arXiv subjects

Jun Xia

Publications and source records attributed to Jun Xia.

At least 73 records · Page 4Linked to original sources

arXiv2024

On the asymptotics of real solutions for the Painlevé I equation

In this paper, we revisit the asymptotic formulas of real Painlevé I transcendents as the independent variable tends to negative infinity, which were initially derived by Kapaev with the complex WKB method. Using the Riemann-Hilbert method, we improve the error estimates of the oscillatory type asymptotics and provide precise error estimates of the singular type asymptotics. We also establish the corresponding asymptotics for the associated Hamiltonians of real Painlevé I transcendents. In addition, two typos in the mentioned asymptotic behaviors in literature are corrected.

math.CA↗

arXiv2024

Towards Energy-Aware Federated Learning via MARL: A Dual-Selection Approach for Model and Client

Although Federated Learning (FL) is promising in knowledge sharing for heterogeneous Artificial Intelligence of Thing (AIoT) devices, their training performance and energy efficacy are severely restricted in practical battery-driven scenarios due to the ``wooden barrel effect'' caused by the mismatch between homogeneous model paradigms and heterogeneous device capability. As a result, due to various kinds of differences among devices, it is hard for existing FL methods to conduct training effectively in energy-constrained scenarios, such as battery constraints of devices. To tackle the above issues, we propose an energy-aware FL framework named DR-FL, which considers the energy constraints in both clients and heterogeneous deep learning models to enable energy-efficient FL. Unlike Vanilla FL, DR-FL adopts our proposed Muti-Agents Reinforcement Learning (MARL)-based dual-selection method, which allows participated devices to make contributions to the global model effectively and adaptively based on their computing capabilities and energy capacities in a MARL-based manner. Experiments conducted with various widely recognized datasets demonstrate that DR-FL has the capability to optimize the exchange of knowledge among diverse models in large-scale AIoT systems while adhering to energy limitations. Additionally, it improves the performance of each individual heterogeneous device's model.

cs.LG↗

arXiv2024

Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective

The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexity. In this work, we reformulate the RNA secondary structure prediction as a K-Rook problem, thereby simplifying the prediction process into probabilistic matching within a finite solution space. Building on this innovative perspective, we introduce RFold, a simple yet effective method that learns to predict the most matching K-Rook solution from the given sequence. RFold employs a bi-dimensional optimization strategy that decomposes the probabilistic matching problem into row-wise and column-wise components to reduce the matching complexity, simplifying the solving process while guaranteeing the validity of the output. Extensive experiments demonstrate that RFold achieves competitive performance and about eight times faster inference efficiency than the state-of-the-art approaches. The code and Colab demo are available in (http://github.com/A4Bio/RFold).

q-bio.BM↗

arXiv2024

A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer

Can we model Non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The Non-Euclidean property have posed a long term challenge in graph modeling. Despite recent graph neural networks and graph transformers efforts encoding graphs as Euclidean vectors, recovering the original graph from vectors remains a challenge. In this paper, we introduce GraphsGPT, featuring an Graph2Seq encoder that transforms Non-Euclidean graphs into learnable Graph Words in the Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from Graph Words to ensure information equivalence. We pretrain GraphsGPT on $100$M molecules and yield some interesting findings: (1) The pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on $8/9$ graph classification and regression tasks. (2) The pretrained GraphGPT serves as a strong graph generator, demonstrated by its strong ability to perform both few-shot and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known Non-Euclidean challenges. (4) The edge-centric pretraining framework GraphsGPT demonstrates its efficacy in graph domain tasks, excelling in both representation and generation. Code is available at \href{https://github.com/A4Bio/GraphsGPT}{GitHub}.

cs.LG↗

arXiv2024

Enabling On-Device Learning via Experience Replay with Efficient Dataset Condensation

Upon deployment to edge devices, it is often desirable for a model to further learn from streaming data to improve accuracy. However, extracting representative features from such data is challenging because it is typically unlabeled, non-independent and identically distributed (non-i.i.d), and is seen only once. To mitigate this issue, a common strategy is to maintain a small data buffer on the edge device to hold the most representative data for further learning. As most data is either never stored or quickly discarded, identifying the most representative data to avoid significant information loss becomes critical. In this paper, we propose an on-device framework that addresses this issue by condensing incoming data into more informative samples. Specifically, to effectively handle unlabeled incoming data, we propose a pseudo-labeling technique designed for unlabeled on-device learning environments. Additionally, we develop a dataset condensation technique that only requires little computation resources. To counteract the effects of noisy labels during the condensation process, we further utilize a contrastive learning objective to improve the purity of class data within the buffer. Our empirical results indicate substantial improvements over existing methods, particularly when buffer capacity is severely restricted. For instance, with a buffer capacity of just one sample per class, our method achieves an accuracy that outperforms the best existing baseline by 58.4% on the CIFAR-10 dataset.

