arXiv subjects

Xiaoxiao Li

Publications and source records attributed to Xiaoxiao Li.

At least 127 records · Page 7Linked to original sources

arXiv2023

Stability and Fluctuations in Complex Ecological Systems

From 08-12 August, 2022, 32 individuals participated in a workshop, Stability and Fluctuations in Complex Ecological Systems, at the Lorentz Center, located in Leiden, The Netherlands. An interdisciplinary dialogue between ecologists, mathematicians, and physicists provided a foundation of important problems to consider over the next 5-10 years. This paper outlines eight areas including (1) improving our understanding of the effect of scale, both temporal and spatial, for both deterministic and stochastic problems; (2) clarifying the different terminologies and definitions used in different scientific fields; (3) developing a comprehensive set of data analysis techniques arising from different fields but which can be used together to improve our understanding of existing data sets; (4) having theoreticians/computational scientists collaborate closely with empirical ecologists to determine what new data should be collected; (5) improving our knowledge of how to protect and/or restore ecosystems; (6) incorporating socio-economic effects into models of ecosystems; (7) improving our understanding of the role of deterministic and stochastic fluctuations; (8) studying the current state of biodiversity at the functional level, taxa level and genome level.

q-bio.PE↗

arXiv2023

Sparse Convolution for Approximate Sparse Instance

Computing the convolution $A \star B$ of two vectors of dimension $n$ is one of the most important computational primitives in many fields. For the non-negative convolution scenario, the classical solution is to leverage the Fast Fourier Transform whose time complexity is $O(n \log n)$. However, the vectors $A$ and $B$ could be very sparse and we can exploit such property to accelerate the computation to obtain the result. In this paper, we show that when $\|A \star B\|_{\geq c_1} = k$ and $\|A \star B\|_{\leq c_2} = n-k$ holds, we can approximately recover the all index in $\mathrm{supp}_{\geq c_1}(A \star B)$ with point-wise error of $o(1)$ in $O(k \log (n) \log(k)\log(k/δ))$ time. We further show that we can iteratively correct the error and recover all index in $\mathrm{supp}_{\geq c_1}(A \star B)$ correctly in $O(k \log(n) \log^2(k) (\log(1/δ) + \log\log(k)))$ time.

cs.DS↗

arXiv2023

Quasi-cyclic perfect codes in Doob graphs and special partitions of Galois rings

The Galois ring GR$(4^Δ)$ is the residue ring $Z_4[x]/(h(x))$, where $h(x)$ is a basic primitive polynomial of degree $Δ$ over $Z_4$. For any odd $Δ$ larger than $1$, we construct a partition of GR$(4^Δ) \backslash \{0\}$ into $6$-subsets of type $\{a,b,-a-b,-a,-b,a+b\}$ and $3$-subsets of type $\{c,-c,2c\}$ such that the partition is invariant under the multiplication by a nonzero element of the Teichmuller set in GR$(4^Δ)$ and, if $Δ$ is not a multiple of $3$, under the action of the automorphism group of GR$(4^Δ)$. As a corollary, this implies the existence of quasi-cyclic additive $1$-perfect codes of index $(2^Δ-1)$ in $D((2^Δ-1)(2^Δ-2)/{6}, 2^Δ-1 )$ where $D(m,n)$ is the Doob metric scheme on $Z^{2m+n}$.

math.CO↗

arXiv2023

Scalable Data Point Valuation in Decentralized Learning

Existing research on data valuation in federated and swarm learning focuses on valuing client contributions and works best when data across clients is independent and identically distributed (IID). In practice, data is rarely distributed IID. We develop an approach called DDVal for decentralized data valuation, capable of valuing individual data points in federated and swarm learning. DDVal is based on sharing deep features and approximating Shapley values through a k-nearest neighbor approximation method. This allows for novel applications, for example, to simultaneously reward institutions and individuals for providing data to a decentralized machine learning task. The valuation of data points through DDVal allows to also draw hierarchical conclusions on the contribution of institutions, and we empirically show that the accuracy of DDVal in estimating institutional contributions is higher than existing Shapley value approximation methods for federated learning. Specifically, it reaches a cosine similarity in approximating Shapley values of 99.969 % in both, IID and non-IID data distributions across institutions, compared with 99.301 % and 97.250 % for the best state of the art methods. DDVal scales with the number of data points instead of the number of clients, and has a loglinear complexity. This scales more favorably than existing approaches with an exponential complexity. We show that DDVal is especially efficient in data distribution scenarios with many clients that have few data points - for example, more than 16 clients with 8,000 data points each. By integrating DDVal into a decentralized system, we show that it is not only suitable for centralized federated learning, but also decentralized swarm learning, which aligns well with the research on emerging internet technologies such as web3 to reward users for providing data to algorithms.

