arXiv subjects

Jian Wu

Publications and source records attributed to Jian Wu.

At least 181 records · Page 10Linked to original sources

arXiv2024

ProtCLIP: Function-Informed Protein Multi-Modal Learning

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.

cs.LG↗

arXiv2024

S$^2$ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning

Antibodies safeguard our health through their precise and potent binding to specific antigens, demonstrating promising therapeutic efficacy in the treatment of numerous diseases, including COVID-19. Recent advancements in biomedical language models have shown the great potential to interpret complex biological structures and functions. However, existing antibody specific models have a notable limitation that they lack explicit consideration for antibody structural information, despite the fact that both 1D sequence and 3D structure carry unique and complementary insights into antibody behavior and functionality. This paper proposes Sequence-Structure multi-level pre-trained Antibody Language Model (S$^2$ALM), combining holistic sequential and structural information in one unified, generic antibody foundation model. We construct a hierarchical pre-training paradigm incorporated with two customized multi-level training objectives to facilitate the modeling of comprehensive antibody representations. S$^2$ALM's representation space uncovers inherent functional binding mechanisms, biological evolution properties and structural interaction patterns. Pre-trained over 75 million sequences and 11.7 million structures, S$^2$ALM can be adopted for diverse downstream tasks: accurately predicting antigen-antibody binding affinities, precisely distinguishing B cell maturation stages, identifying antibody crucial binding positions, and specifically designing novel coronavirus-binding antibodies. Remarkably, S$^2$ALM outperforms well-established and renowned baselines and sets new state-of-the-art performance across extensive antibody specific understanding and generation tasks. S$^2$ALM's ability to model comprehensive and generalized representations further positions its potential to advance real-world therapeutic antibody development, potentially addressing unmet academic, industrial, and clinical needs.

cs.LG↗

arXiv2024

Prediction of Mode Structure Using A Novel Physics-Embedded Neural ODE Method

We designed a new artificial neural network by modifying the neural ordinary differential equation (NODE) framework to successfully predict the time evolution of the 2D mode profile in both the linear growth and nonlinear saturated stages. Starting from the magnetohydrodynamic (MHD) equations, simplifying assumptions were applied based on physical properties and symmetry considerations of the energetic-particle-driven geodesic acoustic mode (EGAM) to reduce complexity. Our approach embeds physical laws directly into the neural network architecture by exposing latent differential states, enabling the model to capture complex features in the nonlinear saturated stage that are difficult to describe analytically, and thus, the new artificial neural network is named as ExpNODE (Exposed latent state Neural ODE). ExpNODE was evaluated using a data set generated from first-principles simulations of the EGAM instability, focusing on the pre-saturated stage and the nonlinear saturated stage where the mode properties are most complex. Compared to state-of-the-art models such as ConvLSTM, ExpNODE with physical information not only achieved lower test loss but also converged faster during training. Specifically, it outperformed ConvLSTM method in both the 20-step and 40-step prediction horizons, demonstrating superior accuracy and efficiency. Additionally, the model exhibited strong generalization capabilities, accurately predicting mode profiles outside the training data set. Visual comparisons between model predictions and ground truth data showed that ExpNODE with physical information closely captured detailed features and asymmetries inherent in the EGAM dynamics that were not adequately captured by other models. These results suggest that integrating physical knowledge into neural ODE frameworks enhances their performance, and provides a powerful tool for modeling complex plasma phenomena.

physics.plasm-ph↗

arXiv2024

PX2Tooth: Reconstructing the 3D Point Cloud Teeth from a Single Panoramic X-ray

Reconstructing the 3D anatomical structures of the oral cavity, which originally reside in the cone-beam CT (CBCT), from a single 2D Panoramic X-ray(PX) remains a critical yet challenging task, as it can effectively reduce radiation risks and treatment costs during the diagnostic in digital dentistry. However, current methods are either error-prone or only trained/evaluated on small-scale datasets (less than 50 cases), resulting in compromised trustworthiness. In this paper, we propose PX2Tooth, a novel approach to reconstruct 3D teeth using a single PX image with a two-stage framework. First, we design the PXSegNet to segment the permanent teeth from the PX images, providing clear positional, morphological, and categorical information for each tooth. Subsequently, we design a novel tooth generation network (TGNet) that learns to transform random point clouds into 3D teeth. TGNet integrates the segmented patch information and introduces a Prior Fusion Module (PFM) to enhance the generation quality, especially in the root apex region. Moreover, we construct a dataset comprising 499 pairs of CBCT and Panoramic X-rays. Extensive experiments demonstrate that PX2Tooth can achieve an Intersection over Union (IoU) of 0.793, significantly surpassing previous methods, underscoring the great potential of artificial intelligence in digital dentistry.

