Yuan He

Yuan He, Jiaoyan Chen, Ernesto Jiménez-Ruiz et al. · oxford

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

Chang Liu, Yinpeng Dong, Wenzhao Xiang et al. · microsoft-research, tsinghua

The robustness of deep neural networks is usually lacking under adversarial examples, common corruptions, and distribution shifts, which becomes an important research problem in the development of deep learning. Although new deep learning methods and robustness improvement techniques have been constantly proposed, the robustness evaluations of existing methods are often inadequate due to their rapid development, diverse noise patterns, and simple evaluation metrics. Without thorough robustness evaluations, it is hard to understand the advances in the field and identify the effective methods. In this paper, we establish a comprehensive robustness benchmark called \textbf{ARES-Bench} on the image classification task. In our benchmark, we evaluate the robustness of 55 typical deep learning models on ImageNet with diverse architectures (e.g., CNNs, Transformers) and learning algorithms (e.g., normal supervised training, pre-training, adversarial training) under numerous adversarial attacks and out-of-distribution (OOD) datasets. Using robustness curves as the major evaluation criteria, we conduct large-scale experiments and draw several important findings, including: 1) there is an inherent trade-off between adversarial and natural robustness for the same model architecture; 2) adversarial training effectively improves adversarial robustness, especially when performed on Transformer architectures; 3) pre-training significantly improves natural robustness based on more training data or self-supervised learning. Based on ARES-Bench, we further analyze the training tricks in large-scale adversarial training on ImageNet. By designing the training settings accordingly, we achieve the new state-of-the-art adversarial robustness. We have made the benchmarking results and code platform publicly available.

Zitai Wang, Qianqian Xu, Zhiyong Yang et al.

Traditional machine learning follows a close-set assumption that the training and test set share the same label space. While in many practical scenarios, it is inevitable that some test samples belong to unknown classes (open-set). To fix this issue, Open-Set Recognition (OSR), whose goal is to make correct predictions on both close-set samples and open-set samples, has attracted rising attention. In this direction, the vast majority of literature focuses on the pattern of open-set samples. However, how to evaluate model performance in this challenging task is still unsolved. In this paper, a systematic analysis reveals that most existing metrics are essentially inconsistent with the aforementioned goal of OSR: (1) For metrics extended from close-set classification, such as Open-set F-score, Youden's index, and Normalized Accuracy, a poor open-set prediction can escape from a low performance score with a superior close-set prediction. (2) Novelty detection AUC, which measures the ranking performance between close-set and open-set samples, ignores the close-set performance. To fix these issues, we propose a novel metric named OpenAUC. Compared with existing metrics, OpenAUC enjoys a concise pairwise formulation that evaluates open-set performance and close-set performance in a coupling manner. Further analysis shows that OpenAUC is free from the aforementioned inconsistency properties. Finally, an end-to-end learning method is proposed to minimize the OpenAUC risk, and the experimental results on popular benchmark datasets speak to its effectiveness. Project Page: https://github.com/wang22ti/OpenAUC.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new BioML track at OAEI 2022.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

Integrating deep learning techniques, particularly language models (LMs), with knowledge representation techniques like ontologies has raised widespread attention, urging the need of a platform that supports both paradigms. Although packages such as OWL API and Jena offer robust support for basic ontology processing features, they lack the capability to transform various types of information within ontologies into formats suitable for downstream deep learning-based applications. Moreover, widely-used ontology APIs are primarily Java-based while deep learning frameworks like PyTorch and Tensorflow are mainly for Python programming. To address the needs, we present DeepOnto, a Python package designed for ontology engineering with deep learning. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to incorporate other essential components including reasoning, verbalisation, normalisation, taxonomy, projection, and more. Building on this module, DeepOnto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methods, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of DeepOnto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).

Hang Dong, Jiaoyan Chen, Yuan He et al. · oxford

Discovering entity mentions that are out of a Knowledge Base (KB) from texts plays a critical role in KB maintenance, but has not yet been fully explored. The current methods are mostly limited to the simple threshold-based approach and feature-based classification, and the datasets for evaluation are relatively rare. We propose BLINKout, a new BERT-based Entity Linking (EL) method which can identify mentions that do not have corresponding KB entities by matching them to a special NIL entity. To better utilize BERT, we propose new techniques including NIL entity representation and classification, with synonym enhancement. We also apply KB Pruning and Versioning strategies to automatically construct out-of-KB datasets from common in-KB EL datasets. Results on five datasets of clinical notes, biomedical publications, and Wikipedia articles in various domains show the advantages of BLINKout over existing methods to identify out-of-KB mentions for the medical ontologies, UMLS, SNOMED CT, and the general KB, WikiData.