cs.LG↗

arXiv2023

Biological Factor Regulatory Neural Network

Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks to provide biological insights for humans due to their black-box nature. Recently, some works integrated biological knowledge with neural networks to improve the transparency and performance of their models. However, these methods can only incorporate partial biological knowledge, leading to suboptimal performance. In this paper, we propose the Biological Factor Regulatory Neural Network (BFReg-NN), a generic framework to model relations among biological factors in cell systems. BFReg-NN starts from gene expression data and is capable of merging most existing biological knowledge into the model, including the regulatory relations among genes or proteins (e.g., gene regulatory networks (GRN), protein-protein interaction networks (PPI)) and the hierarchical relations among genes, proteins and pathways (e.g., several genes/proteins are contained in a pathway). Moreover, BFReg-NN also has the ability to provide new biologically meaningful insights because of its white-box characteristics. Experimental results on different gene expression-based tasks verify the superiority of BFReg-NN compared with baselines. Our case studies also show that the key insights found by BFReg-NN are consistent with the biological literature.

cs.LG↗

arXiv2023

On Fairness of Medical Image Classification with Multiple Sensitive Attributes via Learning Orthogonal Representations

Mitigating the discrimination of machine learning models has gained increasing attention in medical image analysis. However, rare works focus on fair treatments for patients with multiple sensitive demographic ones, which is a crucial yet challenging problem for real-world clinical applications. In this paper, we propose a novel method for fair representation learning with respect to multi-sensitive attributes. We pursue the independence between target and multi-sensitive representations by achieving orthogonality in the representation space. Concretely, we enforce the column space orthogonality by keeping target information on the complement of a low-rank sensitive space. Furthermore, in the row space, we encourage feature dimensions between target and sensitive representations to be orthogonal. The effectiveness of the proposed method is demonstrated with extensive experiments on the CheXpert dataset. To our best knowledge, this is the first work to mitigate unfairness with respect to multiple sensitive attributes in the field of medical imaging.

cs.CV↗

arXiv2023

UniFed: A Unified Framework for Federated Learning on Non-IID Image Features

How to tackle non-iid data is a crucial topic in federated learning. This challenging problem not only affects training process, but also harms performance of clients not participating in training. Existing literature mainly focuses on either side, yet still lacks a unified solution to handle these two types (internal and external) of clients in a joint way. In this work, we propose a unified framework to tackle the non-iid issues for internal and external clients together. Firstly, we propose to use client-specific batch normalization in either internal or external clients to alleviate feature distribution shifts incurred by non-iid data. Then we present theoretical analysis to demonstrate the benefits of client-specific batch normalization. Specifically, we show that our approach promotes convergence speed for federated training and yields lower generalization error bound for external clients. Furthermore, we use causal reasoning to form a causal view to explain the advantages of our framework. At last, we conduct extensive experiments on natural and medical images to evaluate our method, where our method achieves state-of-the-art performance, faster convergence, and shows good compatibility. We also performed comprehensive analytical studies on a real-world medical dataset to demonstrate the effectiveness.

cs.LG↗

arXiv2023

SADM: Sequence-Aware Diffusion Model for Longitudinal Medical Image Generation

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

cs.CV↗

arXiv2023

Transcending XAI Algorithm Boundaries through End-User-Inspired Design

The boundaries of existing explainable artificial intelligence (XAI) algorithms are confined to problems grounded in technical users' demand for explainability. This research paradigm disproportionately ignores the larger group of non-technical end users, who have a much higher demand for AI explanations in diverse explanation goals, such as making safer and better decisions and improving users' predicted outcomes. Lacking explainability-focused functional support for end users may hinder the safe and accountable use of AI in high-stakes domains, such as healthcare, criminal justice, finance, and autonomous driving systems. Built upon prior human factor analysis on end users' requirements for XAI, we identify and model four novel XAI technical problems covering the full spectrum from design to the evaluation of XAI algorithms, including edge-case-based reasoning, customizable counterfactual explanation, collapsible decision tree, and the verifiability metric to evaluate XAI utility. Based on these newly-identified research problems, we also discuss open problems in the technical development of user-centered XAI to inspire future research. Our work bridges human-centered XAI with the technical XAI community, and calls for a new research paradigm on the technical development of user-centered XAI for the responsible use of AI in critical tasks.

