Injecting external knowledge can improve the performance of pre-trained language models (PLMs) on various downstream NLP tasks. However, massive retraining is required to deploy new knowledge injection methods or knowledge bases for downstream tasks. In this work, we are the first to study how to improve the flexibility and efficiency of knowledge injection by reusing existing downstream models. To this end, we explore a new paradigm plug-and-play knowledge injection, where knowledge bases are injected into frozen existing downstream models by a knowledge plugin. Correspondingly, we propose a plug-and-play injection method map-tuning, which trains a mapping of knowledge embeddings to enrich model inputs with mapped embeddings while keeping model parameters frozen. Experimental results on three knowledge-driven NLP tasks show that existing injection methods are not suitable for the new paradigm, while map-tuning effectively improves the performance of downstream models. Moreover, we show that a frozen downstream model can be well adapted to different domains with different mapping networks of domain knowledge. Our code and models are available at https://github.com/THUNLP/Knowledge-Plugin.

Most existing ontology matching methods utilize the literal information to discover alignments. However, some literal information in ontologies may be opaque and some ontologies may not have sufficient literal information. In this paper, these ontologies are named as weak informative ontologies (WIOs) and it is challenging for existing methods to matching WIOs. On one hand, string-based and linguistic-based matching methods cannot work well for WIOs. On the other hand, some matching methods use external resources to improve their performance, but collecting and processing external resources is still time-consuming. To address this issue, this paper proposes a practical method for matching WIOs by employing the ontology structure information to discover alignments. First, the semantic subgraphs are extracted from the ontology graph to capture the precise meanings of ontology elements. Then, a new similarity propagation model is designed for matching WIOs. Meanwhile, in order to avoid meaningless propagation, the similarity propagation is constrained by semantic subgraphs and other conditions. Consequently, the similarity propagation model ensures a balance between efficiency and quality during matching. Finally, the similarity propagation model uses a few credible alignments as seeds to find more alignments, and some useful strategies are adopted to improve the performance. This matching method for WIOs has been implemented in the ontology matching system Lily. Experimental results on public OAEI benchmark datasets demonstrate that Lily significantly outperforms most of the state-of-the-art works in both WIO matching tasks and general ontology matching tasks. In particular, Lily increases the recall by a large margin, while it still obtains high precision of matching results.

Ontology matching (OM) enables semantic interoperability between different ontologies and resolves their conceptual heterogeneity by aligning related entities. OM systems currently have two prevailing design paradigms: conventional knowledge-based expert systems and newer machine learning-based predictive systems. While large language models (LLMs) and LLM-based agents have become revolutionary in data engineering and have been applied creatively in various domains, their potential for OM remains underexplored. This study introduces a novel agent-powered LLM-based design paradigm for OM systems. With thoughtful consideration of several specific challenges to leverage LLMs for OM, we propose a generic framework, namely Agent-OM, consisting of two Siamese agents for retrieval and matching, with a set of simple prompt-based OM tools. Our framework is implemented in a proof-of-concept system. Evaluations of three Ontology Alignment Evaluation Initiative (OAEI) tracks over state-of-the-art OM systems show that our system can achieve very close results to the best long-standing performance on simple OM tasks and significantly improve the performance on complex and few-shot OM tasks.

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are continuously produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph encompassing biological knowledge about RNAs gathered from more than 50 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

The remarkable growth and significant success of machine learning have expanded its applications into programming languages and program analysis. However, a key challenge in adopting the latest machine learning methods is the representation of programming languages, which directly impacts the ability of machine learning methods to reason about programs. The absence of numerical awareness, aggregate data structure information, and improper way of presenting variables in previous representation works have limited their performances. To overcome the limitations and challenges of current program representations, we propose a graph-based program representation called PERFOGRAPH. PERFOGRAPH can capture numerical information and the aggregate data structure by introducing new nodes and edges. Furthermore, we propose an adapted embedding method to incorporate numerical awareness. These enhancements make PERFOGRAPH a highly flexible and scalable representation that effectively captures programs intricate dependencies and semantics. Consequently, it serves as a powerful tool for various applications such as program analysis, performance optimization, and parallelism discovery. Our experimental results demonstrate that PERFOGRAPH outperforms existing representations and sets new state-of-the-art results by reducing the error rate by 7.4% (AMD dataset) and 10% (NVIDIA dataset) in the well-known Device Mapping challenge. It also sets new state-of-the-art results in various performance optimization tasks like Parallelism Discovery and NUMA and Prefetchers Configuration prediction.

