arXiv subjects

Wen Zhang

Publications and source records attributed to Wen Zhang.

At least 127 records · Page 7Linked to original sources

arXiv2024

Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction

The recent focus on microbes in human medicine highlights their potential role in the genetic framework of diseases. To decode the complex interactions among genes, microbes, and diseases, computational predictions of gene-microbe-disease (GMD) associations are crucial. Existing methods primarily address gene-disease and microbe-disease associations, but the more intricate triple-wise GMD associations remain less explored. In this paper, we propose a Heterogeneous Causal Metapath Graph Neural Network (HCMGNN) to predict GMD associations. HCMGNN constructs a heterogeneous graph linking genes, microbes, and diseases through their pairwise associations, and utilizes six predefined causal metapaths to extract directed causal subgraphs, which facilitate the multi-view analysis of causal relations among three entity types. Within each subgraph, we employ a causal semantic sharing message passing network for node representation learning, coupled with an attentive fusion method to integrate these representations for predicting GMD associations. Our extensive experiments show that HCMGNN effectively predicts GMD associations and addresses association sparsity issue by enhancing the graph's semantics and structure.

cs.LG↗

arXiv2024

Start from Zero: Triple Set Prediction for Automatic Knowledge Graph Completion

Knowledge graph (KG) completion aims to find out missing triples in a KG. Some tasks, such as link prediction and instance completion, have been proposed for KG completion. They are triple-level tasks with some elements in a missing triple given to predict the missing element of the triple. However, knowing some elements of the missing triple in advance is not always a realistic setting. In this paper, we propose a novel graph-level automatic KG completion task called Triple Set Prediction (TSP) which assumes none of the elements in the missing triples is given. TSP is to predict a set of missing triples given a set of known triples. To properly and accurately evaluate this new task, we propose 4 evaluation metrics including 3 classification metrics and 1 ranking metric, considering both the partial-open-world and the closed-world assumptions. Furthermore, to tackle the huge candidate triples for prediction, we propose a novel and efficient subgraph-based method GPHT that can predict the triple set fast. To fairly compare the TSP results, we also propose two types of methods RuleTensor-TSP and KGE-TSP applying the existing rule- and embedding-based methods for TSP as baselines. During experiments, we evaluate the proposed methods on two datasets extracted from Wikidata following the relation-similarity partial-open-world assumption proposed by us, and also create a complete family data set to evaluate TSP results following the closed-world assumption. Results prove that the methods can successfully generate a set of missing triples and achieve reasonable scores on the new task, and GPHT performs better than the baselines with significantly shorter prediction time. The datasets and code for experiments are available at https://github.com/zjukg/GPHT-for-TSP.

cs.AI↗

arXiv2024

Liberal Entity Matching as a Compound AI Toolchain

Entity matching (EM), the task of identifying whether two descriptions refer to the same entity, is essential in data management. Traditional methods have evolved from rule-based to AI-driven approaches, yet current techniques using large language models (LLMs) often fall short due to their reliance on static knowledge and rigid, predefined prompts. In this paper, we introduce Libem, a compound AI system designed to address these limitations by incorporating a flexible, tool-oriented approach. Libem supports entity matching through dynamic tool use, self-refinement, and optimization, allowing it to adapt and refine its process based on the dataset and performance metrics. Unlike traditional solo-AI EM systems, which often suffer from a lack of modularity that hinders iterative design improvements and system optimization, Libem offers a composable and reusable toolchain. This approach aims to contribute to ongoing discussions and developments in AI-driven data management.

cs.DB↗

arXiv2024

Know Your Needs Better: Towards Structured Understanding of Marketer Demands with Analogical Reasoning Augmented LLMs

