Daily Papers

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Knowledge Graph Embedding models have become an important area of machine learning.Those models provide a latent representation of entities and relations in a knowledge graph which can then be used in downstream machine learning tasks such as link prediction. The learning process of such models can be performed by contrasting positive and negative triples. While all triples of a KG are considered positive, negative triples are usually not readily available. Therefore, the choice of the sampling method to obtain the negative triples play a crucial role in the performance and effectiveness of Knowledge Graph Embedding models. Most of the current methods fetch negative samples from a random distribution of entities in the underlying Knowledge Graph which also often includes meaningless triples. Other known methods use adversarial techniques or generative neural networks which consequently reduce the efficiency of the process. In this paper, we propose an approach for generating informative negative samples considering available complementary knowledge about entities. Particularly, Pre-trained Language Models are used to form neighborhood clusters by utilizing the distances between entities to obtain representations of symbolic entities via their textual information. Our comprehensive evaluations demonstrate the effectiveness of the proposed approach on benchmark Knowledge Graphs with textual information for the link prediction task.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

Both graph structures and textual information play a critical role in Knowledge Graph Completion (KGC). With the success of Pre-trained Language Models (PLMs) such as BERT, they have been applied for text encoding for KGC. However, the current methods mostly prefer to fine-tune PLMs, leading to huge training costs and limited scalability to larger PLMs. In contrast, we propose to utilize prompts and perform KGC on a frozen PLM with only the prompts trained. Accordingly, we propose a new KGC method named PDKGC with two prompts -- a hard task prompt which is to adapt the KGC task to the PLM pre-training task of token prediction, and a disentangled structure prompt which learns disentangled graph representation so as to enable the PLM to combine more relevant structure knowledge with the text information. With the two prompts, PDKGC builds a textual predictor and a structural predictor, respectively, and their combination leads to more comprehensive entity prediction. Solid evaluation on two widely used KGC datasets has shown that PDKGC often outperforms the baselines including the state-of-the-art, and its components are all effective. Our codes and data are available at https://github.com/genggengcss/PDKGC.

Internet users have been exposing an increasing amount of Personally Identifiable Information (PII) on social media. Such exposed PII can cause severe losses to the users, and informing users of their PII exposure is crucial to raise their privacy awareness and encourage them to take protective measures. To this end, advanced automatic techniques are needed. While Information Extraction (IE) techniques can be used to extract the PII automatically, Deep Learning (DL)-based IE models alleviate the need for feature engineering and further improve the efficiency. However, DL-based IE models often require large-scale labeled data for training, but PII-labeled social media posts are difficult to obtain due to privacy concerns. Also, these models rely heavily on pre-trained word embeddings, while PII in social media often varies in forms and thus has no fixed representations in pre-trained word embeddings. In this study, we propose the Deep Transfer Learning for PII Extraction (DTL-PIIE) framework to address these two limitations. DTL-PIIE transfers knowledge learned from publicly available PII data to social media to address the problem of rare PII-labeled data. Moreover, our framework leverages Graph Convolutional Networks (GCNs) to incorporate syntactic patterns to guide PIIE without relying on pre-trained word embeddings. Evaluation against benchmark IE models indicates that our approach outperforms state-of-the-art DL-based IE models. Our framework can facilitate various applications, such as PII misuse prediction and privacy risk assessment, protecting the privacy of internet users.

Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.

We consider a contrastive learning approach to knowledge graph embedding (KGE) via InfoNCE. For KGE, efficient learning relies on augmenting the training data with negative triples. However, most KGE works overlook the bias from generating the negative triples-false negative triples (factual triples missing from the knowledge graph). We argue that the generation of high-quality (i.e., hard) negative triples might lead to an increase in false negative triples. To mitigate the impact of false negative triples during the generation of hard negative triples, we propose the Hardness and Structure-aware (HaSa) contrastive KGE method, which alleviates the effect of false negative triples while generating the hard negative triples. Experiments show that HaSa improves the performance of InfoNCE-based KGE approaches and achieves state-of-the-art results in several metrics for WN18RR datasets and competitive results for FB15k-237 datasets compared to both classic and pre-trained LM-based KGE methods.

Analogical reasoning is fundamental to human cognition and holds an important place in various fields. However, previous studies mainly focus on single-modal analogical reasoning and ignore taking advantage of structure knowledge. Notably, the research in cognitive psychology has demonstrated that information from multimodal sources always brings more powerful cognitive transfer than single modality sources. To this end, we introduce the new task of multimodal analogical reasoning over knowledge graphs, which requires multimodal reasoning ability with the help of background knowledge. Specifically, we construct a Multimodal Analogical Reasoning dataSet (MARS) and a multimodal knowledge graph MarKG. We evaluate with multimodal knowledge graph embedding and pre-trained Transformer baselines, illustrating the potential challenges of the proposed task. We further propose a novel model-agnostic Multimodal analogical reasoning framework with Transformer (MarT) motivated by the structure mapping theory, which can obtain better performance. Code and datasets are available in https://github.com/zjunlp/MKG_Analogy.

