arXiv subjects

Min Xu

Publications and source records attributed to Min Xu.

At least 145 records · Page 8Linked to original sources

arXiv2024

Enhancing Retrieval and Managing Retrieval: A Four-Module Synergy for Improved Quality and Efficiency in RAG Systems

Retrieval-augmented generation (RAG) techniques leverage the in-context learning capabilities of large language models (LLMs) to produce more accurate and relevant responses. Originating from the simple 'retrieve-then-read' approach, the RAG framework has evolved into a highly flexible and modular paradigm. A critical component, the Query Rewriter module, enhances knowledge retrieval by generating a search-friendly query. This method aligns input questions more closely with the knowledge base. Our research identifies opportunities to enhance the Query Rewriter module to Query Rewriter+ by generating multiple queries to overcome the Information Plateaus associated with a single query and by rewriting questions to eliminate Ambiguity, thereby clarifying the underlying intent. We also find that current RAG systems exhibit issues with Irrelevant Knowledge; to overcome this, we propose the Knowledge Filter. These two modules are both based on the instruction-tuned Gemma-2B model, which together enhance response quality. The final identified issue is Redundant Retrieval; we introduce the Memory Knowledge Reservoir and the Retriever Trigger to solve this. The former supports the dynamic expansion of the RAG system's knowledge base in a parameter-free manner, while the latter optimizes the cost for accessing external knowledge, thereby improving resource utilization and response efficiency. These four RAG modules synergistically improve the response quality and efficiency of the RAG system. The effectiveness of these modules has been validated through experiments and ablation studies across six common QA datasets. The source code can be accessed at https://github.com/Ancientshi/ERM4.

cs.CL↗

arXiv2024

Training-free CryoET Tomogram Segmentation

Cryogenic Electron Tomography (CryoET) is a useful imaging technology in structural biology that is hindered by its need for manual annotations, especially in particle picking. Recent works have endeavored to remedy this issue with few-shot learning or contrastive learning techniques. However, supervised training is still inevitable for them. We instead choose to leverage the power of existing 2D foundation models and present a novel, training-free framework, CryoSAM. In addition to prompt-based single-particle instance segmentation, our approach can automatically search for similar features, facilitating full tomogram semantic segmentation with only one prompt. CryoSAM is composed of two major parts: 1) a prompt-based 3D segmentation system that uses prompts to complete single-particle instance segmentation recursively with Cross-Plane Self-Prompting, and 2) a Hierarchical Feature Matching mechanism that efficiently matches relevant features with extracted tomogram features. They collaborate to enable the segmentation of all particles of one category with just one particle-specific prompt. Our experiments show that CryoSAM outperforms existing works by a significant margin and requires even fewer annotations in particle picking. Further visualizations demonstrate its ability when dealing with full tomogram segmentation for various subcellular structures. Our code is available at: https://github.com/xulabs/aitom

q-bio.QM↗

arXiv2024

ISPO: An Integrated Ontology of Symptom Phenotypes for Semantic Integration of Traditional Chinese Medical Data

Symptom phenotypes are one of the key types of manifestations for diagnosis and treatment of various disease conditions. However, the diversity of symptom terminologies is one of the major obstacles hindering the analysis and knowledge sharing of various types of symptom-related medical data particularly in the fields of Traditional Chinese Medicine (TCM). Objective: This study aimed to construct an Integrated Ontology of symptom phenotypes (ISPO) to support the data mining of Chinese EMRs and real-world study in TCM field. Methods: To construct an integrated ontology of symptom phenotypes (ISPO), we manually annotated classical TCM textbooks and large-scale Chinese electronic medical records (EMRs) to collect symptom terms with support from a medical text annotation system. Furthermore, to facilitate the semantic interoperability between different terminologies, we incorporated public available biomedical vocabularies by manual mapping between Chinese terms and English terms with cross-references to source vocabularies. In addition, we evaluated the ISPO using independent clinical EMRs to provide a high-usable medical ontology for clinical data analysis. Results: By integrating 78,696 inpatient cases of EMRs, 5 biomedical vocabularies, 21 TCM books and dictionaries, ISPO provides 3,147 concepts, 23,475 terms, and 55,552 definition or contextual texts. Adhering to the taxonomical structure of the related anatomical systems of symptom phenotypes, ISPO provides 12 top-level categories and 79 middle-level sub-categories. The validation of data analysis showed the ISPO has a coverage rate of 95.35%, 98.53% and 92.66% for symptom terms with occurrence rates of 0.5% in additional three independent curated clinical datasets, which can demonstrate the significant value of ISPO in mapping clinical terms to ontologies.