Hang Dong, Jiaoyan Chen, Yuan He et al. · oxford

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Shilong Bao, Qianqian Xu, Zhiyong Yang et al.

Collaborative Metric Learning (CML) has recently emerged as a popular method in recommendation systems (RS), closing the gap between metric learning and collaborative filtering. Following the convention of RS, existing practices exploit unique user representation in their model design. This paper focuses on a challenging scenario where a user has multiple categories of interests. Under this setting, the unique user representation might induce preference bias, especially when the item category distribution is imbalanced. To address this issue, we propose a novel method called \textit{Diversity-Promoting Collaborative Metric Learning} (DPCML), with the hope of considering the commonly ignored minority interest of the user. The key idea behind DPCML is to introduce a set of multiple representations for each user in the system where users' preference toward an item is aggregated by taking the minimum item-user distance among their embedding set. Specifically, we instantiate two effective assignment strategies to explore a proper quantity of vectors for each user. Meanwhile, a \textit{Diversity Control Regularization Scheme} (DCRS) is developed to accommodate the multi-vector representation strategy better. Theoretically, we show that DPCML could induce a smaller generalization error than traditional CML. Furthermore, we notice that CML-based approaches usually require \textit{negative sampling} to reduce the heavy computational burden caused by the pairwise objective therein. In this paper, we reveal the fundamental limitation of the widely adopted hard-aware sampling from the One-Way Partial AUC (OPAUC) perspective and then develop an effective sampling alternative for the CML-based paradigm. Finally, comprehensive experiments over a range of benchmark datasets speak to the efficacy of DPCML. Code are available at \url{https://github.com/statusrank/LibCML}.

Shilong Bao, Qianqian Xu, Zhiyong Yang et al.

Collaborative Metric Learning (CML) has recently emerged as a popular method in recommendation systems (RS), closing the gap between metric learning and Collaborative Filtering. Following the convention of RS, existing methods exploit unique user representation in their model design. This paper focuses on a challenging scenario where a user has multiple categories of interests. Under this setting, we argue that the unique user representation might induce preference bias, especially when the item category distribution is imbalanced. To address this issue, we propose a novel method called \textit{Diversity-Promoting Collaborative Metric Learning} (DPCML), with the hope of considering the commonly ignored minority interest of the user. The key idea behind DPCML is to include a multiple set of representations for each user in the system. Based on this embedding paradigm, user preference toward an item is aggregated from different embeddings by taking the minimum item-user distance among the user embedding set. Furthermore, we observe that the diversity of the embeddings for the same user also plays an essential role in the model. To this end, we propose a \textit{diversity control regularization} term to accommodate the multi-vector representation strategy better. Theoretically, we show that DPCML could generalize well to unseen test data by tackling the challenge of the annoying operation that comes from the minimum value. Experiments over a range of benchmark datasets speak to the efficacy of DPCML.

Wenzheng Hou, Qianqian Xu, Zhiyong Yang et al.

It is well-known that deep learning models are vulnerable to adversarial examples. Existing studies of adversarial training have made great progress against this challenge. As a typical trait, they often assume that the class distribution is overall balanced. However, long-tail datasets are ubiquitous in a wide spectrum of applications, where the amount of head class instances is larger than the tail classes. Under such a scenario, AUC is a much more reasonable metric than accuracy since it is insensitive toward class distribution. Motivated by this, we present an early trial to explore adversarial training methods to optimize AUC. The main challenge lies in that the positive and negative examples are tightly coupled in the objective function. As a direct result, one cannot generate adversarial examples without a full scan of the dataset. To address this issue, based on a concavity regularization scheme, we reformulate the AUC optimization problem as a saddle point problem, where the objective becomes an instance-wise function. This leads to an end-to-end training protocol. Furthermore, we provide a convergence guarantee of the proposed algorithm. Our analysis differs from the existing studies since the algorithm is asked to generate adversarial examples by calculating the gradient of a min-max problem. Finally, the extensive experimental results show the performance and robustness of our algorithm in three long-tail datasets.

Zhenyu Li, Zhipeng Zhang, Heng Fan et al.

