arXiv subjects

Wen Zhang

Publications and source records attributed to Wen Zhang.

At least 145 records · Page 8Linked to original sources

arXiv2024

Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation

Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. Furthermore, designing a more fine-grained structure representation learning method is urgently needed as PTM is a biological event that occurs at the atom granularity. In this paper, we propose a PTM site prediction method by Coupling of Multi-Granularity structure and Multi-Scale sequence representation, PTM-CMGMS for brevity. Specifically, multigranularity structure-aware representation learning is designed to learn neighborhood structure representations at the amino acid, atom, and whole protein granularity from AlphaFold predicted structures, followed by utilizing contrastive learning to optimize the structure representations.Additionally, multi-scale sequence representation learning is used to extract context sequence information, and motif generated by aligning all context sequences of PTM sites assists the prediction. Extensive experiments on three datasets show that PTM-CMGMS outperforms the state-of-the-art methods.

q-bio.QM↗

arXiv2023

Decreasing emissions and increasing sink capacity to support China in achieving carbon neutrality before 2060

In September 2020, President Xi Jinping announced that China strives to achieve carbon neutrality before 2060. This ambitious and bold commitment was well received by the global community. However, the technology and pathway are not so clear. Here, we conducted an extensive review covering more than 200 published papers and summarized the key technologies to achieve carbon neutrality. We projected sectoral CO2 emissions for 2020-2050 based on our previous studies and published scenarios. We applied a medium sink scenario for terrestrial sinks due to the potential resource competition and included an ocean sink, which has generally not been included in previous estimates. We analyzed and revisited China's historical terrestrial carbon sink capacity from 1980-2020 based on multiple models and a literature review. To achieve neutrality, it is necessary to increase sink capacity and decrease emissions from many sources. On the one hand, critical measures to reduce emissions include decreasing the use of fossil fuels; substantially increasing the proportion of the renewable energy and nuclear energy. On the other hand, the capacity of future carbon sinks is projected to decrease due to the natural evolution of terrestrial ecosystems, and anthropogenic management practices are needed to increase sink capacity, including increasing the forest sinks through national ecological restoration projects and large-scale land greening campaigns; increasing wood harvesting and storage; and developing CCUS. This paper provides basic source and sink data,and established and promising new technologies for decreasing emissions and increasing sinks for use by the scientific community and policy makers.

physics.ao-ph↗

arXiv2023

Generalizing to Unseen Elements: A Survey on Knowledge Extrapolation for Knowledge Graphs

Knowledge graphs (KGs) have become valuable knowledge resources in various applications, and knowledge graph embedding (KGE) methods have garnered increasing attention in recent years. However, conventional KGE methods still face challenges when it comes to handling unseen entities or relations during model testing. To address this issue, much effort has been devoted to various fields of KGs. In this paper, we use a set of general terminologies to unify these methods and refer to them collectively as Knowledge Extrapolation. We comprehensively summarize these methods, classified by our proposed taxonomy, and describe their interrelationships. Additionally, we introduce benchmarks and provide comparisons of these methods based on aspects that are not captured by the taxonomy. Finally, we suggest potential directions for future research.

cs.CL↗

arXiv2023

Structure-CLIP: Towards Scene Graph Knowledge to Enhance Multi-modal Structured Representations

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

cs.CL↗

arXiv2023

Causal Intervention for Measuring Confidence in Drug-Target Interaction Prediction

Identifying and discovering drug-target interactions(DTIs) are vital steps in drug discovery and development. They play a crucial role in assisting scientists in finding new drugs and accelerating the drug development process. Recently, knowledge graph and knowledge graph embedding (KGE) models have made rapid advancements and demonstrated impressive performance in drug discovery. However, such models lack authenticity and accuracy in drug target identification, leading to an increased misjudgment rate and reduced drug development efficiency. To address these issues, we focus on the problem of drug-target interactions, with knowledge mapping as the core technology. Specifically, a causal intervention-based confidence measure is employed to assess the triplet score to improve the accuracy of the drug-target interaction prediction model. Experimental results demonstrate that the developed confidence measurement method based on causal intervention can significantly enhance the accuracy of DTI link prediction, particularly for high-precision models. The predicted results are more valuable in guiding the design and development of subsequent drug development experiments, thereby significantly improving the efficiency of drug development.