cs.CL↗

arXiv2024

Improving Knowledge Distillation in Transfer Learning with Layer-wise Learning Rates

Transfer learning methods start performing poorly when the complexity of the learning task is increased. Most of these methods calculate the cumulative differences of all the matched features and then use them to back-propagate that loss through all the layers. Contrary to these methods, in this work, we propose a novel layer-wise learning scheme that adjusts learning parameters per layer as a function of the differences in the Jacobian/Attention/Hessian of the output activations w.r.t. the network parameters. We applied this novel scheme for attention map-based and derivative-based (first and second order) transfer learning methods. We received improved learning performance and stability against a wide range of datasets. From extensive experimental evaluation, we observed that the performance boost achieved by our method becomes more significant with the increasing difficulty of the learning task.

cs.LG↗

arXiv2024

Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling

Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology facilitating the study of macromolecular structures at near-atomic resolution. Recent volumetric segmentation approaches on cryo-ET images have drawn widespread interest in biological sector. However, existing methods heavily rely on manually labeled data, which requires highly professional skills, thereby hindering the adoption of fully-supervised approaches for cryo-ET images. Some unsupervised domain adaptation (UDA) approaches have been designed to enhance the segmentation network performance using unlabeled data. However, applying these methods directly to cryo-ET images segmentation tasks remains challenging due to two main issues: 1) the source data, usually obtained through simulation, contain a certain level of noise, while the target data, directly collected from raw-data from real-world scenario, have unpredictable noise levels. 2) the source data used for training typically consists of known macromoleculars, while the target domain data are often unknown, causing the model's segmenter to be biased towards these known macromolecules, leading to a domain shift problem. To address these challenges, in this work, we introduce the first voxel-wise unsupervised domain adaptation approach, termed Vox-UDA, specifically for cryo-ET subtomogram segmentation. Vox-UDA incorporates a noise generation module to simulate target-like noises in the source dataset for cross-noise level adaptation. Additionally, we propose a denoised pseudo-labeling strategy based on improved Bilateral Filter to alleviate the domain shift problem. Experimental results on both simulated and real cryo-ET subtomogram datasets demonstrate the superiority of our proposed approach compared to state-of-the-art UDA methods.

cs.CV↗

arXiv2024

HGTDP-DTA: Hybrid Graph-Transformer with Dynamic Prompt for Drug-Target Binding Affinity Prediction

Drug target binding affinity (DTA) is a key criterion for drug screening. Existing experimental methods are time-consuming and rely on limited structural and domain information. While learning-based methods can model sequence and structural information, they struggle to integrate contextual data and often lack comprehensive modeling of drug-target interactions. In this study, we propose a novel DTA prediction method, termed HGTDP-DTA, which utilizes dynamic prompts within a hybrid Graph-Transformer framework. Our method generates context-specific prompts for each drug-target pair, enhancing the model's ability to capture unique interactions. The introduction of prompt tuning further optimizes the prediction process by filtering out irrelevant noise and emphasizing task-relevant information, dynamically adjusting the input features of the molecular graph. The proposed hybrid Graph-Transformer architecture combines structural information from Graph Convolutional Networks (GCNs) with sequence information captured by Transformers, facilitating the interaction between global and local information. Additionally, we adopted the multi-view feature fusion method to project molecular graph views and affinity subgraph views into a common feature space, effectively combining structural and contextual information. Experiments on two widely used public datasets, Davis and KIBA, show that HGTDP-DTA outperforms state-of-the-art DTA prediction methods in both prediction performance and generalization ability.

cs.LG↗

arXiv2024

Multiscale Tests for Point Processes and Longitudinal Networks

We propose a new testing framework applicable to both the two-sample problem on point processes and the community detection problem on rectangular arrays of point processes, which we refer to as longitudinal networks; the latter problem is useful in situations where we observe interactions among a group of individuals over time. Our framework is based on a multiscale discretization scheme that consider not just the global null but also a collection of nulls local to small regions in the domain; in the two-sample problem, the local rejections tell us where the intensity functions differ and in the longitudinal network problem, the local rejections tell us when the community structure is most salient. We provide theoretical analysis for the two-sample problem and show that our method has minimax optimal power under a Holder continuity condition. We provide extensive simulation and real data analysis demonstrating the practicality of our proposed method.