cs.LG↗

arXiv2024

Enabling On-Device Large Language Model Personalization with Self-Supervised Data Selection and Synthesis

After a large language model (LLM) is deployed on edge devices, it is desirable for these devices to learn from user-generated conversation data to generate user-specific and personalized responses in real-time. However, user-generated data usually contains sensitive and private information, and uploading such data to the cloud for annotation is not preferred if not prohibited. While it is possible to obtain annotation locally by directly asking users to provide preferred responses, such annotations have to be sparse to not affect user experience. In addition, the storage of edge devices is usually too limited to enable large-scale fine-tuning with full user-generated data. It remains an open question how to enable on-device LLM personalization, considering sparse annotation and limited on-device storage. In this paper, we propose a novel framework to select and store the most representative data online in a self-supervised way. Such data has a small memory footprint and allows infrequent requests of user annotations for further fine-tuning. To enhance fine-tuning quality, multiple semantically similar pairs of question texts and expected responses are generated using the LLM. Our experiments show that the proposed framework achieves the best user-specific content-generating capability (accuracy) and fine-tuning speed (performance) compared with vanilla baselines. To the best of our knowledge, this is the very first on-device LLM personalization framework.

cs.CL↗

arXiv2024

Have Your Cake and Eat It Too: Toward Efficient and Accurate Split Federated Learning

Due to its advantages in resource constraint scenarios, Split Federated Learning (SFL) is promising in AIoT systems. However, due to data heterogeneity and stragglers, SFL suffers from the challenges of low inference accuracy and low efficiency. To address these issues, this paper presents a novel SFL approach, named Sliding Split Federated Learning (S$^2$FL), which adopts an adaptive sliding model split strategy and a data balance-based training mechanism. By dynamically dispatching different model portions to AIoT devices according to their computing capability, S$^2$FL can alleviate the low training efficiency caused by stragglers. By combining features uploaded by devices with different data distributions to generate multiple larger batches with a uniform distribution for back-propagation, S$^2$FL can alleviate the performance degradation caused by data heterogeneity. Experimental results demonstrate that, compared to conventional SFL, S$^2$FL can achieve up to 16.5\% inference accuracy improvement and 3.54X training acceleration.

cs.LG↗

arXiv2024

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

q-bio.QM↗

arXiv2024

Advances of Deep Learning in Protein Science: A Comprehensive Survey

Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a powerful tool for protein modeling due to its ability to learn complex patterns and representations from large-scale protein data. This comprehensive survey aims to provide an overview of the recent advances in deep learning techniques applied to protein science. The survey begins by introducing the developments of deep learning based protein models and emphasizes the importance of protein representation learning in drug discovery, protein engineering, and function annotation. It then delves into the fundamentals of deep learning, including convolutional neural networks, recurrent neural networks, attention models, and graph neural networks in modeling protein sequences, structures, and functions, and explores how these techniques can be used to extract meaningful features and capture intricate relationships within protein data. Next, the survey presents various applications of deep learning in the field of proteins, including protein structure prediction, protein-protein interaction prediction, protein function prediction, etc. Furthermore, it highlights the challenges and limitations of these deep learning techniques and also discusses potential solutions and future directions for overcoming these challenges. This comprehensive survey provides a valuable resource for researchers and practitioners in the field of proteins who are interested in harnessing the power of deep learning techniques. By consolidating the latest advancements and discussing potential avenues for improvement, this review contributes to the ongoing progress in protein research and paves the way for future breakthroughs in the field.

q-bio.BM↗

arXiv2024

Deep Manifold Graph Auto-Encoder for Attributed Graph Embedding

Representing graph data in a low-dimensional space for subsequent tasks is the purpose of attributed graph embedding. Most existing neural network approaches learn latent representations by minimizing reconstruction errors. Rare work considers the data distribution and the topological structure of latent codes simultaneously, which often results in inferior embeddings in real-world graph data. This paper proposes a novel Deep Manifold (Variational) Graph Auto-Encoder (DMVGAE/DMGAE) method for attributed graph data to improve the stability and quality of learned representations to tackle the crowding problem. The node-to-node geodesic similarity is preserved between the original and latent space under a pre-defined distribution. The proposed method surpasses state-of-the-art baseline algorithms by a significant margin on different downstream tasks across popular datasets, which validates our solutions. We promise to release the code after acceptance.