cs.AI↗

arXiv2022

Robust Split Federated Learning for U-shaped Medical Image Networks

U-shaped networks are widely used in various medical image tasks, such as segmentation, restoration and reconstruction, but most of them usually rely on centralized learning and thus ignore privacy issues. To address the privacy concerns, federated learning (FL) and split learning (SL) have attracted increasing attention. However, it is hard for both FL and SL to balance the local computational cost, model privacy and parallel training simultaneously. To achieve this goal, in this paper, we propose Robust Split Federated Learning (RoS-FL) for U-shaped medical image networks, which is a novel hybrid learning paradigm of FL and SL. Previous works cannot preserve the data privacy, including the input, model parameters, label and output simultaneously. To effectively deal with all of them, we design a novel splitting method for U-shaped medical image networks, which splits the network into three parts hosted by different parties. Besides, the distributed learning methods usually suffer from a drift between local and global models caused by data heterogeneity. Based on this consideration, we propose a dynamic weight correction strategy (\textbf{DWCS}) to stabilize the training process and avoid model drift. Specifically, a weight correction loss is designed to quantify the drift between the models from two adjacent communication rounds. By minimizing this loss, a correction model is obtained. Then we treat the weighted sum of correction model and final round models as the result. The effectiveness of the proposed RoS-FL is supported by extensive experimental results on different tasks. Related codes will be released at https://github.com/Zi-YuanYang/RoS-FL.

eess.IV↗

arXiv2022

Guidelines and Evaluation of Clinical Explainable AI in Medical Image Analysis

Explainable artificial intelligence (XAI) is essential for enabling clinical users to get informed decision support from AI and comply with evidence-based medical practice. Applying XAI in clinical settings requires proper evaluation criteria to ensure the explanation technique is both technically sound and clinically useful, but specific support is lacking to achieve this goal. To bridge the research gap, we propose the Clinical XAI Guidelines that consist of five criteria a clinical XAI needs to be optimized for. The guidelines recommend choosing an explanation form based on Guideline 1 (G1) Understandability and G2 Clinical relevance. For the chosen explanation form, its specific XAI technique should be optimized for G3 Truthfulness, G4 Informative plausibility, and G5 Computational efficiency. Following the guidelines, we conducted a systematic evaluation on a novel problem of multi-modal medical image explanation with two clinical tasks, and proposed new evaluation metrics accordingly. Sixteen commonly-used heatmap XAI techniques were evaluated and found to be insufficient for clinical use due to their failure in G3 and G4. Our evaluation demonstrated the use of Clinical XAI Guidelines to support the design and evaluation of clinically viable XAI.

cs.LG↗

arXiv2022

A Convergence Theory for Federated Average: Beyond Smoothness

Federated learning enables a large amount of edge computing devices to learn a model without data sharing jointly. As a leading algorithm in this setting, Federated Average FedAvg, which runs Stochastic Gradient Descent (SGD) in parallel on local devices and averages the sequences only once in a while, have been widely used due to their simplicity and low communication cost. However, despite recent research efforts, it lacks theoretical analysis under assumptions beyond smoothness. In this paper, we analyze the convergence of FedAvg. Different from the existing work, we relax the assumption of strong smoothness. More specifically, we assume the semi-smoothness and semi-Lipschitz properties for the loss function, which have an additional first-order term in assumption definitions. In addition, we also assume bound on the gradient, which is weaker than the commonly used bounded gradient assumption in the convergence analysis scheme. As a solution, this paper provides a theoretical convergence study on Federated Learning.

cs.LG↗

arXiv2022

Improving Fairness in Image Classification via Sketching

Fairness is a fundamental requirement for trustworthy and human-centered Artificial Intelligence (AI) system. However, deep neural networks (DNNs) tend to make unfair predictions when the training data are collected from different sub-populations with different attributes (i.e. color, sex, age), leading to biased DNN predictions. We notice that such a troubling phenomenon is often caused by data itself, which means that bias information is encoded to the DNN along with the useful information (i.e. class information, semantic information). Therefore, we propose to use sketching to handle this phenomenon. Without losing the utility of data, we explore the image-to-sketching methods that can maintain useful semantic information for the target classification while filtering out the useless bias information. In addition, we design a fair loss to further improve the model fairness. We evaluate our method through extensive experiments on both general scene dataset and medical scene dataset. Our results show that the desired image-to-sketching method improves model fairness and achieves satisfactory results among state-of-the-art.