q-bio.QM↗

arXiv2023

Sound field reconstruction using neural processes with dynamic kernels

Accurately representing the sound field with the high spatial resolution is critical for immersive and interactive sound field reproduction technology. To minimize experimental effort, data-driven methods have been proposed to estimate sound fields from a small number of discrete observations. In particular, kernel-based methods using Gaussian Processes (GPs) with a covariance function to model spatial correlations have been used for sound field reconstruction. However, these methods have limitations due to the fixed kernels having limited expressiveness, requiring manual identification of optimal kernels for different sound fields. In this work, we propose a new approach that parameterizes GPs using a deep neural network based on Neural Processes (NPs) to reconstruct the magnitude of the sound field. This method has the advantage of dynamically learning kernels from simulated data using an attention mechanism, allowing for greater flexibility and adaptability to the acoustic properties of the sound field. Numerical experiments demonstrate that our proposed approach outperforms current methods in reconstructing accuracy, providing a promising alternative for sound field reconstruction.

eess.AS↗

arXiv2023

CBSiMT: Mitigating Hallucination in Simultaneous Machine Translation with Weighted Prefix-to-Prefix Training

Simultaneous machine translation (SiMT) is a challenging task that requires starting translation before the full source sentence is available. Prefix-to-prefix framework is often applied to SiMT, which learns to predict target tokens using only a partial source prefix. However, due to the word order difference between languages, misaligned prefix pairs would make SiMT models suffer from serious hallucination problems, i.e. target outputs that are unfaithful to source inputs. Such problems can not only produce target tokens that are not supported by the source prefix, but also hinder generating the correct translation by receiving more source words. In this work, we propose a Confidence-Based Simultaneous Machine Translation (CBSiMT) framework, which uses model confidence to perceive hallucination tokens and mitigates their negative impact with weighted prefix-to-prefix training. Specifically, token-level and sentence-level weights are calculated based on model confidence and acted on the loss function. We explicitly quantify the faithfulness of the generated target tokens using the token-level weight, and employ the sentence-level weight to alleviate the disturbance of sentence pairs with serious word order differences on the model. Experimental results on MuST-C English-to-Chinese and WMT15 German-to-English SiMT tasks demonstrate that our method can consistently improve translation quality at most latency regimes, with up to 2 BLEU scores improvement at low latency.

cs.CL↗

arXiv2023

Negative Sampling with Adaptive Denoising Mixup for Knowledge Graph Embedding

Knowledge graph embedding (KGE) aims to map entities and relations of a knowledge graph (KG) into a low-dimensional and dense vector space via contrasting the positive and negative triples. In the training process of KGEs, negative sampling is essential to find high-quality negative triples since KGs only contain positive triples. Most existing negative sampling methods assume that non-existent triples with high scores are high-quality negative triples. However, negative triples sampled by these methods are likely to contain noise. Specifically, they ignore that non-existent triples with high scores might also be true facts due to the incompleteness of KGs, which are usually called false negative triples. To alleviate the above issue, we propose an easily pluggable denoising mixup method called DeMix, which generates high-quality triples by refining sampled negative triples in a self-supervised manner. Given a sampled unlabeled triple, DeMix firstly classifies it into a marginal pseudo-negative triple or a negative triple based on the judgment of the KGE model itself. Secondly, it selects an appropriate mixup partner for the current triple to synthesize a partially positive or a harder negative triple. Experimental results on the knowledge graph completion task show that the proposed DeMix is superior to other negative sampling techniques, ensuring corresponding KGEs a faster convergence and better link prediction results.

cs.AI↗

arXiv2023

DeepKE: A Deep Learning Based Knowledge Extraction Toolkit for Knowledge Base Population

We present an open-source and extensible knowledge extraction toolkit DeepKE, supporting complicated low-resource, document-level and multimodal scenarios in the knowledge base population. DeepKE implements various information extraction tasks, including named entity recognition, relation extraction and attribute extraction. With a unified framework, DeepKE allows developers and researchers to customize datasets and models to extract information from unstructured data according to their requirements. Specifically, DeepKE not only provides various functional modules and model implementation for different tasks and scenarios but also organizes all components by consistent frameworks to maintain sufficient modularity and extensibility. We release the source code at GitHub in https://github.com/zjunlp/DeepKE with Google Colab tutorials and comprehensive documents for beginners. Besides, we present an online system in http://deepke.openkg.cn/EN/re_doc_show.html for real-time extraction of various tasks, and a demo video.

