/kong13661/PIA}}.

cs.SD↗

arXiv2023

Federated Deep Multi-View Clustering with Global Self-Supervision

Federated multi-view clustering has the potential to learn a global clustering model from data distributed across multiple devices. In this setting, label information is unknown and data privacy must be preserved, leading to two major challenges. First, views on different clients often have feature heterogeneity, and mining their complementary cluster information is not trivial. Second, the storage and usage of data from multiple clients in a distributed environment can lead to incompleteness of multi-view data. To address these challenges, we propose a novel federated deep multi-view clustering method that can mine complementary cluster structures from multiple clients, while dealing with data incompleteness and privacy concerns. Specifically, in the server environment, we propose sample alignment and data extension techniques to explore the complementary cluster structures of multiple views. The server then distributes global prototypes and global pseudo-labels to each client as global self-supervised information. In the client environment, multiple clients use the global self-supervised information and deep autoencoders to learn view-specific cluster assignments and embedded features, which are then uploaded to the server for refining the global self-supervised information. Finally, the results of our extensive experiments demonstrate that our proposed method exhibits superior performance in addressing the challenges of incomplete multi-view data in distributed environments.

cs.LG↗

arXiv2023

Zero-shot information extraction from radiological reports using ChatGPT

Electronic health records contain an enormous amount of valuable information, but many are recorded in free text. Information extraction is the strategy to transform the sequence of characters into structured data, which can be employed for secondary analysis. However, the traditional information extraction components, such as named entity recognition and relation extraction, require annotated data to optimize the model parameters, which has become one of the major bottlenecks in building information extraction systems. With the large language models achieving good performances on various downstream NLP tasks without parameter tuning, it becomes possible to use large language models for zero-shot information extraction. In this study, we aim to explore whether the most popular large language model, ChatGPT, can extract useful information from the radiological reports. We first design the prompt template for the interested information in the CT reports. Then, we generate the prompts by combining the prompt template with the CT reports as the inputs of ChatGPT to obtain the responses. A post-processing module is developed to transform the responses into structured extraction results. We conducted the experiments with 847 CT reports collected from Peking University Cancer Hospital. The experimental results indicate that ChatGPT can achieve competitive performances for some extraction tasks compared with the baseline information extraction system, but some limitations need to be further improved.

cs.CL↗

arXiv2023

Unsupervised Multiplex Graph Learning with Complementary and Consistent Information

Unsupervised multiplex graph learning (UMGL) has been shown to achieve significant effectiveness for different downstream tasks by exploring both complementary information and consistent information among multiple graphs. However, previous methods usually overlook the issues in practical applications, i.e., the out-of-sample issue and the noise issue. To address the above issues, in this paper, we propose an effective and efficient UMGL method to explore both complementary and consistent information. To do this, our method employs multiple MLP encoders rather than graph convolutional network (GCN) to conduct representation learning with two constraints, i.e., preserving the local graph structure among nodes to handle the out-of-sample issue, and maximizing the correlation of multiple node representations to handle the noise issue. Comprehensive experiments demonstrate that our proposed method achieves superior effectiveness and efficiency over the comparison methods and effectively tackles those two issues. Code is available at https://github.com/LarryUESTC/CoCoMG.

cs.LG↗

arXiv2023

A Universal Unbiased Method for Classification from Aggregate Observations

In conventional supervised classification, true labels are required for individual instances. However, it could be prohibitive to collect the true labels for individual instances, due to privacy concerns or unaffordable annotation costs. This motivates the study on classification from aggregate observations (CFAO), where the supervision is provided to groups of instances, instead of individual instances. CFAO is a generalized learning framework that contains various learning problems, such as multiple-instance learning and learning from label proportions. The goal of this paper is to present a novel universal method of CFAO, which holds an unbiased estimator of the classification risk for arbitrary losses -- previous research failed to achieve this goal. Practically, our method works by weighing the importance of each label for each instance in the group, which provides purified supervision for the classifier to learn. Theoretically, our proposed method not only guarantees the risk consistency due to the unbiased risk estimator but also can be compatible with arbitrary losses. Extensive experiments on various problems of CFAO demonstrate the superiority of our proposed method.