Knowledge graphs (KGs) consist of links that describe relationships between entities. Due to the difficulty of manually enumerating all relationships between entities, automatically completing them is essential for KGs. Knowledge Graph Completion (KGC) is a task that infers unseen relationships between entities in a KG. Traditional embedding-based KGC methods, such as RESCAL, TransE, DistMult, ComplEx, RotatE, HAKE, HousE, etc., infer missing links using only the knowledge from training data. In contrast, the recent Pre-trained Language Model (PLM)-based KGC utilizes knowledge obtained during pre-training. Therefore, PLM-based KGC can estimate missing links between entities by reusing memorized knowledge from pre-training without inference. This approach is problematic because building KGC models aims to infer unseen links between entities. However, conventional evaluations in KGC do not consider inference and memorization abilities separately. Thus, a PLM-based KGC method, which achieves high performance in current KGC evaluations, may be ineffective in practical applications. To address this issue, we analyze whether PLM-based KGC methods make inferences or merely access memorized knowledge. For this purpose, we propose a method for constructing synthetic datasets specified in this analysis and conclude that PLMs acquire the inference abilities required for KGC through pre-training, even though the performance improvements mostly come from textual information of entities and relations.

Pre-trained language representation models (PLMs) cannot well capture factual knowledge from text. In contrast, knowledge embedding (KE) methods can effectively represent the relational facts in knowledge graphs (KGs) with informative entity embeddings, but conventional KE models cannot take full advantage of the abundant textual information. In this paper, we propose a unified model for Knowledge Embedding and Pre-trained LanguagE Representation (KEPLER), which can not only better integrate factual knowledge into PLMs but also produce effective text-enhanced KE with the strong PLMs. In KEPLER, we encode textual entity descriptions with a PLM as their embeddings, and then jointly optimize the KE and language modeling objectives. Experimental results show that KEPLER achieves state-of-the-art performances on various NLP tasks, and also works remarkably well as an inductive KE model on KG link prediction. Furthermore, for pre-training and evaluating KEPLER, we construct Wikidata5M, a large-scale KG dataset with aligned entity descriptions, and benchmark state-of-the-art KE methods on it. It shall serve as a new KE benchmark and facilitate the research on large KG, inductive KE, and KG with text. The source code can be obtained from https://github.com/THU-KEG/KEPLER.

The goal of knowledge graph completion (KGC) is to predict missing links in a KG using trained facts that are already known. In recent, pre-trained language model (PLM) based methods that utilize both textual and structural information are emerging, but their performances lag behind state-of-the-art (SOTA) structure-based methods or some methods lose their inductive inference capabilities in the process of fusing structure embedding to text encoder. In this paper, we propose a novel method to effectively unify structure information and language semantics without losing the power of inductive reasoning. We adopt entity anchors and these anchors and textual description of KG elements are fed together into the PLM-based encoder to learn unified representations. In addition, the proposed method utilizes additional random negative samples which can be reused in the each mini-batch during contrastive learning to learn a generalized entity representations. We verify the effectiveness of the our proposed method through various experiments and analysis. The experimental results on standard benchmark widely used in link prediction task show that the proposed model outperforms existing the SOTA KGC models. Especially, our method show the largest performance improvement on FB15K-237, which is competitive to the SOTA of structure-based KGC methods.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

While Language Models have become workhorses for NLP, their interplay with textual knowledge graphs (KGs) - structured memories of general or domain knowledge - is actively researched. Current embedding methodologies for such graphs typically either (i) linearize graphs for embedding them using sequential Language Models (LMs), which underutilize structural information, or (ii) use Graph Neural Networks (GNNs) to preserve graph structure, while GNNs cannot represent textual features as well as a pre-trained LM could. In this work we introduce a novel language model, the Graph Language Model (GLM), that integrates the strengths of both approaches, while mitigating their weaknesses. The GLM parameters are initialized from a pretrained LM, to facilitate nuanced understanding of individual concepts and triplets. Simultaneously, its architectural design incorporates graph biases, thereby promoting effective knowledge distribution within the graph. Empirical evaluations on relation classification tasks on ConceptNet subgraphs reveal that GLM embeddings surpass both LM- and GNN-based baselines in supervised and zero-shot settings.

We introduce the Scene Language, a visual scene representation that concisely and precisely describes the structure, semantics, and identity of visual scenes. It represents a scene with three key components: a program that specifies the hierarchical and relational structure of entities in the scene, words in natural language that summarize the semantic class of each entity, and embeddings that capture the visual identity of each entity. This representation can be inferred from pre-trained language models via a training-free inference technique, given text or image inputs. The resulting scene can be rendered into images using traditional, neural, or hybrid graphics renderers. Together, this forms a robust, automated system for high-quality 3D and 4D scene generation. Compared with existing representations like scene graphs, our proposed Scene Language generates complex scenes with higher fidelity, while explicitly modeling the scene structures to enable precise control and editing.