cs.CV↗

arXiv2022

Efficient Medical Image Assessment via Self-supervised Learning

High-performance deep learning methods typically rely on large annotated training datasets, which are difficult to obtain in many clinical applications due to the high cost of medical image labeling. Existing data assessment methods commonly require knowing the labels in advance, which are not feasible to achieve our goal of 'knowing which data to label.' To this end, we formulate and propose a novel and efficient data assessment strategy, EXponentiAl Marginal sINgular valuE (EXAMINE) score, to rank the quality of unlabeled medical image data based on their useful latent representations extracted via Self-supervised Learning (SSL) networks. Motivated by theoretical implication of SSL embedding space, we leverage a Masked Autoencoder for feature extraction. Furthermore, we evaluate data quality based on the marginal change of the largest singular value after excluding the data point in the dataset. We conduct extensive experiments on a pathology dataset. Our results indicate the effectiveness and efficiency of our proposed methods for selecting the most valuable data to label.

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

Federated Adversarial Learning: A Framework with Convergence Analysis

Federated learning (FL) is a trending training paradigm to utilize decentralized training data. FL allows clients to update model parameters locally for several epochs, then share them to a global model for aggregation. This training paradigm with multi-local step updating before aggregation exposes unique vulnerabilities to adversarial attacks. Adversarial training is a popular and effective method to improve the robustness of networks against adversaries. In this work, we formulate a general form of federated adversarial learning (FAL) that is adapted from adversarial learning in the centralized setting. On the client side of FL training, FAL has an inner loop to generate adversarial samples for adversarial training and an outer loop to update local model parameters. On the server side, FAL aggregates local model updates and broadcast the aggregated model. We design a global robust training loss and formulate FAL training as a min-max optimization problem. Unlike the convergence analysis in classical centralized training that relies on the gradient direction, it is significantly harder to analyze the convergence in FAL for three reasons: 1) the complexity of min-max optimization, 2) model not updating in the gradient direction due to the multi-local updates on the client-side before aggregation and 3) inter-client heterogeneity. We address these challenges by using appropriate gradient approximation and coupling techniques and present the convergence analysis in the over-parameterized regime. Our main result theoretically shows that the minimum loss under our algorithm can converge to $ε$ small with chosen learning rate and communication rounds. It is noteworthy that our analysis is feasible for non-IID clients.

cs.LG↗

arXiv2022

Exploring Resolution and Degradation Clues as Self-supervised Signal for Low Quality Object Detection

Image restoration algorithms such as super resolution (SR) are indispensable pre-processing modules for object detection in low quality images. Most of these algorithms assume the degradation is fixed and known a priori. However, in practical, either the real degradation or optimal up-sampling ratio rate is unknown or differs from assumption, leading to a deteriorating performance for both the pre-processing module and the consequent high-level task such as object detection. Here, we propose a novel self-supervised framework to detect objects in degraded low resolution images. We utilizes the downsampling degradation as a kind of transformation for self-supervised signals to explore the equivariant representation against various resolutions and other degradation conditions. The Auto Encoding Resolution in Self-supervision (AERIS) framework could further take the advantage of advanced SR architectures with an arbitrary resolution restoring decoder to reconstruct the original correspondence from the degraded input image. Both the representation learning and object detection are optimized jointly in an end-to-end training fashion. The generic AERIS framework could be implemented on various mainstream object detection architectures with different backbones. The extensive experiments show that our methods has achieved superior performance compared with existing methods when facing variant degradation situations. Code would be released at https://github.com/cuiziteng/ECCV_AERIS.

cs.CV↗

arXiv2022

Backdoor Attack is a Devil in Federated GAN-based Medical Image Synthesis

Deep Learning-based image synthesis techniques have been applied in healthcare research for generating medical images to support open research. Training generative adversarial neural networks (GAN) usually requires large amounts of training data. Federated learning (FL) provides a way of training a central model using distributed data from different medical institutions while keeping raw data locally. However, FL is vulnerable to backdoor attack, an adversarial by poisoning training data, given the central server cannot access the original data directly. Most backdoor attack strategies focus on classification models and centralized domains. In this study, we propose a way of attacking federated GAN (FedGAN) by treating the discriminator with a commonly used data poisoning strategy in backdoor attack classification models. We demonstrate that adding a small trigger with size less than 0.5 percent of the original image size can corrupt the FL-GAN model. Based on the proposed attack, we provide two effective defense strategies: global malicious detection and local training regularization. We show that combining the two defense strategies yields a robust medical image generation.

cs.CV↗