stat.ME↗

arXiv2024

Synergistic Global-space Camera and Human Reconstruction from Videos

Remarkable strides have been made in reconstructing static scenes or human bodies from monocular videos. Yet, the two problems have largely been approached independently, without much synergy. Most visual SLAM methods can only reconstruct camera trajectories and scene structures up to scale, while most HMR methods reconstruct human meshes in metric scale but fall short in reasoning with cameras and scenes. This work introduces Synergistic Camera and Human Reconstruction (SynCHMR) to marry the best of both worlds. Specifically, we design Human-aware Metric SLAM to reconstruct metric-scale camera poses and scene point clouds using camera-frame HMR as a strong prior, addressing depth, scale, and dynamic ambiguities. Conditioning on the dense scene recovered, we further learn a Scene-aware SMPL Denoiser to enhance world-frame HMR by incorporating spatio-temporal coherency and dynamic scene constraints. Together, they lead to consistent reconstructions of camera trajectories, human meshes, and dense scene point clouds in a common world frame. Project page: https://paulchhuang.github.io/synchmr

cs.CV↗

arXiv2024

MediCLIP: Adapting CLIP for Few-shot Medical Image Anomaly Detection

In the field of medical decision-making, precise anomaly detection in medical imaging plays a pivotal role in aiding clinicians. However, previous work is reliant on large-scale datasets for training anomaly detection models, which increases the development cost. This paper first focuses on the task of medical image anomaly detection in the few-shot setting, which is critically significant for the medical field where data collection and annotation are both very expensive. We propose an innovative approach, MediCLIP, which adapts the CLIP model to few-shot medical image anomaly detection through self-supervised fine-tuning. Although CLIP, as a vision-language model, demonstrates outstanding zero-/fewshot performance on various downstream tasks, it still falls short in the anomaly detection of medical images. To address this, we design a series of medical image anomaly synthesis tasks to simulate common disease patterns in medical imaging, transferring the powerful generalization capabilities of CLIP to the task of medical image anomaly detection. When only few-shot normal medical images are provided, MediCLIP achieves state-of-the-art performance in anomaly detection and location compared to other methods. Extensive experiments on three distinct medical anomaly detection tasks have demonstrated the superiority of our approach. The code is available at https://github.com/cnulab/MediCLIP.

cs.CV↗

arXiv2024

Conditional Local Feature Encoding for Graph Neural Networks

Graph neural networks (GNNs) have shown great success in learning from graph-based data. The key mechanism of current GNNs is message passing, where a node's feature is updated based on the information passing from its local neighbourhood. A limitation of this mechanism is that node features become increasingly dominated by the information aggregated from the neighbourhood as we use more rounds of message passing. Consequently, as the GNN layers become deeper, adjacent node features tends to be similar, making it more difficult for GNNs to distinguish adjacent nodes, thereby, limiting the performance of GNNs. In this paper, we propose conditional local feature encoding (CLFE) to help prevent the problem of node features being dominated by the information from local neighbourhood. The idea of our method is to extract the node hidden state embedding from message passing process and concatenate it with the nodes feature from previous stage, then we utilise linear transformation to form a CLFE based on the concatenated vector. The CLFE will form the layer output to better preserve node-specific information, thus help to improve the performance of GNN models. To verify the feasibility of our method, we conducted extensive experiments on seven benchmark datasets for four graph domain tasks: super-pixel graph classification, node classification, link prediction, and graph regression. The experimental results consistently demonstrate that our method improves model performance across a variety of baseline GNN models for all four tasks.

cs.LG↗

arXiv2024

ERAGent: Enhancing Retrieval-Augmented Language Models with Improved Accuracy, Efficiency, and Personalization

Retrieval-augmented generation (RAG) for language models significantly improves language understanding systems. The basic retrieval-then-read pipeline of response generation has evolved into a more extended process due to the integration of various components, sometimes even forming loop structures. Despite its advancements in improving response accuracy, challenges like poor retrieval quality for complex questions that require the search of multifaceted semantic information, inefficiencies in knowledge re-retrieval during long-term serving, and lack of personalized responses persist. Motivated by transcending these limitations, we introduce ERAGent, a cutting-edge framework that embodies an advancement in the RAG area. Our contribution is the introduction of the synergistically operated module: Enhanced Question Rewriter and Knowledge Filter, for better retrieval quality. Retrieval Trigger is incorporated to curtail extraneous external knowledge retrieval without sacrificing response quality. ERAGent also personalizes responses by incorporating a learned user profile. The efficiency and personalization characteristics of ERAGent are supported by the Experiential Learner module which makes the AI assistant being capable of expanding its knowledge and modeling user profile incrementally. Rigorous evaluations across six datasets and three question-answering tasks prove ERAGent's superior accuracy, efficiency, and personalization, emphasizing its potential to advance the RAG field and its applicability in practical systems.