cs.CV↗

arXiv2024

Bridge-IF: Learning Inverse Protein Folding with Markov Bridges

Inverse protein folding is a fundamental task in computational protein design, which aims to design protein sequences that fold into the desired backbone structures. While the development of machine learning algorithms for this task has seen significant success, the prevailing approaches, which predominantly employ a discriminative formulation, frequently encounter the error accumulation issue and often fail to capture the extensive variety of plausible sequences. To fill these gaps, we propose Bridge-IF, a generative diffusion bridge model for inverse folding, which is designed to learn the probabilistic dependency between the distributions of backbone structures and protein sequences. Specifically, we harness an expressive structure encoder to propose a discrete, informative prior derived from structures, and establish a Markov bridge to connect this prior with native sequences. During the inference stage, Bridge-IF progressively refines the prior sequence, culminating in a more plausible design. Moreover, we introduce a reparameterization perspective on Markov bridge models, from which we derive a simplified loss function that facilitates more effective training. We also modulate protein language models (PLMs) with structural conditions to precisely approximate the Markov bridge process, thereby significantly enhancing generation performance while maintaining parameter-efficient training. Extensive experiments on well-established benchmarks demonstrate that Bridge-IF predominantly surpasses existing baselines in sequence recovery and excels in the design of plausible proteins with high foldability. The code is available at https://github.com/violet-sto/Bridge-IF.

cs.LG↗

arXiv2024

Joint Explicit and Implicit Cross-Modal Interaction Network for Anterior Chamber Inflammation Diagnosis

Uveitis demands the precise diagnosis of anterior chamber inflammation (ACI) for optimal treatment. However, current diagnostic methods only rely on a limited single-modal disease perspective, which leads to poor performance. In this paper, we investigate a promising yet challenging way to fuse multimodal data for ACI diagnosis. Notably, existing fusion paradigms focus on empowering implicit modality interactions (i.e., self-attention and its variants), but neglect to inject explicit modality interactions, especially from clinical knowledge and imaging property. To this end, we propose a jointly Explicit and implicit Cross-Modal Interaction Network (EiCI-Net) for Anterior Chamber Inflammation Diagnosis that uses anterior segment optical coherence tomography (AS-OCT) images, slit-lamp images, and clinical data jointly. Specifically, we first develop CNN-Based Encoders and Tabular Processing Module (TPM) to extract efficient feature representations in different modalities. Then, we devise an Explicit Cross-Modal Interaction Module (ECIM) to generate attention maps as a kind of explicit clinical knowledge based on the tabular feature maps, then integrated them into the slit-lamp feature maps, allowing the CNN-Based Encoder to focus on more effective informativeness of the slit-lamp images. After that, the Implicit Cross-Modal Interaction Module (ICIM), a transformer-based network, further implicitly enhances modality interactions. Finally, we construct a considerable real-world dataset from our collaborative hospital and conduct sufficient experiments to demonstrate the superior performance of our proposed EiCI-Net compared with the state-of-the-art classification methods in various metrics.

cs.CV↗

arXiv2024

Enhancing Semi-Supervised Learning via Representative and Diverse Sample Selection

Semi-Supervised Learning (SSL) has become a preferred paradigm in many deep learning tasks, which reduces the need for human labor. Previous studies primarily focus on effectively utilising the labelled and unlabeled data to improve performance. However, we observe that how to select samples for labelling also significantly impacts performance, particularly under extremely low-budget settings. The sample selection task in SSL has been under-explored for a long time. To fill in this gap, we propose a Representative and Diverse Sample Selection approach (RDSS). By adopting a modified Frank-Wolfe algorithm to minimise a novel criterion $α$-Maximum Mean Discrepancy ($α$-MMD), RDSS samples a representative and diverse subset for annotation from the unlabeled data. We demonstrate that minimizing $α$-MMD enhances the generalization ability of low-budget learning. Experimental results show that RDSS consistently improves the performance of several popular SSL frameworks and outperforms the state-of-the-art sample selection approaches used in Active Learning (AL) and Semi-Supervised Active Learning (SSAL), even with constrained annotation budgets.