In this paper, we explore a new way for user targeting, where non-expert marketers could select their target users solely given demands in natural language form. The key to this issue is how to transform natural languages into practical structured logical languages, i.e., the structured understanding of marketer demands. In practical scenarios, the demands of non-expert marketers are often abstract and diverse. Considering the impressive natural language processing ability of large language models (LLMs), we try to leverage LLMs to solve this issue. To stimulate the LLMs' reasoning ability, the chain-of-thought (CoT) prompting method is widely used, but existing methods still have some limitations in our scenario: (1) Previous methods either use simple "Let's think step by step" spells or provide fixed examples in demonstrations without considering compatibility between prompts and concrete questions, making LLMs ineffective when the marketers' demands are abstract and diverse. (2) Previous methods are often implemented in closed-source models or excessively large models, which is not suitable in industrial practical scenarios. Based on these, we propose ARALLM (i.e., Analogical Reasoning Augmented Large Language Models) consisting of two modules: Analogical Reasoning based Prompting and Reasoning-Augmented Multi-Task Model Distillation. Part of our data and code can be found at https://github.com/alipay/Analogic-Reasoning-Augmented-Large-Language-Model.

cs.CL↗

arXiv2024

Knowledgeable Preference Alignment for LLMs in Domain-specific Question Answering

Deploying large language models (LLMs) to real scenarios for domain-specific question answering (QA) is a key thrust for LLM applications, which poses numerous challenges, especially in ensuring that responses are both accommodating to user requirements and appropriately leveraging domain-specific knowledge bases. They are the two major difficulties for LLM application as vanilla fine-tuning falls short of addressing. Combining these requirements, we conceive of them as the requirement for the model's preference to be harmoniously aligned with humans'. Thus, we introduce Knowledgeable Preference AlignmenT (KnowPAT), which constructs two kinds of preference sets to tackle the two issues. Besides, we design a new alignment objective to align the LLM preference with different human preferences uniformly, aiming to optimize LLM performance in real-world, domain-specific QA settings. Adequate experiments and comprehensive comparisons with 15 baseline methods illustrate that our KnowPAT is a superior pipeline for real-scenario domain-specific QA with LLMs.

cs.CL↗

arXiv2024

Improving Paratope and Epitope Prediction by Multi-Modal Contrastive Learning and Interaction Informativeness Estimation

Accurately predicting antibody-antigen binding residues, i.e., paratopes and epitopes, is crucial in antibody design. However, existing methods solely focus on uni-modal data (either sequence or structure), disregarding the complementary information present in multi-modal data, and most methods predict paratopes and epitopes separately, overlooking their specific spatial interactions. In this paper, we propose a novel Multi-modal contrastive learning and Interaction informativeness estimation-based method for Paratope and Epitope prediction, named MIPE, by using both sequence and structure data of antibodies and antigens. MIPE implements a multi-modal contrastive learning strategy, which maximizes representations of binding and non-binding residues within each modality and meanwhile aligns uni-modal representations towards effective modal representations. To exploit the spatial interaction information, MIPE also incorporates an interaction informativeness estimation that computes the estimated interaction matrices between antibodies and antigens, thereby approximating them to the actual ones. Extensive experiments demonstrate the superiority of our method compared to baselines. Additionally, the ablation studies and visualizations demonstrate the superiority of MIPE owing to the better representations acquired through multi-modal contrastive learning and the interaction patterns comprehended by the interaction informativeness estimation.

q-bio.BM↗

arXiv2024

Multi-domain Knowledge Graph Collaborative Pre-training and Prompt Tuning for Diverse Downstream Tasks

Knowledge graphs (KGs) provide reliable external knowledge for a wide variety of AI tasks in the form of structured triples. Knowledge graph pre-training (KGP) aims to pre-train neural networks on large-scale KGs and provide unified interfaces to enhance different downstream tasks, which is a key direction for KG management, maintenance, and applications. Existing works often focus on purely research questions in open domains, or they are not open source due to data security and privacy in real scenarios. Meanwhile, existing studies have not explored the training efficiency and transferability of KGP models in depth. To address these problems, We propose a framework MuDoK to achieve multi-domain collaborative pre-training and efficient prefix prompt tuning to serve diverse downstream tasks like recommendation and text understanding. Our design is a plug-and-play prompt learning approach that can be flexibly adapted to different downstream task backbones. In response to the lack of open-source benchmarks, we constructed a new multi-domain KGP benchmark called KPI with two large-scale KGs and six different sub-domain tasks to evaluate our method and open-sourced it for subsequent research. We evaluated our approach based on constructed KPI benchmarks using diverse backbone models in heterogeneous downstream tasks. The experimental results show that our framework brings significant performance gains, along with its generality, efficiency, and transferability.