cs.CL↗

arXiv2023

A Comprehensive Study on Knowledge Graph Embedding over Relational Patterns Based on Rule Learning

Knowledge Graph Embedding (KGE) has proven to be an effective approach to solving the Knowledge Graph Completion (KGC) task. Relational patterns which refer to relations with specific semantics exhibiting graph patterns are an important factor in the performance of KGE models. Though KGE models' capabilities are analyzed over different relational patterns in theory and a rough connection between better relational patterns modeling and better performance of KGC has been built, a comprehensive quantitative analysis on KGE models over relational patterns remains absent so it is uncertain how the theoretical support of KGE to a relational pattern contributes to the performance of triples associated to such a relational pattern. To address this challenge, we evaluate the performance of 7 KGE models over 4 common relational patterns on 2 benchmarks, then conduct an analysis in theory, entity frequency, and part-to-whole three aspects and get some counterintuitive conclusions. Finally, we introduce a training-free method Score-based Patterns Adaptation (SPA) to enhance KGE models' performance over various relational patterns. This approach is simple yet effective and can be applied to KGE models without additional training. Our experimental results demonstrate that our method generally enhances performance over specific relational patterns. Our source code is available from GitHub at https://github.com/zjukg/Comprehensive-Study-over-Relational-Patterns.

cs.AI↗

arXiv2023

MACO: A Modality Adversarial and Contrastive Framework for Modality-missing Multi-modal Knowledge Graph Completion

Recent years have seen significant advancements in multi-modal knowledge graph completion (MMKGC). MMKGC enhances knowledge graph completion (KGC) by integrating multi-modal entity information, thereby facilitating the discovery of unobserved triples in the large-scale knowledge graphs (KGs). Nevertheless, existing methods emphasize the design of elegant KGC models to facilitate modality interaction, neglecting the real-life problem of missing modalities in KGs. The missing modality information impedes modal interaction, consequently undermining the model's performance. In this paper, we propose a modality adversarial and contrastive framework (MACO) to solve the modality-missing problem in MMKGC. MACO trains a generator and discriminator adversarially to generate missing modality features that can be incorporated into the MMKGC model. Meanwhile, we design a cross-modal contrastive loss to improve the performance of the generator. Experiments on public benchmarks with further explorations demonstrate that MACO could achieve state-of-the-art results and serve as a versatile framework to bolster various MMKGC models. Our code and benchmark data are available at https://github.com/zjukg/MACO.

cs.CL↗

arXiv2023

Large Language Models and Knowledge Graphs: Opportunities and Challenges

Large Language Models (LLMs) have taken Knowledge Representation -- and the world -- by storm. This inflection point marks a shift from explicit knowledge representation to a renewed focus on the hybrid representation of both explicit knowledge and parametric knowledge. In this position paper, we will discuss some of the common debate points within the community on LLMs (parametric knowledge) and Knowledge Graphs (explicit knowledge) and speculate on opportunities and visions that the renewed focus brings, as well as related research topics and challenges.

cs.AI↗

arXiv2023

Rethinking Uncertainly Missing and Ambiguous Visual Modality in Multi-Modal Entity Alignment

As a crucial extension of entity alignment (EA), multi-modal entity alignment (MMEA) aims to identify identical entities across disparate knowledge graphs (KGs) by exploiting associated visual information. However, existing MMEA approaches primarily concentrate on the fusion paradigm of multi-modal entity features, while neglecting the challenges presented by the pervasive phenomenon of missing and intrinsic ambiguity of visual images. In this paper, we present a further analysis of visual modality incompleteness, benchmarking latest MMEA models on our proposed dataset MMEA-UMVM, where the types of alignment KGs covering bilingual and monolingual, with standard (non-iterative) and iterative training paradigms to evaluate the model performance. Our research indicates that, in the face of modality incompleteness, models succumb to overfitting the modality noise, and exhibit performance oscillations or declines at high rates of missing modality. This proves that the inclusion of additional multi-modal data can sometimes adversely affect EA. To address these challenges, we introduce UMAEA , a robust multi-modal entity alignment approach designed to tackle uncertainly missing and ambiguous visual modalities. It consistently achieves SOTA performance across all 97 benchmark splits, significantly surpassing existing baselines with limited parameters and time consumption, while effectively alleviating the identified limitations of other models. Our code and benchmark data are available at https://github.com/zjukg/UMAEA.