In this paper, we improve the challenging monocular 3D object detection problem with a general semi-supervised framework. Specifically, having observed that the bottleneck of this task lies in lacking reliable and informative samples to train the detector, we introduce a novel, simple, yet effective `Augment and Criticize' framework that explores abundant informative samples from unlabeled data for learning more robust detection models. In the `Augment' stage, we present the Augmentation-based Prediction aGgregation (APG), which aggregates detections from various automatically learned augmented views to improve the robustness of pseudo label generation. Since not all pseudo labels from APG are beneficially informative, the subsequent `Criticize' phase is presented. In particular, we introduce the Critical Retraining Strategy (CRS) that, unlike simply filtering pseudo labels using a fixed threshold (e.g., classification score) as in 2D semi-supervised tasks, leverages a learnable network to evaluate the contribution of unlabeled images at different training timestamps. This way, the noisy samples prohibitive to model evolution could be effectively suppressed. To validate our framework, we apply it to MonoDLE and MonoFlex. The two new detectors, dubbed 3DSeMo_DLE and 3DSeMo_FLEX, achieve state-of-the-art results with remarkable improvements for over 3.5% AP_3D/BEV (Easy) on KITTI, showing its effectiveness and generality. Code and models will be released.

Linfeng Zhang, Yukang Shi, Hung-Shuo Tai et al.

Detecting 3D objects from multi-view images is a fundamental problem in 3D computer vision. Recently, significant breakthrough has been made in multi-view 3D detection tasks. However, the unprecedented detection performance of these vision BEV (bird's-eye-view) detection models is accompanied with enormous parameters and computation, which make them unaffordable on edge devices. To address this problem, in this paper, we propose a structured knowledge distillation framework, aiming to improve the efficiency of modern vision-only BEV detection models. The proposed framework mainly includes: (a) spatial-temporal distillation which distills teacher knowledge of information fusion from different timestamps and views, (b) BEV response distillation which distills teacher response to different pillars, and (c) weight-inheriting which solves the problem of inconsistent inputs between students and teacher in modern transformer architectures. Experimental results show that our method leads to an average improvement of 2.16 mAP and 2.27 NDS on the nuScenes benchmark, outperforming multiple baselines by a large margin.

Mengyao Lyu, Yuhong Yang, Haiwen Hong et al.

The prevalent use of commercial and open-source diffusion models (DMs) for text-to-image generation prompts risk mitigation to prevent undesired behaviors. Existing concept erasing methods in academia are all based on full parameter or specification-based fine-tuning, from which we observe the following issues: 1) Generation alternation towards erosion: Parameter drift during target elimination causes alternations and potential deformations across all generations, even eroding other concepts at varying degrees, which is more evident with multi-concept erased; 2) Transfer inability & deployment inefficiency: Previous model-specific erasure impedes the flexible combination of concepts and the training-free transfer towards other models, resulting in linear cost growth as the deployment scenarios increase. To achieve non-invasive, precise, customizable, and transferable elimination, we ground our erasing framework on one-dimensional adapters to erase multiple concepts from most DMs at once across versatile erasing applications. The concept-SemiPermeable structure is injected as a Membrane (SPM) into any DM to learn targeted erasing, and meantime the alteration and erosion phenomenon is effectively mitigated via a novel Latent Anchoring fine-tuning strategy. Once obtained, SPMs can be flexibly combined and plug-and-play for other DMs without specific re-tuning, enabling timely and efficient adaptation to diverse scenarios. During generation, our Facilitated Transport mechanism dynamically regulates the permeability of each SPM to respond to different input prompts, further minimizing the impact on other concepts. Quantitative and qualitative results across ~40 concepts, 7 DMs and 4 erasing applications have demonstrated the superior erasing of SPM. Our code and pre-tuned SPMs are available on the project page https://lyumengyao.github.io/projects/spm.

Chang Liu, Wenzhao Xiang, Yuan He et al.

Deep neural networks (DNNs) may suffer from significantly degenerated performance when the training and test data are of different underlying distributions. Despite the importance of model generalization to out-of-distribution (OOD) data, the accuracy of state-of-the-art (SOTA) models on OOD data can plummet. Recent work has demonstrated that regular or off-manifold adversarial examples, as a special case of data augmentation, can be used to improve OOD generalization. Inspired by this, we theoretically prove that on-manifold adversarial examples can better benefit OOD generalization. Nevertheless, it is nontrivial to generate on-manifold adversarial examples because the real manifold is generally complex. To address this issue, we proposed a novel method of Augmenting data with Adversarial examples via a Wavelet module (AdvWavAug), an on-manifold adversarial data augmentation technique that is simple to implement. In particular, we project a benign image into a wavelet domain. With the assistance of the sparsity characteristic of wavelet transformation, we can modify an image on the estimated data manifold. We conduct adversarial augmentation based on AdvProp training framework. Extensive experiments on different models and different datasets, including ImageNet and its distorted versions, demonstrate that our method can improve model generalization, especially on OOD data. By integrating AdvWavAug into the training process, we have achieved SOTA results on some recent transformer-based models.