cs.LG↗

arXiv2023

Self-Paced Neutral Expression-Disentangled Learning for Facial Expression Recognition

The accuracy of facial expression recognition is typically affected by the following factors: high similarities across different expressions, disturbing factors, and micro-facial movement of rapid and subtle changes. One potentially viable solution for addressing these barriers is to exploit the neutral information concealed in neutral expression images. To this end, in this paper we propose a self-Paced Neutral Expression-Disentangled Learning (SPNDL) model. SPNDL disentangles neutral information from facial expressions, making it easier to extract key and deviation features. Specifically, it allows to capture discriminative information among similar expressions and perceive micro-facial movements. In order to better learn these neutral expression-disentangled features (NDFs) and to alleviate the non-convex optimization problem, a self-paced learning (SPL) strategy based on NDFs is proposed in the training stage. SPL learns samples from easy to complex by increasing the number of samples selected into the training process, which enables to effectively suppress the negative impacts introduced by low-quality samples and inconsistently distributed NDFs. Experiments on three popular databases (i.e., CK+, Oulu-CASIA, and RAF-DB) show the effectiveness of our proposed method.

cs.CV↗

arXiv2022

GATE: Graph CCA for Temporal SElf-supervised Learning for Label-efficient fMRI Analysis

In this work, we focus on the challenging task, neuro-disease classification, using functional magnetic resonance imaging (fMRI). In population graph-based disease analysis, graph convolutional neural networks (GCNs) have achieved remarkable success. However, these achievements are inseparable from abundant labeled data and sensitive to spurious signals. To improve fMRI representation learning and classification under a label-efficient setting, we propose a novel and theory-driven self-supervised learning (SSL) framework on GCNs, namely Graph CCA for Temporal self-supervised learning on fMRI analysis GATE. Concretely, it is demanding to design a suitable and effective SSL strategy to extract formation and robust features for fMRI. To this end, we investigate several new graph augmentation strategies from fMRI dynamic functional connectives (FC) for SSL training. Further, we leverage canonical-correlation analysis (CCA) on different temporal embeddings and present the theoretical implications. Consequently, this yields a novel two-step GCN learning procedure comprised of (i) SSL on an unlabeled fMRI population graph and (ii) fine-tuning on a small labeled fMRI dataset for a classification task. Our method is tested on two independent fMRI datasets, demonstrating superior performance on autism and dementia diagnosis.

cs.LG↗

arXiv2022

FedNI: Federated Graph Learning with Network Inpainting for Population-Based Disease Prediction

Graph Convolutional Neural Networks (GCNs) are widely used for graph analysis. Specifically, in medical applications, GCNs can be used for disease prediction on a population graph, where graph nodes represent individuals and edges represent individual similarities. However, GCNs rely on a vast amount of data, which is challenging to collect for a single medical institution. In addition, a critical challenge that most medical institutions continue to face is addressing disease prediction in isolation with incomplete data information. To address these issues, Federated Learning (FL) allows isolated local institutions to collaboratively train a global model without data sharing. In this work, we propose a framework, FedNI, to leverage network inpainting and inter-institutional data via FL. Specifically, we first federatively train missing node and edge predictor using a graph generative adversarial network (GAN) to complete the missing information of local networks. Then we train a global GCN node classifier across institutions using a federated graph learning platform. The novel design enables us to build more accurate machine learning models by leveraging federated learning and also graph learning approaches. We demonstrate that our federated model outperforms local and baseline FL methods with significant margins on two public neuroimaging datasets.

cs.LG↗

arXiv2022

Multi-level Feature Learning for Contrastive Multi-view Clustering

Multi-view clustering can explore common semantics from multiple views and has attracted increasing attention. However, existing works punish multiple objectives in the same feature space, where they ignore the conflict between learning consistent common semantics and reconstructing inconsistent view-private information. In this paper, we propose a new framework of multi-level feature learning for contrastive multi-view clustering to address the aforementioned issue. Our method learns different levels of features from the raw features, including low-level features, high-level features, and semantic labels/features in a fusion-free manner, so that it can effectively achieve the reconstruction objective and the consistency objectives in different feature spaces. Specifically, the reconstruction objective is conducted on the low-level features. Two consistency objectives based on contrastive learning are conducted on the high-level features and the semantic labels, respectively. They make the high-level features effectively explore the common semantics and the semantic labels achieve the multi-view clustering. As a result, the proposed framework can reduce the adverse influence of view-private information. Extensive experiments on public datasets demonstrate that our method achieves state-of-the-art clustering effectiveness.