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

While carbon accounting plays a fundamental role in our fight against climate change, it is not without its challenges. We begin the paper with a critique of the conventional carbon accounting practices, after which we proceed to introduce the E-liability carbon accounting methodology and Emissions Liability Management (ELM) originally proposed by Kaplan and Ramanna, highlighting their strengths. Recognizing the immense value of this novel approach for real-world carbon accounting improvement, we introduce a novel data-driven integrative framework that leverages AI and computation - the E-Liability Knowledge Graph framework - to achieve real-world implementation of the E-liability carbon accounting methodology. In addition to providing a path-to-implementation, our proposed framework brings clarity to the complex environmental interactions within supply chains, thus enabling better informed and more responsible decision-making. We analyze the implementation aspects of this framework and conclude with a discourse on the role of this AI-aided knowledge graph in ensuring the transparency and decarbonization of global supply chains.

Inconsistency handling is an important issue in knowledge management. Especially in ontology engineering, logical inconsistencies may occur during ontology construction. A natural way to reason with an inconsistent ontology is to utilize the maximal consistent subsets of the ontology. However, previous studies on selecting maximum consistent subsets have rarely considered the semantics of the axioms, which may result in irrational inference. In this paper, we propose a novel approach to reasoning with inconsistent ontologies in description logics based on the embeddings of axioms. We first give a method for turning axioms into distributed semantic vectors to compute the semantic connections between the axioms. We then define an embedding-based method for selecting the maximum consistent subsets and use it to define an inconsistency-tolerant inference relation. We show the rationality of our inference relation by considering some logical properties. Finally, we conduct experiments on several ontologies to evaluate the reasoning power of our inference relation. The experimental results show that our embedding-based method can outperform existing inconsistency-tolerant reasoning methods based on maximal consistent subsets.

As the immense opportunities enabled by large language models become more apparent, NLP systems will be increasingly expected to excel in real-world settings. However, in many instances, powerful models alone will not yield translational NLP solutions, especially if the formulated problem is not well aligned with the real-world task. In this work, we study the case of UMLS vocabulary insertion, an important real-world task in which hundreds of thousands of new terms, referred to as atoms, are added to the UMLS, one of the most comprehensive open-source biomedical knowledge bases. Previous work aimed to develop an automated NLP system to make this time-consuming, costly, and error-prone task more efficient. Nevertheless, practical progress in this direction has been difficult to achieve due to a problem formulation and evaluation gap between research output and the real-world task. In order to address this gap, we introduce a new formulation for UMLS vocabulary insertion which mirrors the real-world task, datasets which faithfully represent it and several strong baselines we developed through re-purposing existing solutions. Additionally, we propose an effective rule-enhanced biomedical language model which enables important new model behavior, outperforms all strong baselines and provides measurable qualitative improvements to editors who carry out the UVI task. We hope this case study provides insight into the considerable importance of problem formulation for the success of translational NLP solutions.

Individuals and organizations cope with an always-growing amount of data, which is heterogeneous in its contents and formats. An adequate data management process yielding data quality and control over its lifecycle is a prerequisite to getting value out of this data and minimizing inherent risks related to multiple usages. Common data governance frameworks rely on people, policies, and processes that fall short of the overwhelming complexity of data. Yet, harnessing this complexity is necessary to achieve high-quality standards. The latter will condition any downstream data usage outcome, including generative artificial intelligence trained on this data. In this paper, we report our concrete experience establishing a simple, cost-efficient framework that enables metadata-driven, agile and (semi-)automated data governance (i.e. Data Governance 4.0). We explain how we implement and use this framework to integrate 25 years of clinical study data at an enterprise scale in a fully productive environment. The framework encompasses both methodologies and technologies leveraging semantic web principles. We built a knowledge graph describing avatars of data assets in their business context, including governance principles. Multiple ontologies articulated by an enterprise upper ontology enable key governance actions such as FAIRification, lifecycle management, definition of roles and responsibilities, lineage across transformations and provenance from source systems. This metadata model is the keystone to data governance 4.0: a semi-automatised data management process that considers the business context in an agile manner to adapt governance constraints to each use case and dynamically tune it based on business changes.