cs.CL↗

arXiv2024

Physical Vapor Deposition of High Mobility P-type Tellurium and its Applications for Gate-tunable van der Waals PN Photodiodes

Recently tellurium (Te) has attracted resurgent interests due to its p-type characteristics and outstanding ambient environmental stability. Here we present a substrate engineering based physical vapor deposition method to synthesize high-quality Te nanoflakes and achieved a field-effect hole mobility of 1500 cm2/Vs, which is, to the best of our knowledge, the highest among the existing synthesized van der Waals p-type semiconductors. The high mobility Te enables the fabrication of Te/MoS2 pn diodes with highly gate-tunable electronic and optoelectronic characteristics. The Te/MoS2 heterostructure can be used as a visible range photodetector with a current responsivity up to 630 A/W, which is about one order of magnitude higher than the one achieved using p-type Si-MoS2 PN photodiodes. The photo response of the Te/MoS2 heterojunction also exhibits strong gate tunability due to their ultrathin thickness and unique band structures. The successful synthesis of high mobility Te and the enabled Te/MoS2 photodiodes show promise for the development of highly tunable and ultrathin photodetectors.

physics.app-ph↗

arXiv2024

One-Prompt to Segment All Medical Images

Large foundation models, known for their strong zero-shot generalization, have excelled in visual and language applications. However, applying them to medical image segmentation, a domain with diverse imaging types and target labels, remains an open challenge. Current approaches, such as adapting interactive segmentation models like Segment Anything Model (SAM), require user prompts for each sample during inference. Alternatively, transfer learning methods like few/one-shot models demand labeled samples, leading to high costs. This paper introduces a new paradigm toward the universal medical image segmentation, termed 'One-Prompt Segmentation.' One-Prompt Segmentation combines the strengths of one-shot and interactive methods. In the inference stage, with just \textbf{one prompted sample}, it can adeptly handle the unseen task in a single forward pass. We train One-Prompt Model on 64 open-source medical datasets, accompanied by the collection of over 3,000 clinician-labeled prompts. Tested on 14 previously unseen datasets, the One-Prompt Model showcases superior zero-shot segmentation capabilities, outperforming a wide range of related methods. The code and data is released as https://github.com/KidsWithTokens/one-prompt.

eess.IV↗

arXiv2024

RandAlign: A Parameter-Free Method for Regularizing Graph Convolutional Networks

Studies continually find that message-passing graph convolutional networks suffer from the over-smoothing issue. Basically, the issue of over-smoothing refers to the phenomenon that the learned embeddings for all nodes can become very similar to one another and therefore are uninformative after repeatedly applying message passing iterations. Intuitively, we can expect the generated embeddings become smooth asymptotically layerwisely, that is each layer of graph convolution generates a smoothed version of embeddings as compared to that generated by the previous layer. Based on this intuition, we propose RandAlign, a stochastic regularization method for graph convolutional networks. The idea of RandAlign is to randomly align the learned embedding for each node with that of the previous layer using randomly interpolation in each graph convolution layer. Through alignment, the smoothness of the generated embeddings is explicitly reduced. To better maintain the benefit yielded by the graph convolution, in the alignment step we introduce to first scale the embedding of the previous layer to the same norm as the generated embedding and then perform random interpolation for aligning the generated embedding. RandAlign is a parameter-free method and can be directly applied without introducing additional trainable weights or hyper-parameters. We experimentally evaluate RandAlign on different graph domain tasks on seven benchmark datasets. The experimental results show that RandAlign is a general method that improves the generalization performance of various graph convolutional network models and also improves the numerical stability of optimization, advancing the state of the art performance for graph representation learning.

cs.LG↗

arXiv2024

Neighbour-level Message Interaction Encoding for Improved Representation Learning on Graphs