Yunqing Hu, Xuan Jin, Yin Zhang et al.

Previous works on multi-label image recognition (MLIR) usually use CNNs as a starting point for research. In this paper, we take pure Vision Transformer (ViT) as the research base and make full use of the advantages of Transformer with long-range dependency modeling to circumvent the disadvantages of CNNs limited to local receptive field. However, for multi-label images containing multiple objects from different categories, scales, and spatial relations, it is not optimal to use global information alone. Our goal is to leverage ViT's patch tokens and self-attention mechanism to mine rich instances in multi-label images, named diverse instance discovery (DiD). To this end, we propose a semantic category-aware module and a spatial relationship-aware module, respectively, and then combine the two by a re-constraint strategy to obtain instance-aware attention maps. Finally, we propose a weakly supervised object localization-based approach to extract multi-scale local features, to form a multi-view pipeline. Our method requires only weakly supervised information at the label level, no additional knowledge injection or other strongly supervised information is required. Experiments on three benchmark datasets show that our method significantly outperforms previous works and achieves state-of-the-art results under fair experimental comparisons.

Chao Lin, Zhao Li, Sheng Zhou et al.

Virtual try-on(VTON) aims at fitting target clothes to reference person images, which is widely adopted in e-commerce.Existing VTON approaches can be narrowly categorized into Parser-Based(PB) and Parser-Free(PF) by whether relying on the parser information to mask the persons' clothes and synthesize try-on images. Although abandoning parser information has improved the applicability of PF methods, the ability of detail synthesizing has also been sacrificed. As a result, the distraction from original cloth may persistin synthesized images, especially in complicated postures and high resolution applications. To address the aforementioned issue, we propose a novel PF method named Regional Mask Guided Network(RMGN). More specifically, a regional mask is proposed to explicitly fuse the features of target clothes and reference persons so that the persisted distraction can be eliminated. A posture awareness loss and a multi-level feature extractor are further proposed to handle the complicated postures and synthesize high resolution images. Extensive experiments demonstrate that our proposed RMGN outperforms both state-of-the-art PB and PF methods.Ablation studies further verify the effectiveness ofmodules in RMGN.

Hui Yang, Jiaoyan Chen, Yuan He et al. · oxford

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.

Xingyue Huang, Xianglong Hu, Zifeng Ding et al.

Large language models (LLMs) often struggle with mathematical problems that require exact computation or multi-step algebraic reasoning. Tool-integrated reasoning (TIR) offers a promising solution by leveraging external tools such as code interpreters to ensure correctness, but it introduces inference-time dependencies that hinder scalability and deployment. In this work, we propose a new paradigm for distilling tool knowledge into LLMs purely through natural language. We first construct a Solver Agent that solves math problems by interleaving planning, symbolic tool calls, and reflective reasoning. Then, using a back-translation pipeline powered by multiple LLM-based agents, we convert interleaved TIR traces into natural language reasoning traces. A Translator Agent generates explanations for individual tool calls, while a Rephrase Agent merges them into a fluent and globally coherent narrative. Empirically, we show that fine-tuning a small open-source model on these synthesized traces enables it to internalize both tool knowledge and structured reasoning patterns, yielding gains on competition-level math benchmarks without requiring tool access at inference.

Qilong Zhang, Xiaodan Li, Yuefeng Chen et al.

Adversarial examples have posed a severe threat to deep neural networks due to their transferable nature. Currently, various works have paid great efforts to enhance the cross-model transferability, which mostly assume the substitute model is trained in the same domain as the target model. However, in reality, the relevant information of the deployed model is unlikely to leak. Hence, it is vital to build a more practical black-box threat model to overcome this limitation and evaluate the vulnerability of deployed models. In this paper, with only the knowledge of the ImageNet domain, we propose a Beyond ImageNet Attack (BIA) to investigate the transferability towards black-box domains (unknown classification tasks). Specifically, we leverage a generative model to learn the adversarial function for disrupting low-level features of input images. Based on this framework, we further propose two variants to narrow the gap between the source and target domains from the data and model perspectives, respectively. Extensive experiments on coarse-grained and fine-grained domains demonstrate the effectiveness of our proposed methods. Notably, our methods outperform state-of-the-art approaches by up to 7.71\% (towards coarse-grained domains) and 25.91\% (towards fine-grained domains) on average. Our code is available at \url{https://github.com/qilong-zhang/Beyond-ImageNet-Attack}.

