Geometric relational embeddings map relational data as geometric objects that combine vector information suitable for machine learning and structured/relational information for structured/relational reasoning, typically in low dimensions. Their preservation of relational structures and their appealing properties and interpretability have led to their uptake for tasks such as knowledge graph completion, ontology and hierarchy reasoning, logical query answering, and hierarchical multi-label classification. We survey methods that underly geometric relational embeddings and categorize them based on (i) the embedding geometries that are used to represent the data; and (ii) the relational reasoning tasks that they aim to improve. We identify the desired properties (i.e., inductive biases) of each kind of embedding and discuss some potential future work.

Complex logical query answering (CLQA) is a recently emerged task of graph machine learning that goes beyond simple one-hop link prediction and solves a far more complex task of multi-hop logical reasoning over massive, potentially incomplete graphs in a latent space. The task received a significant traction in the community; numerous works expanded the field along theoretical and practical axes to tackle different types of complex queries and graph modalities with efficient systems. In this paper, we provide a holistic survey of CLQA with a detailed taxonomy studying the field from multiple angles, including graph types (modality, reasoning domain, background semantics), modeling aspects (encoder, processor, decoder), supported queries (operators, patterns, projected variables), datasets, evaluation metrics, and applications. Refining the CLQA task, we introduce the concept of Neural Graph Databases (NGDBs). Extending the idea of graph databases (graph DBs), NGDB consists of a Neural Graph Storage and a Neural Graph Engine. Inside Neural Graph Storage, we design a graph store, a feature store, and further embed information in a latent embedding store using an encoder. Given a query, Neural Query Engine learns how to perform query planning and execution in order to efficiently retrieve the correct results by interacting with the Neural Graph Storage. Compared with traditional graph DBs, NGDBs allow for a flexible and unified modeling of features in diverse modalities using the embedding store. Moreover, when the graph is incomplete, they can provide robust retrieval of answers which a normal graph DB cannot recover. Finally, we point out promising directions, unsolved problems and applications of NGDB for future research.

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining.

Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational queries are often observed in real-world KG applications, and existing approaches for approximate query answering cannot make use of qualifier pairs. In this work, we bridge this gap and extend the multi-hop reasoning problem to hyper-relational KGs allowing to tackle this new type of complex queries. Building upon recent advancements in Graph Neural Networks and query embedding techniques, we study how to embed and answer hyper-relational conjunctive queries. Besides that, we propose a method to answer such queries and demonstrate in our experiments that qualifiers improve query answering on a diverse set of query patterns.

Finding out the differences and commonalities between the knowledge of two parties is an important task. Such a comparison becomes necessary, when one party wants to determine how much it is worth to acquire the knowledge of the second party, or similarly when two parties try to determine, whether a collaboration could be beneficial. When these two parties cannot trust each other (for example, due to them being competitors) performing such a comparison is challenging as neither of them would be willing to share any of their assets. This paper addresses this problem for knowledge graphs, without a need for non-disclosure agreements nor a third party during the protocol. During the protocol, the intersection between the two knowledge graphs is determined in a privacy preserving fashion. This is followed by the computation of various metrics, which give an indication of the potential gain from obtaining the other parties knowledge graph, while still keeping the actual knowledge graph contents secret. The protocol makes use of blind signatures and (counting) Bloom filters to reduce the amount of leaked information. Finally, the party who wants to obtain the other's knowledge graph can get a part of such in a way that neither party is able to know beforehand which parts of the graph are obtained (i.e., they cannot choose to only get or share the good parts). After inspection of the quality of this part, the Buyer can decide to proceed with the transaction. The analysis of the protocol indicates that the developed protocol is secure against malicious participants. Further experimental analysis shows that the resource consumption scales linear with the number of statements in the knowledge graph.