cs.CL↗

arXiv2024

Coefficient Decomposition for Spectral Graph Convolution

Spectral graph convolutional network (SGCN) is a kind of graph neural networks (GNN) based on graph signal filters, and has shown compelling expressivity for modeling graph-structured data. Most SGCNs adopt polynomial filters and learn the coefficients from the training data. Many of them focus on which polynomial basis leads to optimal expressive power and models' architecture is little discussed. In this paper, we propose a general form in terms of spectral graph convolution, where the coefficients of polynomial basis are stored in a third-order tensor. Then, we show that the convolution block in existing SGCNs can be derived by performing a certain coefficient decomposition operation on the coefficient tensor. Based on the generalized view, we develop novel spectral graph convolutions CoDeSGC-CP and -Tucker by tensor decomposition CP and Tucker on the coefficient tensor. Extensive experimental results demonstrate that the proposed convolutions achieve favorable performance improvements.

cs.LG↗

arXiv2024

Making Large Language Models Perform Better in Knowledge Graph Completion

Large language model (LLM) based knowledge graph completion (KGC) aims to predict the missing triples in the KGs with LLMs. However, research about LLM-based KGC fails to sufficiently harness LLMs' inference proficiencies, overlooking critical structural information integral to KGs. In this paper, we explore methods to incorporate structural information into the LLMs, with the overarching goal of facilitating structure-aware reasoning. We first discuss on the existing LLM paradigms like in-context learning and instruction tuning, proposing basic structural information injection approaches. Then we propose a Knowledge Prefix Adapter (KoPA) to fulfill this stated goal. The KoPA uses a structural pre-training phase to comprehend the intricate entities and relations within KGs, representing them as structural embeddings. Then KoPA communicates such cross-modal structural information understanding to the LLMs through a knowledge prefix adapter which projects the structural embeddings into the textual space and obtains virtual knowledge tokens positioned as a prefix of the input prompt. We conduct comprehensive experiments and provide incisive analysis concerning how the introduction of cross-modal structural information would be better for LLM's factual knowledge reasoning ability. Our code and data are available at https://github.com/zjukg/KoPA .

cs.CL↗

arXiv2024

Distributed Representations of Entities in Open-World Knowledge Graphs

Graph neural network (GNN)-based methods have demonstrated remarkable performance in various knowledge graph (KG) tasks. However, most existing approaches rely on observing all entities during training, posing a challenge in real-world knowledge graphs where new entities emerge frequently. To address this limitation, we introduce Decentralized Attention Network (DAN). DAN leverages neighbor context as the query vector to score the neighbors of an entity, thereby distributing the entity semantics only among its neighbor embeddings. To effectively train a DAN, we introduce self-distillation, a technique that guides the network in generating desired representations. Theoretical analysis validates the effectiveness of our approach. We implement an end-to-end framework and conduct extensive experiments to evaluate our method, showcasing competitive performance on conventional entity alignment and entity prediction tasks. Furthermore, our method significantly outperforms existing methods in open-world settings.

cs.LG↗

arXiv2024

NativE: Multi-modal Knowledge Graph Completion in the Wild

Multi-modal knowledge graph completion (MMKGC) aims to automatically discover the unobserved factual knowledge from a given multi-modal knowledge graph by collaboratively modeling the triple structure and multi-modal information from entities. However, real-world MMKGs present challenges due to their diverse and imbalanced nature, which means that the modality information can span various types (e.g., image, text, numeric, audio, video) but its distribution among entities is uneven, leading to missing modalities for certain entities. Existing works usually focus on common modalities like image and text while neglecting the imbalanced distribution phenomenon of modal information. To address these issues, we propose a comprehensive framework NativE to achieve MMKGC in the wild. NativE proposes a relation-guided dual adaptive fusion module that enables adaptive fusion for any modalities and employs a collaborative modality adversarial training framework to augment the imbalanced modality information. We construct a new benchmark called WildKGC with five datasets to evaluate our method. The empirical results compared with 21 recent baselines confirm the superiority of our method, consistently achieving state-of-the-art performance across different datasets and various scenarios while keeping efficient and generalizable. Our code and data are released at https://github.com/zjukg/NATIVE