cs.LG↗

arXiv2024

Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer

Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding site. Previous studies have utilized complex techniques to generate CDRs, but they suffer from inadequate geometric modeling. Moreover, the common iterative refinement strategies lead to an inefficient inference. In this paper, we propose a \textit{simple yet effective} model that can co-design 1D sequences and 3D structures of CDRs in a one-shot manner. To achieve this, we decouple the antibody CDR design problem into two stages: (i) geometric modeling of protein complex structures and (ii) sequence-structure co-learning. We develop a novel macromolecular structure invariant embedding, typically for protein complexes, that captures both intra- and inter-component interactions among the backbone atoms, including C$α$, N, C, and O atoms, to achieve comprehensive geometric modeling. Then, we introduce a simple cross-gate MLP for sequence-structure co-learning, allowing sequence and structure representations to implicitly refine each other. This enables our model to design desired sequences and structures in a one-shot manner. Extensive experiments are conducted to evaluate our results at both the sequence and structure levels, which demonstrate that our model achieves superior performance compared to the state-of-the-art antibody CDR design methods.

q-bio.BM↗

arXiv2024

Masked Modeling for Self-supervised Representation Learning on Vision and Beyond

As the deep learning revolution marches on, self-supervised learning has garnered increasing attention in recent years thanks to its remarkable representation learning ability and the low dependence on labeled data. Among these varied self-supervised techniques, masked modeling has emerged as a distinctive approach that involves predicting parts of the original data that are proportionally masked during training. This paradigm enables deep models to learn robust representations and has demonstrated exceptional performance in the context of computer vision, natural language processing, and other modalities. In this survey, we present a comprehensive review of the masked modeling framework and its methodology. We elaborate on the details of techniques within masked modeling, including diverse masking strategies, recovering targets, network architectures, and more. Then, we systematically investigate its wide-ranging applications across domains. Furthermore, we also explore the commonalities and differences between masked modeling methods in different fields. Toward the end of this paper, we conclude by discussing the limitations of current techniques and point out several potential avenues for advancing masked modeling research. A paper list project with this survey is available at \url{https://github.com/Lupin1998/Awesome-MIM}.

cs.CV↗

arXiv2024

Graph-level Protein Representation Learning by Structure Knowledge Refinement

This paper focuses on learning representation on the whole graph level in an unsupervised manner. Learning graph-level representation plays an important role in a variety of real-world issues such as molecule property prediction, protein structure feature extraction, and social network analysis. The mainstream method is utilizing contrastive learning to facilitate graph feature extraction, known as Graph Contrastive Learning (GCL). GCL, although effective, suffers from some complications in contrastive learning, such as the effect of false negative pairs. Moreover, augmentation strategies in GCL are weakly adaptive to diverse graph datasets. Motivated by these problems, we propose a novel framework called Structure Knowledge Refinement (SKR) which uses data structure to determine the probability of whether a pair is positive or negative. Meanwhile, we propose an augmentation strategy that naturally preserves the semantic meaning of the original data and is compatible with our SKR framework. Furthermore, we illustrate the effectiveness of our SKR framework through intuition and experiments. The experimental results on the tasks of graph-level classification demonstrate that our SKR framework is superior to most state-of-the-art baselines.

cs.LG↗

arXiv2023

AdapterFL: Adaptive Heterogeneous Federated Learning for Resource-constrained Mobile Computing Systems

Federated Learning (FL) enables collaborative learning of large-scale distributed clients without data sharing. However, due to the disparity of computing resources among massive mobile computing devices, the performance of traditional homogeneous model-based Federated Learning (FL) is seriously limited. On the one hand, to achieve model training in all the diverse clients, mobile computing systems can only use small low-performance models for collaborative learning. On the other hand, devices with high computing resources cannot train a high-performance large model with their insufficient raw data. To address the resource-constrained problem in mobile computing systems, we present a novel heterogeneous FL approach named AdapterFL, which uses a model reassemble strategy to facilitate collaborative training of massive heterogeneous mobile devices adaptively. Specifically, we select multiple candidate heterogeneous models based on the computing performance of massive mobile devices and then divide each heterogeneous model into two partitions. By reassembling the partitions, we can generate models with varied sizes that are combined by the partial parameters of the large model with the partial parameters of the small model. Using these reassembled models for FL training, we can train the partial parameters of the large model using low-performance devices. In this way, we can alleviate performance degradation in large models due to resource constraints. The experimental results show that AdapterFL can achieve up to 12\% accuracy improvement compared to the state-of-the-art heterogeneous federated learning methods in resource-constrained scenarios.