cs.LG↗

arXiv2024

KA$^2$ER: Knowledge Adaptive Amalgamation of ExpeRts for Medical Images Segmentation

Recently, many foundation models for medical image analysis such as MedSAM, SwinUNETR have been released and proven to be useful in multiple tasks. However, considering the inherent heterogeneity and inhomogeneity of real-world medical data, directly applying these models to specific medical image segmentation tasks often leads to negative domain shift effects, which can severely weaken the model's segmentation capabilities. To this end, we propose an adaptive amalgamation knowledge framework that aims to train a versatile foundation model to handle the joint goals of multiple expert models, each specialized for a distinct task. Specifically, we first train an nnUNet-based expert model for each task, and reuse the pre-trained SwinUNTER as the target foundation model. Then, the input data for all challenging tasks are encoded in the foundation model and the expert models, respectively, and their backbone features are jointly projected into the adaptive amalgamation layer. Within the hidden layer, the hierarchical attention mechanisms are designed to achieve adaptive merging of the target model to the hidden layer feature knowledge of all experts, which significantly reduces the domain shift arising from the inter-task differences. Finally, the gold amalgamated features and the prompt features are fed into the mask decoder to obtain the segmentation results. Extensive experiments conducted in these challenging tasks demonstrate the effectiveness and adaptability of our foundation model for real-world medical image segmentation.

cs.CV↗

arXiv2024

Cofca: A Step-Wise Counterfactual Multi-hop QA benchmark

While Large Language Models (LLMs) excel in question-answering (QA) tasks, their real reasoning abilities on multiple evidence retrieval and integration on Multi-hop QA tasks remain less explored. Firstly, LLMs sometimes generate answers that rely on internal memory rather than retrieving evidence and reasoning in the given context, which brings concerns about the evaluation quality of real reasoning abilities. Although previous counterfactual QA benchmarks can separate the internal memory of LLMs, they focus solely on final QA performance, which is insufficient for reporting LLMs' real reasoning abilities. Because LLMs are expected to engage in intricate reasoning processes that involve evidence retrieval and answering a series of sub-questions from given passages. Moreover, current factual Multi-hop QA (MHQA) benchmarks are annotated on open-source corpora such as Wikipedia, although useful for multi-step reasoning evaluation, they show limitations due to the potential data contamination in LLMs' pre-training stage. To address these issues, we introduce a Step-wise Counterfactual benchmark (CofCA), a novel evaluation benchmark consisting of factual data and counterfactual data that reveals LLMs' real reasoning abilities on multi-step reasoning and reasoning chain evaluation. Our experimental results reveal a significant performance gap of several LLMs between Wikipedia-based factual data and counterfactual data, deeming data contamination issues in existing benchmarks. Moreover, we observe that LLMs usually bypass the correct reasoning chain, showing an inflated multi-step reasoning performance. We believe that our CofCA benchmark will enhance and facilitate the evaluations of trustworthy LLMs.

cs.CL↗

arXiv2024

MedThink: Explaining Medical Visual Question Answering via Multimodal Decision-Making Rationale

Medical Visual Question Answering (MedVQA), which offers language responses to image-based medical inquiries, represents a challenging task and significant advancement in healthcare. It assists medical experts to swiftly interpret medical images, thereby enabling faster and more accurate diagnoses. However, the model interpretability and transparency of existing MedVQA solutions are often limited, posing challenges in understanding their decision-making processes. To address this issue, we devise a semi-automated annotation process to streamline data preparation and build new benchmark MedVQA datasets R-RAD, R-SLAKE and R-Path. These datasets provide intermediate medical decision-making rationales generated by multimodal large language models and human annotations for question-answering pairs in existing MedVQA datasets, i.e., VQA-RAD, SLAKE and PathVQA. Moreover, we design a novel framework, MedThink, which finetunes lightweight pretrained generative models by incorporating medical decision-making rationales. MedThink includes three distinct strategies to generate decision outcomes and corresponding rationales, thereby clearly showcasing the medical decision-making process during reasoning. Our comprehensive experiments show that our method achieves an accuracy of 83.5% on R-RAD, 86.3% on R-SLAKE and 87.2% on R-Path. These results significantly exceed those of existing state-of-the-art models with comparable parameters. Datasets and code will be released.