cs.MM↗

arXiv2024

Prompt-fused framework for Inductive Logical Query Answering

Answering logical queries on knowledge graphs (KG) poses a significant challenge for machine reasoning. The primary obstacle in this task stems from the inherent incompleteness of KGs. Existing research has predominantly focused on addressing the issue of missing edges in KGs, thereby neglecting another aspect of incompleteness: the emergence of new entities. Furthermore, most of the existing methods tend to reason over each logical operator separately, rather than comprehensively analyzing the query as a whole during the reasoning process. In this paper, we propose a query-aware prompt-fused framework named Pro-QE, which could incorporate existing query embedding methods and address the embedding of emerging entities through contextual information aggregation. Additionally, a query prompt, which is generated by encoding the symbolic query, is introduced to gather information relevant to the query from a holistic perspective. To evaluate the efficacy of our model in the inductive setting, we introduce two new challenging benchmarks. Experimental results demonstrate that our model successfully handles the issue of unseen entities in logical queries. Furthermore, the ablation study confirms the efficacy of the aggregator and prompt components.

cs.LG↗

arXiv2024

InBox: Recommendation with Knowledge Graph using Interest Box Embedding

Knowledge graphs (KGs) have become vitally important in modern recommender systems, effectively improving performance and interpretability. Fundamentally, recommender systems aim to identify user interests based on historical interactions and recommend suitable items. However, existing works overlook two key challenges: (1) an interest corresponds to a potentially large set of related items, and (2) the lack of explicit, fine-grained exploitation of KG information and interest connectivity. This leads to an inability to reflect distinctions between entities and interests when modeling them in a single way. Additionally, the granularity of concepts in the knowledge graphs used for recommendations tends to be coarse, failing to match the fine-grained nature of user interests. This homogenization limits the precise exploitation of knowledge graph data and interest connectivity. To address these limitations, we introduce a novel embedding-based model called InBox. Specifically, various knowledge graph entities and relations are embedded as points or boxes, while user interests are modeled as boxes encompassing interaction history. Representing interests as boxes enables containing collections of item points related to that interest. We further propose that an interest comprises diverse basic concepts, and box intersection naturally supports concept combination. Across three training steps, InBox significantly outperforms state-of-the-art methods like HAKG and KGIN on recommendation tasks. Further analysis provides meaningful insights into the variable value of different KG data for recommendations. In summary, InBox advances recommender systems through box-based interest and concept modeling for sophisticated knowledge graph exploitation.

cs.IR↗

arXiv2024

Knowledge Graphs Meet Multi-Modal Learning: A Comprehensive Survey

Knowledge Graphs (KGs) play a pivotal role in advancing various AI applications, with the semantic web community's exploration into multi-modal dimensions unlocking new avenues for innovation. In this survey, we carefully review over 300 articles, focusing on KG-aware research in two principal aspects: KG-driven Multi-Modal (KG4MM) learning, where KGs support multi-modal tasks, and Multi-Modal Knowledge Graph (MM4KG), which extends KG studies into the MMKG realm. We begin by defining KGs and MMKGs, then explore their construction progress. Our review includes two primary task categories: KG-aware multi-modal learning tasks, such as Image Classification and Visual Question Answering, and intrinsic MMKG tasks like Multi-modal Knowledge Graph Completion and Entity Alignment, highlighting specific research trajectories. For most of these tasks, we provide definitions, evaluation benchmarks, and additionally outline essential insights for conducting relevant research. Finally, we discuss current challenges and identify emerging trends, such as progress in Large Language Modeling and Multi-modal Pre-training strategies. This survey aims to serve as a comprehensive reference for researchers already involved in or considering delving into KG and multi-modal learning research, offering insights into the evolving landscape of MMKG research and supporting future work.

cs.AI↗

arXiv2024

Revisit and Outstrip Entity Alignment: A Perspective of Generative Models

Recent embedding-based methods have achieved great successes in exploiting entity alignment from knowledge graph (KG) embeddings of multiple modalities. In this paper, we study embedding-based entity alignment (EEA) from a perspective of generative models. We show that EEA shares similarities with typical generative models and prove the effectiveness of the recently developed generative adversarial network (GAN)-based EEA methods theoretically. We then reveal that their incomplete objective limits the capacity on both entity alignment and entity synthesis (i.e., generating new entities). We mitigate this problem by introducing a generative EEA (GEEA) framework with the proposed mutual variational autoencoder (M-VAE) as the generative model. M-VAE enables entity conversion between KGs and generation of new entities from random noise vectors. We demonstrate the power of GEEA with theoretical analysis and empirical experiments on both entity alignment and entity synthesis tasks.