Message passing has become the dominant framework in graph representation learning. The essential idea of the message-passing framework is to update node embeddings based on the information aggregated from local neighbours. However, most existing aggregation methods have not encoded neighbour-level message interactions into the aggregated message, resulting in an information lost in embedding generation. And this information lost could be accumulated and become more serious as more layers are added to the graph network model. To address this issue, we propose a neighbour-level message interaction information encoding method for improving graph representation learning. For messages that are aggregated at a node, we explicitly generate an encoding between each message and the rest messages using an encoding function. Then we aggregate these learned encodings and take the sum of the aggregated encoding and the aggregated message to update the embedding for the node. By this way, neighbour-level message interaction information is integrated into the generated node embeddings. The proposed encoding method is a generic method which can be integrated into message-passing graph convolutional networks. Extensive experiments are conducted on six popular benchmark datasets across four highly-demanded tasks. The results show that integrating neighbour-level message interactions achieves improved performance of the base models, advancing the state of the art results for representation learning over graphs.

cs.LG↗

arXiv2024

CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders

Cryo-electron microscopy (cryo-EM) emerges as a pivotal technology for determining the architecture of cells, viruses, and protein assemblies at near-atomic resolution. Traditional particle picking, a key step in cryo-EM, struggles with manual effort and automated methods' sensitivity to low signal-to-noise ratio (SNR) and varied particle orientations. Furthermore, existing neural network (NN)-based approaches often require extensive labeled datasets, limiting their practicality. To overcome these obstacles, we introduce cryoMAE, a novel approach based on few-shot learning that harnesses the capabilities of Masked Autoencoders (MAE) to enable efficient selection of single particles in cryo-EM images. Contrary to conventional NN-based techniques, cryoMAE requires only a minimal set of positive particle images for training yet demonstrates high performance in particle detection. Furthermore, the implementation of a self-cross similarity loss ensures distinct features for particle and background regions, thereby enhancing the discrimination capability of cryoMAE. Experiments on large-scale cryo-EM datasets show that cryoMAE outperforms existing state-of-the-art (SOTA) methods, improving 3D reconstruction resolution by up to 22.4%.

q-bio.BM↗

arXiv2024

RealNet: A Feature Selection Network with Realistic Synthetic Anomaly for Anomaly Detection

Self-supervised feature reconstruction methods have shown promising advances in industrial image anomaly detection and localization. Despite this progress, these methods still face challenges in synthesizing realistic and diverse anomaly samples, as well as addressing the feature redundancy and pre-training bias of pre-trained feature. In this work, we introduce RealNet, a feature reconstruction network with realistic synthetic anomaly and adaptive feature selection. It is incorporated with three key innovations: First, we propose Strength-controllable Diffusion Anomaly Synthesis (SDAS), a diffusion process-based synthesis strategy capable of generating samples with varying anomaly strengths that mimic the distribution of real anomalous samples. Second, we develop Anomaly-aware Features Selection (AFS), a method for selecting representative and discriminative pre-trained feature subsets to improve anomaly detection performance while controlling computational costs. Third, we introduce Reconstruction Residuals Selection (RRS), a strategy that adaptively selects discriminative residuals for comprehensive identification of anomalous regions across multiple levels of granularity. We assess RealNet on four benchmark datasets, and our results demonstrate significant improvements in both Image AUROC and Pixel AUROC compared to the current state-o-the-art methods. The code, data, and models are available at https://github.com/cnulab/RealNet.

cs.CV↗

arXiv2024

Not just Birds and Cars: Generic, Scalable and Explainable Models for Professional Visual Recognition

Some visual recognition tasks are more challenging then the general ones as they require professional categories of images. The previous efforts, like fine-grained vision classification, primarily introduced models tailored to specific tasks, like identifying bird species or car brands with limited scalability and generalizability. This paper aims to design a scalable and explainable model to solve Professional Visual Recognition tasks from a generic standpoint. We introduce a biologically-inspired structure named Pro-NeXt and reveal that Pro-NeXt exhibits substantial generalizability across diverse professional fields such as fashion, medicine, and art-areas previously considered disparate. Our basic-sized Pro-NeXt-B surpasses all preceding task-specific models across 12 distinct datasets within 5 diverse domains. Furthermore, we find its good scaling property that scaling up Pro-NeXt in depth and width with increasing GFlops can consistently enhances its accuracy. Beyond scalability and adaptability, the intermediate features of Pro-NeXt achieve reliable object detection and segmentation performance without extra training, highlighting its solid explainability. We will release the code to foster further research in this area.

cs.CV↗