Hang Dong, Jiaoyan Chen, Yuan He et al. · oxford

We investigate the task of inserting new concepts extracted from texts into an ontology using language models. We explore an approach with three steps: edge search which is to find a set of candidate locations to insert (i.e., subsumptions between concepts), edge formation and enrichment which leverages the ontological structure to produce and enhance the edge candidates, and edge selection which eventually locates the edge to be placed into. In all steps, we propose to leverage neural methods, where we apply embedding-based methods and contrastive learning with Pre-trained Language Models (PLMs) such as BERT for edge search, and adapt a BERT fine-tuning-based multi-label Edge-Cross-encoder, and Large Language Models (LLMs) such as GPT series, FLAN-T5, and Llama 2, for edge selection. We evaluate the methods on recent datasets created using the SNOMED CT ontology and the MedMentions entity linking benchmark. The best settings in our framework use fine-tuned PLM for search and a multi-label Cross-encoder for selection. Zero-shot prompting of LLMs is still not adequate for the task, and we propose explainable instruction tuning of LLMs for improved performance. Our study shows the advantages of PLMs and highlights the encouraging performance of LLMs that motivates future studies.

Bohui Zhang, Yuan He, Lydia Pintscher et al.

Schemas play a vital role in ensuring data quality and supporting usability in the Semantic Web and natural language processing. Traditionally, their creation demands substantial involvement from knowledge engineers and domain experts. Leveraging the impressive capabilities of large language models (LLMs) in tasks like ontology engineering, we explore schema generation using LLMs. To bridge the resource gap, we introduce two datasets: YAGO Schema and Wikidata EntitySchema, along with novel evaluation metrics. The LLM-based pipelines utilize local and global information from knowledge graphs (KGs) to generate schemas in Shape Expressions (ShEx). Experiments demonstrate LLMs' strong potential in producing high-quality ShEx schemas, paving the way for scalable, automated schema generation for large KGs. Furthermore, our benchmark introduces a new challenge for structured generation, pushing the limits of LLMs on syntactically rich formalisms.

Zifeng Ding, Shenyang Huang, Zeyu Cao et al. · cambridge

Forecasting future links is a central task in temporal graph (TG) reasoning, requiring models to leverage historical interactions to predict upcoming ones. Traditional neural approaches, such as temporal graph neural networks, achieve strong performance but lack explainability and cannot be applied to unseen graphs without retraining. Recent studies have begun to explore using large language models (LLMs) for graph reasoning, but most of them are constrained to static graphs or small synthetic TGs and lack the evaluation of the quality of reasoning traces generated by LLMs. In this work, we present Reasoning-Enhanced Learning for Temporal Graphs (ReaL-TG), a reinforcement learning framework that fine-tunes LLMs to perform explainable link forecasting on real-world TGs. ReaL-TG uses outcome-based reward to encourage models to self-explore reasoning strategies from graph structure and to produce explanations that directly justify their predictions. To enable evaluation on LLM-generated reasoning traces, we propose a new evaluation protocol combining ranking metrics with an LLM-as-a-Judge system that assesses both the quality of reasoning and the impact of hallucinations. Experiments with ReaL-TG-4B, obtained by fine-tuning Qwen3-4B under our framework, show that it outperforms much larger frontier LLMs, including GPT-5 mini, on ranking metrics, while producing high-quality explanations confirmed by both the LLM judge and human evaluation.

Jiaoyan Chen, Olga Mashkova, Fernando Zhapa-Camacho et al.

Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e., ontology embedding has been widely investigated. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies and formally defines ontology embedding as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies they aim at and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL and discusses the challenges and future directions.

Jiaoyan Chen, Yuan He, Yuxia Geng et al.

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.

Jiaoyan Chen, Yuxia Geng, Zhuo Chen et al.

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

Yuan He, Jiaoyan Chen, Denvar Antonyrajah et al.

Ontology alignment (a.k.a ontology matching (OM)) plays a critical role in knowledge integration. Owing to the success of machine learning in many domains, it has been applied in OM. However, the existing methods, which often adopt ad-hoc feature engineering or non-contextual word embeddings, have not yet outperformed rule-based systems especially in an unsupervised setting. In this paper, we propose a novel OM system named BERTMap which can support both unsupervised and semi-supervised settings. It first predicts mappings using a classifier based on fine-tuning the contextual embedding model BERT on text semantics corpora extracted from ontologies, and then refines the mappings through extension and repair by utilizing the ontology structure and logic. Our evaluation with three alignment tasks on biomedical ontologies demonstrates that BERTMap can often perform better than the leading OM systems LogMap and AML.