cs.CL↗

arXiv2024

Unleashing the Power of Imbalanced Modality Information for Multi-modal Knowledge Graph Completion

Multi-modal knowledge graph completion (MMKGC) aims to predict the missing triples in the multi-modal knowledge graphs by incorporating structural, visual, and textual information of entities into the discriminant models. The information from different modalities will work together to measure the triple plausibility. Existing MMKGC methods overlook the imbalance problem of modality information among entities, resulting in inadequate modal fusion and inefficient utilization of the raw modality information. To address the mentioned problems, we propose Adaptive Multi-modal Fusion and Modality Adversarial Training (AdaMF-MAT) to unleash the power of imbalanced modality information for MMKGC. AdaMF-MAT achieves multi-modal fusion with adaptive modality weights and further generates adversarial samples by modality-adversarial training to enhance the imbalanced modality information. Our approach is a co-design of the MMKGC model and training strategy which can outperform 19 recent MMKGC methods and achieve new state-of-the-art results on three public MMKGC benchmarks. Our code and data have been released at https://github.com/zjukg/AdaMF-MAT.

cs.AI↗

arXiv2024

Computational Fluid Dynamics: its Carbon Footprint and Role in Carbon Emission Reduction

Turbulent flow physics regulates the aerodynamic properties of lifting surfaces, the thermodynamic efficiency of vapor power systems, and exchanges of natural and anthropogenic quantities between the atmosphere and ocean, to name just a few applications. The dynamics of turbulent flows are described via numerical integration of the non-linear Navier-Stokes equation -- a procedure known as computational fluid dynamics (CFD). At the dawn of scientific computing in the late 1950s, it would be many decades before terms such as ``carbon footprint'' or ``sustainability'' entered the lexicon, and longer still before these themes attained national priority throughout advanced economies. This paper introduces a framework designed to calculate the carbon footprint of CFD and its contribution to carbon emission reduction strategies. We will distinguish between "hero" and "routine" calculations, noting that the carbon footprint of hero calculations is largely determined by the energy source mix utilized. We will also review CFD of flows where turbulence effects are modeled, thus reducing the degrees of freedom. Estimates of the carbon footprint are presented for such fully- and partially-resolved simulations as functions of turbulence activity and calculation year, demonstrating a reduction in carbon emissions by two to five orders of magnitude at practical conditions. Beyond analyzing CO2 emissions, we quantify the benefits of applying CFD towards overall carbon emission reduction. The community's effort to avoid redundant calculations via turbulence databases merits particular attention, with estimates indicating that a single database could potentially reduce CO2 emissions by approximately O(1) million metric tons. Additionally, implementing CFD in the fluids industry has markedly decreased dependence on wind tunnel testing, which is anticipated to lead to CO2 emission reduction.

physics.soc-ph↗

arXiv2024

A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation

Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only utilize sequence or structure information alone, which hinders the performance in generation. In this study, we propose a Multi-Modal Contrastive Diffusion model (MMCD), fusing both sequence and structure modalities in a diffusion framework to co-generate novel peptide sequences and structures. Specifically, MMCD constructs the sequence-modal and structure-modal diffusion models, respectively, and devises a multi-modal contrastive learning strategy with intercontrastive and intra-contrastive in each diffusion timestep, aiming to capture the consistency between two modalities and boost model performance. The inter-contrastive aligns sequences and structures of peptides by maximizing the agreement of their embeddings, while the intra-contrastive differentiates therapeutic and non-therapeutic peptides by maximizing the disagreement of their sequence/structure embeddings simultaneously. The extensive experiments demonstrate that MMCD performs better than other state-of-theart deep generative methods in generating therapeutic peptides across various metrics, including antimicrobial/anticancer score, diversity, and peptide-docking.

q-bio.QM↗