cs.CV↗

arXiv2024

Unraveling Babel: Exploring Multilingual Activation Patterns of LLMs and Their Applications

Recently, large language models (LLMs) have achieved tremendous breakthroughs in the field of NLP, but still lack understanding of their internal neuron activities when processing different languages. We designed a method to convert dense LLMs into fine-grained MoE architectures, and then visually studied the multilingual activation patterns of LLMs through expert activation frequency heatmaps. Through comprehensive experiments on different model families, different model sizes, and different variants, we analyzed the similarities and differences in the internal neuron activation patterns of LLMs when processing different languages. Specifically, we investigated the distribution of high-frequency activated experts, multilingual shared experts, whether multilingual activation patterns are related to language families, and the impact of instruction tuning on activation patterns. We further explored leveraging the discovered differences in expert activation frequencies to guide sparse activation and pruning. Experimental results demonstrated that our method significantly outperformed random expert pruning and even exceeded the performance of unpruned models in some languages. Additionally, we found that configuring different pruning rates for different layers based on activation level differences could achieve better results. Our findings reveal the multilingual processing mechanisms within LLMs and utilize these insights to offer new perspectives for applications such as sparse activation and model pruning.

cs.CL↗

arXiv2024

[Re] Network Deconvolution

Our work aims to reproduce the set of findings published in "Network Deconvolution" by Ye et al. (2020)[1]. That paper proposes an optimization technique for model training in convolutional neural networks. The proposed technique "network deconvolution" is used in convolutional neural networks to remove pixel-wise and channel-wise correlations before data is fed into each layer. In particular, we interrogate the validity of the authors' claim that using network deconvolution instead of batch normalization improves deep learning model performance. Our effort confirms the validity of this claim, successfully reproducing the results reported in Tables 1 and 2 of the original paper. Our study involved 367 unique experiments across multiple architectures, datasets, and hyper parameter configurations. For Table 1, while there were some minor deviations in accuracy when compared to the original values (within 10%), the overall trend was consistent with the original study's findings when training the models with epochs 20 and 100. For Table 2, all 14 reproduced values were consistent with the original values. Additionally, we document the training and testing times for each architecture in Table 1 with 1, 20, and 100 epoch settings for both CIFAR-10 and CIFAR-100 datasets. We document the total execution times for Table 2 architectures with the ImageNet dataset. The data and software used for this reproducibility study are publicly available at https://github.com/lamps-lab/rep-network-deconvolution.

cs.CV↗

arXiv2024

GraphRevisedIE: Multimodal Information Extraction with Graph-Revised Network

Key information extraction (KIE) from visually rich documents (VRD) has been a challenging task in document intelligence because of not only the complicated and diverse layouts of VRD that make the model hard to generalize but also the lack of methods to exploit the multimodal features in VRD. In this paper, we propose a light-weight model named GraphRevisedIE that effectively embeds multimodal features such as textual, visual, and layout features from VRD and leverages graph revision and graph convolution to enrich the multimodal embedding with global context. Extensive experiments on multiple real-world datasets show that GraphRevisedIE generalizes to documents of varied layouts and achieves comparable or better performance compared to previous KIE methods. We also publish a business license dataset that contains both real-life and synthesized documents to facilitate research of document KIE.

cs.IR↗

arXiv2024

Multi-rater Prompting for Ambiguous Medical Image Segmentation

Multi-rater annotations commonly occur when medical images are independently annotated by multiple experts (raters). In this paper, we tackle two challenges arisen in multi-rater annotations for medical image segmentation (called ambiguous medical image segmentation): (1) How to train a deep learning model when a group of raters produces a set of diverse but plausible annotations, and (2) how to fine-tune the model efficiently when computation resources are not available for re-training the entire model on a different dataset domain. We propose a multi-rater prompt-based approach to address these two challenges altogether. Specifically, we introduce a series of rater-aware prompts that can be plugged into the U-Net model for uncertainty estimation to handle multi-annotation cases. During the prompt-based fine-tuning process, only 0.3% of learnable parameters are required to be updated comparing to training the entire model. Further, in order to integrate expert consensus and disagreement, we explore different multi-rater incorporation strategies and design a mix-training strategy for comprehensive insight learning. Extensive experiments verify the effectiveness of our new approach for ambiguous medical image segmentation on two public datasets while alleviating the heavy burden of model re-training.