cs.LG↗

arXiv2023

AcademicGPT: Empowering Academic Research

Large Language Models (LLMs) have demonstrated exceptional capabilities across various natural language processing tasks. Yet, many of these advanced LLMs are tailored for broad, general-purpose applications. In this technical report, we introduce AcademicGPT, designed specifically to empower academic research. AcademicGPT is a continual training model derived from LLaMA2-70B. Our training corpus mainly consists of academic papers, thesis, content from some academic domain, high-quality Chinese data and others. While it may not be extensive in data scale, AcademicGPT marks our initial venture into a domain-specific GPT tailored for research area. We evaluate AcademicGPT on several established public benchmarks such as MMLU and CEval, as well as on some specialized academic benchmarks like PubMedQA, SCIEval, and our newly-created ComputerScienceQA, to demonstrate its ability from general knowledge ability, to Chinese ability, and to academic ability. Building upon AcademicGPT's foundation model, we also developed several applications catered to the academic area, including General Academic Question Answering, AI-assisted Paper Reading, Paper Review, and AI-assisted Title and Abstract Generation.

cs.CL↗

arXiv2023

CONVERT:Contrastive Graph Clustering with Reliable Augmentation

Contrastive graph node clustering via learnable data augmentation is a hot research spot in the field of unsupervised graph learning. The existing methods learn the sampling distribution of a pre-defined augmentation to generate data-driven augmentations automatically. Although promising clustering performance has been achieved, we observe that these strategies still rely on pre-defined augmentations, the semantics of the augmented graph can easily drift. The reliability of the augmented view semantics for contrastive learning can not be guaranteed, thus limiting the model performance. To address these problems, we propose a novel CONtrastiVe Graph ClustEring network with Reliable AugmenTation (CONVERT). Specifically, in our method, the data augmentations are processed by the proposed reversible perturb-recover network. It distills reliable semantic information by recovering the perturbed latent embeddings. Moreover, to further guarantee the reliability of semantics, a novel semantic loss is presented to constrain the network via quantifying the perturbation and recovery. Lastly, a label-matching mechanism is designed to guide the model by clustering information through aligning the semantic labels and the selected high-confidence clustering pseudo labels. Extensive experimental results on seven datasets demonstrate the effectiveness of the proposed method. We release the code and appendix of CONVERT at https://github.com/xihongyang1999/CONVERT on GitHub.

cs.LG↗

arXiv2023

WaveAttack: Asymmetric Frequency Obfuscation-based Backdoor Attacks Against Deep Neural Networks

Due to the popularity of Artificial Intelligence (AI) technology, numerous backdoor attacks are designed by adversaries to mislead deep neural network predictions by manipulating training samples and training processes. Although backdoor attacks are effective in various real scenarios, they still suffer from the problems of both low fidelity of poisoned samples and non-negligible transfer in latent space, which make them easily detectable by existing backdoor detection algorithms. To overcome the weakness, this paper proposes a novel frequency-based backdoor attack method named WaveAttack, which obtains image high-frequency features through Discrete Wavelet Transform (DWT) to generate backdoor triggers. Furthermore, we introduce an asymmetric frequency obfuscation method, which can add an adaptive residual in the training and inference stage to improve the impact of triggers and further enhance the effectiveness of WaveAttack. Comprehensive experimental results show that WaveAttack not only achieves higher stealthiness and effectiveness, but also outperforms state-of-the-art (SOTA) backdoor attack methods in the fidelity of images by up to 28.27\% improvement in PSNR, 1.61\% improvement in SSIM, and 70.59\% reduction in IS.

cs.CV↗

arXiv2023

A Survey of Deep Graph Clustering: Taxonomy, Challenge, Application, and Open Resource

Graph clustering, which aims to divide nodes in the graph into several distinct clusters, is a fundamental yet challenging task. Benefiting from the powerful representation capability of deep learning, deep graph clustering methods have achieved great success in recent years. However, the corresponding survey paper is relatively scarce, and it is imminent to make a summary of this field. From this motivation, we conduct a comprehensive survey of deep graph clustering. Firstly, we introduce formulaic definition, evaluation, and development in this field. Secondly, the taxonomy of deep graph clustering methods is presented based on four different criteria, including graph type, network architecture, learning paradigm, and clustering method. Thirdly, we carefully analyze the existing methods via extensive experiments and summarize the challenges and opportunities from five perspectives, including graph data quality, stability, scalability, discriminative capability, and unknown cluster number. Besides, the applications of deep graph clustering methods in six domains, including computer vision, natural language processing, recommendation systems, social network analyses, bioinformatics, and medical science, are presented. Last but not least, this paper provides open resource supports, including 1) a collection (\url{https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering}) of state-of-the-art deep graph clustering methods (papers, codes, and datasets) and 2) a unified framework (\url{https://github.com/Marigoldwu/A-Unified-Framework-for-Deep-Attribute-Graph-Clustering}) of deep graph clustering. We hope this work can serve as a quick guide and help researchers overcome challenges in this vibrant field.

cs.LG↗