cs.AI↗

arXiv2023

MEAformer: Multi-modal Entity Alignment Transformer for Meta Modality Hybrid

Multi-modal entity alignment (MMEA) aims to discover identical entities across different knowledge graphs (KGs) whose entities are associated with relevant images. However, current MMEA algorithms rely on KG-level modality fusion strategies for multi-modal entity representation, which ignores the variations of modality preferences of different entities, thus compromising robustness against noise in modalities such as blurry images and relations. This paper introduces MEAformer, a multi-modal entity alignment transformer approach for meta modality hybrid, which dynamically predicts the mutual correlation coefficients among modalities for more fine-grained entity-level modality fusion and alignment. Experimental results demonstrate that our model not only achieves SOTA performance in multiple training scenarios, including supervised, unsupervised, iterative, and low-resource settings, but also has a limited number of parameters, efficient runtime, and interpretability. Our code is available at https://github.com/zjukg/MEAformer.

cs.AI↗

arXiv2023

Target-oriented Sentiment Classification with Sequential Cross-modal Semantic Graph

Multi-modal aspect-based sentiment classification (MABSC) is task of classifying the sentiment of a target entity mentioned in a sentence and an image. However, previous methods failed to account for the fine-grained semantic association between the image and the text, which resulted in limited identification of fine-grained image aspects and opinions. To address these limitations, in this paper we propose a new approach called SeqCSG, which enhances the encoder-decoder sentiment classification framework using sequential cross-modal semantic graphs. SeqCSG utilizes image captions and scene graphs to extract both global and local fine-grained image information and considers them as elements of the cross-modal semantic graph along with tokens from tweets. The sequential cross-modal semantic graph is represented as a sequence with a multi-modal adjacency matrix indicating relationships between elements. Experimental results show that the approach outperforms existing methods and achieves state-of-the-art performance on two standard datasets. Further analysis has demonstrated that the model can implicitly learn the correlation between fine-grained information of the image and the text with the given target. Our code is available at https://github.com/zjukg/SeqCSG.

cs.CV↗

arXiv2023

CausE: Towards Causal Knowledge Graph Embedding

Knowledge graph embedding (KGE) focuses on representing the entities and relations of a knowledge graph (KG) into the continuous vector spaces, which can be employed to predict the missing triples to achieve knowledge graph completion (KGC). However, KGE models often only briefly learn structural correlations of triple data and embeddings would be misled by the trivial patterns and noisy links in real-world KGs. To address this issue, we build the new paradigm of KGE in the context of causality and embedding disentanglement. We further propose a Causality-enhanced knowledge graph Embedding (CausE) framework. CausE employs causal intervention to estimate the causal effect of the confounder embeddings and design new training objectives to make stable predictions. Experimental results demonstrate that CausE could outperform the baseline models and achieve state-of-the-art KGC performance. We release our code in https://github.com/zjukg/CausE.

cs.CL↗

arXiv2023

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction.

cs.LG↗

arXiv2023

Exploring Better Text Image Translation with Multimodal Codebook

Text image translation (TIT) aims to translate the source texts embedded in the image to target translations, which has a wide range of applications and thus has important research value. However, current studies on TIT are confronted with two main bottlenecks: 1) this task lacks a publicly available TIT dataset, 2) dominant models are constructed in a cascaded manner, which tends to suffer from the error propagation of optical character recognition (OCR). In this work, we first annotate a Chinese-English TIT dataset named OCRMT30K, providing convenience for subsequent studies. Then, we propose a TIT model with a multimodal codebook, which is able to associate the image with relevant texts, providing useful supplementary information for translation. Moreover, we present a multi-stage training framework involving text machine translation, image-text alignment, and TIT tasks, which fully exploits additional bilingual texts, OCR dataset and our OCRMT30K dataset to train our model. Extensive experiments and in-depth analyses strongly demonstrate the effectiveness of our proposed model and training framework.

cs.CL↗