The integration of Artificial Intelligence (AI) into the field of drug discovery has been a growing area of interdisciplinary scientific research. However, conventional AI models are heavily limited in handling complex biomedical structures (such as 2D or 3D protein and molecule structures) and providing interpretations for outputs, which hinders their practical application. As of late, Graph Machine Learning (GML) has gained considerable attention for its exceptional ability to model graph-structured biomedical data and investigate their properties and functional relationships. Despite extensive efforts, GML methods still suffer from several deficiencies, such as the limited ability to handle supervision sparsity and provide interpretability in learning and inference processes, and their ineffectiveness in utilising relevant domain knowledge. In response, recent studies have proposed integrating external biomedical knowledge into the GML pipeline to realise more precise and interpretable drug discovery with limited training instances. However, a systematic definition for this burgeoning research direction is yet to be established. This survey presents a comprehensive overview of long-standing drug discovery principles, provides the foundational concepts and cutting-edge techniques for graph-structured data and knowledge databases, and formally summarises Knowledge-augmented Graph Machine Learning (KaGML) for drug discovery. we propose a thorough review of related KaGML works, collected following a carefully designed search methodology, and organise them into four categories following a novel-defined taxonomy. To facilitate research in this promptly emerging field, we also share collected practical resources that are valuable for intelligent drug discovery and provide an in-depth discussion of the potential avenues for future advancements.

As the volume of data on the web grows, the web structure graph, which is a graph representation of the web, continues to evolve. The structure of this graph has gradually shifted from content-based to non-content-based. Furthermore, spam data, such as noisy hyperlinks, in the web structure graph adversely affect the speed and efficiency of information retrieval and link mining algorithms. Previous works in this area have focused on removing noisy hyperlinks using structural and string approaches. However, these approaches may incorrectly remove useful links or be unable to detect noisy hyperlinks in certain circumstances. In this paper, a data collection of hyperlinks is initially constructed using an interactive crawler. The semantic and relatedness structure of the hyperlinks is then studied through semantic web approaches and tools such as the DBpedia ontology. Finally, the removal process of noisy hyperlinks is carried out using a reasoner on the DBpedia ontology. Our experiments demonstrate the accuracy and ability of semantic web technologies to remove noisy hyperlinks

This vision paper proposes KGNet, an on-demand graph machine learning (GML) as a service on top of RDF engines to support GML-enabled SPARQL queries. KGNet automates the training of GML models on a KG by identifying a task-specific subgraph. This helps reduce the task-irrelevant KG structure and properties for better scalability and accuracy. While training a GML model on KG, KGNet collects metadata of trained models in the form of an RDF graph called KGMeta, which is interlinked with the relevant subgraphs in KG. Finally, all trained models are accessible via a SPARQL-like query. We call it a GML-enabled query and refer to it as SPARQLML. KGNet supports SPARQLML on top of existing RDF engines as an interface for querying and inferencing over KGs using GML models. The development of KGNet poses research opportunities in several areas, including meta-sampling for identifying task-specific subgraphs, GML pipeline automation with computational constraints, such as limited time and memory budget, and SPARQLML query optimization. KGNet supports different GML tasks, such as node classification, link prediction, and semantic entity matching. We evaluated KGNet using two real KGs of different application domains. Compared to training on the entire KG, KGNet significantly reduced training time and memory usage while maintaining comparable or improved accuracy. The KGNet source-code is available for further study

Concept learning deals with learning description logic concepts from a background knowledge and input examples. The goal is to learn a concept that covers all positive examples, while not covering any negative examples. This non-trivial task is often formulated as a search problem within an infinite quasi-ordered concept space. Although state-of-the-art models have been successfully applied to tackle this problem, their large-scale applications have been severely hindered due to their excessive exploration incurring impractical runtimes. Here, we propose a remedy for this limitation. We reformulate the learning problem as a multi-label classification problem and propose a neural embedding model (NERO) that learns permutation-invariant embeddings for sets of examples tailored towards predicting $F_1$ scores of pre-selected description logic concepts. By ranking such concepts in descending order of predicted scores, a possible goal concept can be detected within few retrieval operations, i.e., no excessive exploration. Importantly, top-ranked concepts can be used to start the search procedure of state-of-the-art symbolic models in multiple advantageous regions of a concept space, rather than starting it in the most general concept $\top$. Our experiments on 5 benchmark datasets with 770 learning problems firmly suggest that NERO significantly (p-value <1%) outperforms the state-of-the-art models in terms of $F_1$ score, the number of explored concepts, and the total runtime. We provide an open-source implementation of our approach.

We describe the translation of the Suggested Upper Merged Ontology (SUMO) to Typed First-order Form (TFF) with level 0 polymorphism. Building on our prior work to create a TPTP FOF translation of SUMO for use in the E and Vampire theorem provers, we detail the transformations required to handle an explicitly typed logic, and express SUMO's type hierarchy for numbers in a manner consistent with its intended semantics and the three numerical classes allowed in TFF. We provide description of the open source code and an example proof in Vampire on the resulting theory.