Large, heterogeneous datasets are characterized by missing or even erroneous information. This is more evident when they are the product of community effort or automatic fact extraction methods from external sources, such as text. A special case of the aforementioned phenomenon can be seen in knowledge graphs, where this mostly appears in the form of missing or incorrect edges and nodes. Structured querying on such incomplete graphs will result in incomplete sets of answers, even if the correct entities exist in the graph, since one or more edges needed to match the pattern are missing. To overcome this problem, several algorithms for approximate structured query answering have been proposed. Inspired by modern Information Retrieval metrics, these algorithms produce a ranking of all entities in the graph, and their performance is further evaluated based on how high in this ranking the correct answers appear. In this work we take a critical look at this way of evaluation. We argue that performing a ranking-based evaluation is not sufficient to assess methods for complex query answering. To solve this, we introduce Message Passing Query Boxes (MPQB), which takes binary classification metrics back into use and shows the effect this has on the recently proposed query embedding method MPQE.

Neural link predictors are immensely useful for identifying missing edges in large scale Knowledge Graphs. However, it is still not clear how to use these models for answering more complex queries that arise in a number of domains, such as queries using logical conjunctions, disjunctions, and existential quantifiers, while accounting for missing edges. In this work, we propose a framework for efficiently answering complex queries on incomplete Knowledge Graphs. We translate each query into an end-to-end differentiable objective, where the truth value of each atom is computed by a pre-trained neural link predictor. We then analyse two solutions to the optimisation problem, including gradient-based and combinatorial search. In our experiments, the proposed approach produces more accurate results than state-of-the-art methods -- black-box neural models trained on millions of generated queries -- without the need of training on a large and diverse set of complex queries. Using orders of magnitude less training data, we obtain relative improvements ranging from 8% up to 40% in Hits@3 across different knowledge graphs containing factual information. Finally, we demonstrate that it is possible to explain the outcome of our model in terms of the intermediate solutions identified for each of the complex query atoms.

We present a method for learning representations of entities, that uses a Transformer-based architecture as an entity encoder, and link prediction training on a knowledge graph with textual entity descriptions. We demonstrate that our approach can be applied effectively for link prediction in different inductive settings involving entities not seen during training, outperforming related state-of-the-art methods (22% MRR improvement on average). We provide evidence that the learned representations transfer to other tasks that do not require fine-tuning the entity encoder. In an entity classification task we obtain an average improvement of 16% accuracy compared with baselines that also employ pre-trained models. For an information retrieval task, significant improvements of up to 8.8% in NDCG@10 were obtained for natural language queries.

In order to facilitate the accesses of general users to knowledge graphs, an increasing effort is being exerted to construct graph-structured queries of given natural language questions. At the core of the construction is to deduce the structure of the target query and determine the vertices/edges which constitute the query. Existing query construction methods rely on question understanding and conventional graph-based algorithms which lead to inefficient and degraded performances facing complex natural language questions over knowledge graphs with large scales. In this paper, we focus on this problem and propose a novel framework standing on recent knowledge graph embedding techniques. Our framework first encodes the underlying knowledge graph into a low-dimensional embedding space by leveraging generalized local knowledge graphs. Given a natural language question, the learned embedding representations of the knowledge graph are utilized to compute the query structure and assemble vertices/edges into the target query. Extensive experiments were conducted on the benchmark dataset, and the results demonstrate that our framework outperforms state-of-the-art baseline models regarding effectiveness and efficiency.

Question answering over knowledge graphs (KGQA) has evolved from simple single-fact questions to complex questions that require graph traversal and aggregation. We propose a novel approach for complex KGQA that uses unsupervised message passing, which propagates confidence scores obtained by parsing an input question and matching terms in the knowledge graph to a set of possible answers. First, we identify entity, relationship, and class names mentioned in a natural language question, and map these to their counterparts in the graph. Then, the confidence scores of these mappings propagate through the graph structure to locate the answer entities. Finally, these are aggregated depending on the identified question type. This approach can be efficiently implemented as a series of sparse matrix multiplications mimicking joins over small local subgraphs. Our evaluation results show that the proposed approach outperforms the state-of-the-art on the LC-QuAD benchmark. Moreover, we show that the performance of the approach depends only on the quality of the question interpretation results, i.e., given a correct relevance score distribution, our approach always produces a correct answer ranking. Our error analysis reveals correct answers missing from the benchmark dataset and inconsistencies in the DBpedia knowledge graph. Finally, we provide a comprehensive evaluation of the proposed approach accompanied with an ablation study and an error analysis, which showcase the pitfalls for each of the question answering components in more detail.