Several recent efforts have been devoted to enhancing pre-trained language models (PLMs) by utilizing extra heterogeneous knowledge in knowledge graphs (KGs) and achieved consistent improvements on various knowledge-driven NLP tasks. However, most of these knowledge-enhanced PLMs embed static sub-graphs of KGs ("knowledge context"), regardless of that the knowledge required by PLMs may change dynamically according to specific text ("textual context"). In this paper, we propose a novel framework named Coke to dynamically select contextual knowledge and embed knowledge context according to textual context for PLMs, which can avoid the effect of redundant and ambiguous knowledge in KGs that cannot match the input text. Our experimental results show that Coke outperforms various baselines on typical knowledge-driven NLP tasks, indicating the effectiveness of utilizing dynamic knowledge context for language understanding. Besides the performance improvements, the dynamically selected knowledge in Coke can describe the semantics of text-related knowledge in a more interpretable form than the conventional PLMs. Our source code and datasets will be available to provide more details for Coke.

Graph Convolutional Networks (GCN) have achieved state-of-art results on single text classification tasks like sentiment analysis, emotion detection, etc. However, the performance is achieved by testing and reporting on resource-rich languages like English. Applying GCN for multi-task text classification is an unexplored area. Moreover, training a GCN or adopting an English GCN for Indian languages is often limited by data availability, rich morphological variation, syntax, and semantic differences. In this paper, we study the use of GCN for the Telugu language in single and multi-task settings for four natural language processing (NLP) tasks, viz. sentiment analysis (SA), emotion identification (EI), hate-speech (HS), and sarcasm detection (SAR). In order to evaluate the performance of GCN with one of the Indian languages, Telugu, we analyze the GCN based models with extensive experiments on four downstream tasks. In addition, we created an annotated Telugu dataset, TEL-NLP, for the four NLP tasks. Further, we propose a supervised graph reconstruction method, Multi-Task Text GCN (MT-Text GCN) on the Telugu that leverages to simultaneously (i) learn the low-dimensional word and sentence graph embeddings from word-sentence graph reconstruction using graph autoencoder (GAE) and (ii) perform multi-task text classification using these latent sentence graph embeddings. We argue that our proposed MT-Text GCN achieves significant improvements on TEL-NLP over existing Telugu pretrained word embeddings, and multilingual pretrained Transformer models: mBERT, and XLM-R. On TEL-NLP, we achieve a high F1-score for four NLP tasks: SA (0.84), EI (0.55), HS (0.83) and SAR (0.66). Finally, we show our model's quantitative and qualitative analysis on the four NLP tasks in Telugu.

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

Representation learning is a critical ingredient for natural language processing systems. Recent Transformer language models like BERT learn powerful textual representations, but these models are targeted towards token- and sentence-level training objectives and do not leverage information on inter-document relatedness, which limits their document-level representation power. For applications on scientific documents, such as classification and recommendation, the embeddings power strong performance on end tasks. We propose SPECTER, a new method to generate document-level embedding of scientific documents based on pretraining a Transformer language model on a powerful signal of document-level relatedness: the citation graph. Unlike existing pretrained language models, SPECTER can be easily applied to downstream applications without task-specific fine-tuning. Additionally, to encourage further research on document-level models, we introduce SciDocs, a new evaluation benchmark consisting of seven document-level tasks ranging from citation prediction, to document classification and recommendation. We show that SPECTER outperforms a variety of competitive baselines on the benchmark.

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

Contrastive learning (CL) is a prevalent technique for training embedding models, which pulls semantically similar examples (positives) closer in the representation space while pushing dissimilar ones (negatives) further apart. A key source of negatives are 'in-batch' examples, i.e., positives from other examples in the batch. Effectiveness of such models is hence strongly influenced by the size and quality of training batches. In this work, we propose 'Breaking the Batch Barrier' (B3), a novel batch construction strategy designed to curate high-quality batches for CL. Our approach begins by using a pretrained teacher embedding model to rank all examples in the dataset, from which a sparse similarity graph is constructed. A community detection algorithm is then applied to this graph to identify clusters of examples that serve as strong negatives for one another. The clusters are then used to construct batches that are rich in in-batch negatives. Empirical results on the MMEB multimodal embedding benchmark (36 tasks) demonstrate that our method sets a new state of the art, outperforming previous best methods by +1.3 and +2.9 points at the 7B and 2B model scales, respectively. Notably, models trained with B3 surpass existing state-of-the-art results even with a batch size as small as 64, which is 4-16x smaller than that required by other methods.

Term clustering is important in biomedical knowledge graph construction. Using similarities between terms embedding is helpful for term clustering. State-of-the-art term embeddings leverage pretrained language models to encode terms, and use synonyms and relation knowledge from knowledge graphs to guide contrastive learning. These embeddings provide close embeddings for terms belonging to the same concept. However, from our probing experiments, these embeddings are not sensitive to minor textual differences which leads to failure for biomedical term clustering. To alleviate this problem, we adjust the sampling strategy in pretraining term embeddings by providing dynamic hard positive and negative samples during contrastive learning to learn fine-grained representations which result in better biomedical term clustering. We name our proposed method as CODER++, and it has been applied in clustering biomedical concepts in the newly released Biomedical Knowledge Graph named BIOS.