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.

One of the significant barriers to the training of statistical models on knowledge graphs is the difficulty that scientists have in finding the best input data to address their prediction goal. In addition to this, a key challenge is to determine how to manipulate these relational data, which are often in the form of particular triples (i.e., subject, predicate, object), to enable the learning process. Currently, many high-quality catalogs of knowledge graphs, are available. However, their primary goal is the re-usability of these resources, and their interconnection, in the context of the Semantic Web. This paper describes the LiveSchema initiative, namely, a first version of a gateway that has the main scope of leveraging the gold mine of data collected by many existing catalogs collecting relational data like ontologies and knowledge graphs. At the current state, LiveSchema contains - 1000 datasets from 4 main sources and offers some key facilities, which allow to: i) evolving LiveSchema, by aggregating other source catalogs and repositories as input sources; ii) querying all the collected resources; iii) transforming each given dataset into formal concept analysis matrices that enable analysis and visualization services; iv) generating models and tensors from each given dataset.

The availability of representative datasets is an essential prerequisite for many successful artificial intelligence and machine learning models. However, in real life applications these models often encounter scenarios that are inadequately represented in the data used for training. There are various reasons for the absence of sufficient data, ranging from time and cost constraints to ethical considerations. As a consequence, the reliable usage of these models, especially in safety-critical applications, is still a tremendous challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches. Knowledge augmented machine learning approaches offer the possibility of compensating for deficiencies, errors, or ambiguities in the data, thus increasing the generalization capability of the applied models. Even more, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-driven models with existing knowledge. The identified approaches are structured according to the categories knowledge integration, extraction and conformity. In particular, we address the application of the presented methods in the field of autonomous driving.

Recent years witnessed a rising interest towards Datalog-based ontological reasoning systems, both in academia and industry. These systems adopt languages, often shared under the collective name of Datalog$+/-$, that extend Datalog with the essential feature of existential quantification, while introducing syntactic limitations to sustain reasoning decidability and achieve a good trade-off between expressive power and computational complexity. From an implementation perspective, modern reasoners borrow the vast experience of the database community in developing streaming-based data processing systems, such as volcano-iterator architectures, that sustain a limited memory footprint and good scalability. In this paper, we focus on two extremely promising, expressive, and tractable languages, namely, Shy and Warded Datalog$+/-$. We leverage their theoretical underpinnings to introduce novel reasoning techniques, technically, "chase variants", that are particularly fit for efficient reasoning in streaming-based architectures. We then implement them in Vadalog, our reference streaming-based engine, to efficiently solve ontological reasoning tasks over real-world settings.