cs.LG↗

arXiv2021

Self-paced Resistance Learning against Overfitting on Noisy Labels

Noisy labels composed of correct and corrupted ones are pervasive in practice. They might significantly deteriorate the performance of convolutional neural networks (CNNs), because CNNs are easily overfitted on corrupted labels. To address this issue, inspired by an observation, deep neural networks might first memorize the probably correct-label data and then corrupt-label samples, we propose a novel yet simple self-paced resistance framework to resist corrupted labels, without using any clean validation data. The proposed framework first utilizes the memorization effect of CNNs to learn a curriculum, which contains confident samples and provides meaningful supervision for other training samples. Then it adopts selected confident samples and a proposed resistance loss to update model parameters; the resistance loss tends to smooth model parameters' update or attain equivalent prediction over each class, thereby resisting model overfitting on corrupted labels. Finally, we unify these two modules into a single loss function and optimize it in an alternative learning. Extensive experiments demonstrate the significantly superior performance of the proposed framework over recent state-of-the-art methods on noisy-label data. Source codes of the proposed method are available on https://github.com/xsshi2015/Self-paced-Resistance-Learning.

cs.CV↗

arXiv2021

Multi-VAE: Learning Disentangled View-common and View-peculiar Visual Representations for Multi-view Clustering

Multi-view clustering, a long-standing and important research problem, focuses on mining complementary information from diverse views. However, existing works often fuse multiple views' representations or handle clustering in a common feature space, which may result in their entanglement especially for visual representations. To address this issue, we present a novel VAE-based multi-view clustering framework (Multi-VAE) by learning disentangled visual representations. Concretely, we define a view-common variable and multiple view-peculiar variables in the generative model. The prior of view-common variable obeys approximately discrete Gumbel Softmax distribution, which is introduced to extract the common cluster factor of multiple views. Meanwhile, the prior of view-peculiar variable follows continuous Gaussian distribution, which is used to represent each view's peculiar visual factors. By controlling the mutual information capacity to disentangle the view-common and view-peculiar representations, continuous visual information of multiple views can be separated so that their common discrete cluster information can be effectively mined. Experimental results demonstrate that Multi-VAE enjoys the disentangled and explainable visual representations, while obtaining superior clustering performance compared with state-of-the-art methods.

cs.CV↗

arXiv2021

Self-paced Principal Component Analysis

Principal Component Analysis (PCA) has been widely used for dimensionality reduction and feature extraction. Robust PCA (RPCA), under different robust distance metrics, such as l1-norm and l2, p-norm, can deal with noise or outliers to some extent. However, real-world data may display structures that can not be fully captured by these simple functions. In addition, existing methods treat complex and simple samples equally. By contrast, a learning pattern typically adopted by human beings is to learn from simple to complex and less to more. Based on this principle, we propose a novel method called Self-paced PCA (SPCA) to further reduce the effect of noise and outliers. Notably, the complexity of each sample is calculated at the beginning of each iteration in order to integrate samples from simple to more complex into training. Based on an alternating optimization, SPCA finds an optimal projection matrix and filters out outliers iteratively. Theoretical analysis is presented to show the rationality of SPCA. Extensive experiments on popular data sets demonstrate that the proposed method can improve the state of-the-art results considerably.

cs.LG↗

arXiv2021

Structured Graph Learning for Scalable Subspace Clustering: From Single-view to Multi-view

Graph-based subspace clustering methods have exhibited promising performance. However, they still suffer some of these drawbacks: encounter the expensive time overhead, fail in exploring the explicit clusters, and cannot generalize to unseen data points. In this work, we propose a scalable graph learning framework, seeking to address the above three challenges simultaneously. Specifically, it is based on the ideas of anchor points and bipartite graph. Rather than building a $n\times n$ graph, where $n$ is the number of samples, we construct a bipartite graph to depict the relationship between samples and anchor points. Meanwhile, a connectivity constraint is employed to ensure that the connected components indicate clusters directly. We further establish the connection between our method and the K-means clustering. Moreover, a model to process multi-view data is also proposed, which is linear scaled with respect to $n$. Extensive experiments demonstrate the efficiency and effectiveness of our approach with respect to many state-of-the-art clustering methods.