cs.CV↗

arXiv2024

Simple but Efficient: A Multi-Scenario Nearline Retrieval Framework for Recommendation on Taobao

In recommendation systems, the matching stage is becoming increasingly critical, serving as the upper limit for the entire recommendation process. Recently, some studies have started to explore the use of multi-scenario information for recommendations, such as model-based and data-based approaches. However, the matching stage faces significant challenges due to the need for ultra-large-scale retrieval and meeting low latency requirements. As a result, the methods applied at this stage (collaborative filtering and two-tower models) are often designed to be lightweight, hindering the full utilization of extensive information. On the other hand, the ranking stage features the most sophisticated models with the strongest scoring capabilities, but due to the limited screen size of mobile devices, most of the ranked results may not gain exposure or be displayed. In this paper, we introduce an innovative multi-scenario nearline retrieval framework. It operates by harnessing ranking logs from various scenarios through Flink, allowing us to incorporate finely ranked results from other scenarios into our matching stage in near real-time. Besides, we propose a streaming scoring module, which selects a crucial subset from the candidate pool. Implemented on the "Guess You Like" (homepage of the Taobao APP), China's premier e-commerce platform, our method has shown substantial improvements-most notably, a 5% uptick in product transactions. Furthermore, the proposed approach is not only model-free but also highly efficient, suggesting it can be quickly implemented in diverse scenarios and demonstrate promising performance.

cs.IR↗

arXiv2024

TeleOR: Real-time Telemedicine System for Full-Scene Operating Room

The advent of telemedicine represents a transformative development in leveraging technology to extend the reach of specialized medical expertise to remote surgeries, a field where the immediacy of expert guidance is paramount. However, the intricate dynamics of Operating Room (OR) scene pose unique challenges for telemedicine, particularly in achieving high-fidelity, real-time scene reconstruction and transmission amidst obstructions and bandwidth limitations. This paper introduces TeleOR, a pioneering system designed to address these challenges through real-time OR scene reconstruction for Tele-intervention. TeleOR distinguishes itself with three innovative approaches: dynamic self-calibration, which leverages inherent scene features for calibration without the need for preset markers, allowing for obstacle avoidance and real-time camera adjustment; selective OR reconstruction, focusing on dynamically changing scene segments to reduce reconstruction complexity; and viewport-adaptive transmission, optimizing data transmission based on real-time client feedback to efficiently deliver high-quality 3D reconstructions within bandwidth constraints. Comprehensive experiments on the 4D-OR surgical scene dataset demostrate the superiority and applicability of TeleOR, illuminating the potential to revolutionize tele-interventions by overcoming the spatial and technical barriers inherent in remote surgical guidance.

eess.IV↗

arXiv2024

Multi-Modal CLIP-Informed Protein Editing

Proteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.

cs.AI↗

arXiv2024

ExcelFormer: A neural network surpassing GBDTs on tabular data

Data organized in tabular format is ubiquitous in real-world applications, and users often craft tables with biased feature definitions and flexibly set prediction targets of their interests. Thus, a rapid development of a robust, effective, dataset-versatile, user-friendly tabular prediction approach is highly desired. While Gradient Boosting Decision Trees (GBDTs) and existing deep neural networks (DNNs) have been extensively utilized by professional users, they present several challenges for casual users, particularly: (i) the dilemma of model selection due to their different dataset preferences, and (ii) the need for heavy hyperparameter searching, failing which their performances are deemed inadequate. In this paper, we delve into this question: Can we develop a deep learning model that serves as a "sure bet" solution for a wide range of tabular prediction tasks, while also being user-friendly for casual users? We delve into three key drawbacks of deep tabular models, encompassing: (P1) lack of rotational variance property, (P2) large data demand, and (P3) over-smooth solution. We propose ExcelFormer, addressing these challenges through a semi-permeable attention module that effectively constrains the influence of less informative features to break the DNNs' rotational invariance property (for P1), data augmentation approaches tailored for tabular data (for P2), and attentive feedforward network to boost the model fitting capability (for P3). These designs collectively make ExcelFormer a "sure bet" solution for diverse tabular datasets. Extensive and stratified experiments conducted on real-world datasets demonstrate that our model outperforms previous approaches across diverse tabular data prediction tasks, and this framework can be friendly to casual users, offering ease of use without the heavy hyperparameter tuning.

cs.LG↗