Values, as intended in ethics, determine the shape and validity of moral and social norms, grounding our everyday individual and community behavior on commonsense knowledge. Formalising latent moral content in human interaction is an appealing perspective that would enable a deeper understanding of both social dynamics and individual cognitive and behavioral dimension. To tackle this problem, several theoretical frameworks offer different values models, and organize them into different taxonomies. The problem of the most used theories is that they adopt a cultural-independent perspective while many entities that are considered "values" are grounded in commonsense knowledge and expressed in everyday life interaction. We propose here two ontological modules, FOLK, an ontology for values intended in their broad sense, and That's All Folks, a module for lexical and factual folk value triggers, whose purpose is to complement the main theories, providing a method for identifying the values that are not contemplated by the major value theories, but which nonetheless play a key role in daily human interactions, and shape social structures, cultural biases, and personal beliefs. The resource is tested via performing automatic detection of values from text with a frame-based approach.

OWL ontologies are a quite popular way to describe structured knowledge in terms of classes, relations among classes and class instances. In this paper, given a target class T of an OWL ontology, with a focus on ontologies with real- and boolean-valued data properties, we address the problem of learning graded fuzzy concept inclusion axioms with the aim of describing enough conditions for being an individual classified as instance of the class T. To do so, we present PN-OWL that is a two-stage learning algorithm made of a P-stage and an N-stage. Roughly, in the P-stage the algorithm tries to cover as many positive examples as possible (increase recall), without compromising too much precision, while in the N-stage, the algorithm tries to rule out as many false positives, covered by the P-stage, as possible. PN-OWL then aggregates the fuzzy inclusion axioms learnt at the P-stage and the N-stage by combining them via aggregation functions to allow for a final decision whether an individual is instance of T or not. We also illustrate its effectiveness by means of an experimentation. An interesting feature is that fuzzy datatypes are built automatically, the learnt fuzzy concept inclusions can be represented directly into Fuzzy OWL 2 and, thus, any Fuzzy OWL 2 reasoner can then be used to automatically determine/classify (and to which degree) whether an individual belongs to the target class T or not.

The main goal of this paper is to evaluate knowledge base schemas, modeled as a set of entity types, each such type being associated with a set of properties, according to their focus. We intuitively model the notion of focus as ''the state or quality of being relevant in storing and retrieving information''. This definition of focus is adapted from the notion of ''categorization purpose'', as first defined in cognitive psychology, thus giving us a high level of understandability on the side of users. In turn, this notion is formalized based on a set of knowledge metrics that, for any given focus, rank knowledge base schemas according to their quality. We apply the proposed methodology to more than 200 state-of-the-art knowledge base schemas. The experimental results show the utility of our approach

The tractability of the lightweight description logic EL has allowed for the construction of large and widely used ontologies that support semantic interoperability. However, comprehensive domains with a broad user base are often at odds with strong axiomatisations otherwise useful for inferencing, since these are usually context-dependent and subject to diverging perspectives. In this paper we introduce Standpoint EL, a multi-modal extension of EL that allows for the integrated representation of domain knowledge relative to diverse, possibly conflicting standpoints (or contexts), which can be hierarchically organised and put in relation to each other. We establish that Standpoint EL still exhibits EL's favourable PTime standard reasoning, whereas introducing additional features like empty standpoints, rigid roles, and nominals makes standard reasoning tasks intractable.

Structured and unstructured data and facts about drugs, genes, protein, viruses, and their mechanism are spread across a huge number of scientific articles. These articles are a large-scale knowledge source and can have a huge impact on disseminating knowledge about the mechanisms of certain biological processes. A domain-specific knowledge graph~(KG) is an explicit conceptualization of a specific subject-matter domain represented w.r.t semantically interrelated entities and relations. A KG can be constructed by integrating such facts and data and be used for data integration, exploration, and federated queries. However, exploration and querying large-scale KGs is tedious for certain groups of users due to a lack of knowledge about underlying data assets or semantic technologies. Such a KG will not only allow deducing new knowledge and question answering(QA) but also allows domain experts to explore. Since cross-disciplinary explanations are important for accurate diagnosis, it is important to query the KG to provide interactive explanations about learned biomarkers. Inspired by these, we construct a domain-specific KG, particularly for cancer-specific biomarker discovery. The KG is constructed by integrating cancer-related knowledge and facts from multiple sources. First, we construct a domain-specific ontology, which we call OncoNet Ontology (ONO). The ONO ontology is developed to enable semantic reasoning for verification of the predictions for relations between diseases and genes. The KG is then developed and enriched by harmonizing the ONO, additional metadata schemas, ontologies, controlled vocabularies, and additional concepts from external sources using a BERT-based information extraction method. BioBERT and SciBERT are finetuned with the selected articles crawled from PubMed. We listed down some queries and some examples of QA and deducing knowledge based on the KG.