cs.LG↗

arXiv2020

Joint Prediction and Time Estimation of COVID-19 Developing Severe Symptoms using Chest CT Scan

With the rapidly worldwide spread of Coronavirus disease (COVID-19), it is of great importance to conduct early diagnosis of COVID-19 and predict the time that patients might convert to the severe stage, for designing effective treatment plan and reducing the clinicians' workloads. In this study, we propose a joint classification and regression method to determine whether the patient would develop severe symptoms in the later time, and if yes, predict the possible conversion time that the patient would spend to convert to the severe stage. To do this, the proposed method takes into account 1) the weight for each sample to reduce the outliers' influence and explore the problem of imbalance classification, and 2) the weight for each feature via a sparsity regularization term to remove the redundant features of high-dimensional data and learn the shared information across the classification task and the regression task. To our knowledge, this study is the first work to predict the disease progression and the conversion time, which could help clinicians to deal with the potential severe cases in time or even save the patients' lives. Experimental analysis was conducted on a real data set from two hospitals with 422 chest computed tomography (CT) scans, where 52 cases were converted to severe on average 5.64 days and 34 cases were severe at admission. Results show that our method achieves the best classification (e.g., 85.91% of accuracy) and regression (e.g., 0.462 of the correlation coefficient) performance, compared to all comparison methods. Moreover, our proposed method yields 76.97% of accuracy for predicting the severe cases, 0.524 of the correlation coefficient, and 0.55 days difference for the converted time.

eess.IV↗

arXiv2020

Neural Network Retraining for Model Serving

We propose incremental (re)training of a neural network model to cope with a continuous flow of new data in inference during model serving. As such, this is a life-long learning process. We address two challenges of life-long retraining: catastrophic forgetting and efficient retraining. If we combine all past and new data it can easily become intractable to retrain the neural network model. On the other hand, if the model is retrained using only new data, it can easily suffer catastrophic forgetting and thus it is paramount to strike the right balance. Moreover, if we retrain all weights of the model every time new data is collected, retraining tends to require too many computing resources. To solve these two issues, we propose a novel retraining model that can select important samples and important weights utilizing multi-armed bandits. To further address forgetting, we propose a new regularization term focusing on synapse and neuron importance. We analyze multiple datasets to document the outcome of the proposed retraining methods. Various experiments demonstrate that our retraining methodologies mitigate the catastrophic forgetting problem while boosting model performance.

cs.LG↗

arXiv2020

Listwise Learning to Rank by Exploring Unique Ratings

In this paper, we propose new listwise learning-to-rank models that mitigate the shortcomings of existing ones. Existing listwise learning-to-rank models are generally derived from the classical Plackett-Luce model, which has three major limitations. (1) Its permutation probabilities overlook ties, i.e., a situation when more than one document has the same rating with respect to a query. This can lead to imprecise permutation probabilities and inefficient training because of selecting documents one by one. (2) It does not favor documents having high relevance. (3) It has a loose assumption that sampling documents at different steps is independent. To overcome the first two limitations, we model ranking as selecting documents from a candidate set based on unique rating levels in decreasing order. The number of steps in training is determined by the number of unique rating levels. We propose a new loss function and associated four models for the entire sequence of weighted classification tasks by assigning high weights to the selected documents with high ratings for optimizing Normalized Discounted Cumulative Gain (NDCG). To overcome the final limitation, we further propose a novel and efficient way of refining prediction scores by combining an adapted Vanilla Recurrent Neural Network (RNN) model with pooling given selected documents at previous steps. We encode all of the documents already selected by an RNN model. In a single step, we rank all of the documents with the same ratings using the last cell of the RNN multiple times. We have implemented our models using three settings: neural networks, neural networks with gradient boosting, and regression trees with gradient boosting. We have conducted experiments on four public datasets. The experiments demonstrate that the models notably outperform state-of-the-art learning-to-rank models.

cs.IR↗