GNN2R: Weakly-Supervised Rationale-Providing Question Answering over Knowledge Graphs

Most current methods for multi-hop question answering (QA) over knowledge graphs (KGs) only provide final conclusive answers without explanations, such as a set of KG entities that is difficult for normal users to review and comprehend. This issue severely limits the application of KG-based QA in real-world scenarios. However, it is non-trivial to solve due to two challenges: First, annotations of reasoning chains of multi-hop questions, which could serve as supervision for explanation generation, are usually lacking. Second, it is difficult to maintain high efficiency when explicit KG triples need to be retrieved to generate explanations. In this paper, we propose a novel Graph Neural Network-based Two-Step Reasoning model (GNN2R) to solve this issue. GNN2R can provide both final answers and reasoning subgraphs as a rationale behind final answers efficiently with only weak supervision that is available through question-final answer pairs. We extensively evaluated GNN2R with detailed analyses in experiments. The results demonstrate that, in terms of effectiveness, efficiency, and quality of generated explanations, GNN2R outperforms existing state-of-the-art methods that are applicable to this task. Our code and pre-trained models are available at https://github.com/ruijie-wang-uzh/GNN2R.

DONUT-hole: DONUT Sparsification by Harnessing Knowledge and Optimizing Learning Efficiency

This paper introduces DONUT-hole, a sparse OCR-free visual document understanding (VDU) model that addresses the limitations of its predecessor model, dubbed DONUT. The DONUT model, leveraging a transformer architecture, overcoming the challenges of separate optical character recognition (OCR) and visual semantic understanding (VSU) components. However, its deployment in production environments and edge devices is hindered by high memory and computational demands, particularly in large-scale request services. To overcome these challenges, we propose an optimization strategy based on knowledge distillation and model pruning. Our paradigm to produce DONUT-hole, reduces the model denisty by 54\% while preserving performance. We also achieve a global representational similarity index between DONUT and DONUT-hole based on centered kernel alignment (CKA) metric of 0.79. Moreover, we evaluate the effectiveness of DONUT-hole in the document image key information extraction (KIE) task, highlighting its potential for developing more efficient VDU systems for logistic companies.

Approximate Answering of Graph Queries

Knowledge graphs (KGs) are inherently incomplete because of incomplete world knowledge and bias in what is the input to the KG. Additionally, world knowledge constantly expands and evolves, making existing facts deprecated or introducing new ones. However, we would still want to be able to answer queries as if the graph were complete. In this chapter, we will give an overview of several methods which have been proposed to answer queries in such a setting. We will first provide an overview of the different query types which can be supported by these methods and datasets typically used for evaluation, as well as an insight into their limitations. Then, we give an overview of the different approaches and describe them in terms of expressiveness, supported graph types, and inference capabilities.

BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphs

Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to predict new links in such graphs. Some methods ignore valuable attribute data associated with entities in biomedical KGs, such as protein sequences, or molecular graphs. Other works incorporate such data, but assume that entities can be represented with the same data modality. This is not always the case for biomedical KGs, where entities exhibit heterogeneous modalities that are central to their representation in the subject domain. We propose a modular framework for learning embeddings in KGs with entity attributes, that allows encoding attribute data of different modalities while also supporting entities with missing attributes. We additionally propose an efficient pretraining strategy for reducing the required training runtime. We train models using a biomedical KG containing approximately 2 million triples, and evaluate the performance of the resulting entity embeddings on the tasks of link prediction, and drug-protein interaction prediction, comparing against methods that do not take attribute data into account. In the standard link prediction evaluation, the proposed method results in competitive, yet lower performance than baselines that do not use attribute data. When evaluated in the task of drug-protein interaction prediction, the method compares favorably with the baselines. We find settings involving low degree entities, which make up for a substantial amount of the set of entities in the KG, where our method outperforms the baselines. Our proposed pretraining strategy yields significantly higher performance while reducing the required training runtime. Our implementation is available at https://github.com/elsevier-AI-Lab/BioBLP .

Geometric Relational Embeddings: A Survey

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.

Neural Graph Reasoning: Complex Logical Query Answering Meets Graph Databases

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.

A Biomedical Knowledge Graph for Biomarker Discovery in Cancer

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.

Explainable AI for Bioinformatics: Methods, Tools, and Applications

Artificial intelligence(AI) systems based on deep neural networks (DNNs) and machine learning (ML) algorithms are increasingly used to solve critical problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNN or ML models that are unavoidably opaque and perceived as black-box methods, may not be able to explain why and how they make certain decisions. Such black-box models are difficult to comprehend not only for targeted users and decision-makers but also for AI developers. Besides, in sensitive areas like healthcare, explainability and accountability are not only desirable properties of AI but also legal requirements -- especially when AI may have significant impacts on human lives. Explainable artificial intelligence (XAI) is an emerging field that aims to mitigate the opaqueness of black-box models and make it possible to interpret how AI systems make their decisions with transparency. An interpretable ML model can explain how it makes predictions and which factors affect the model's outcomes. The majority of state-of-the-art interpretable ML methods have been developed in a domain-agnostic way and originate from computer vision, automated reasoning, or even statistics. Many of these methods cannot be directly applied to bioinformatics problems, without prior customization, extension, and domain adoption. In this paper, we discuss the importance of explainability with a focus on bioinformatics. We analyse and comprehensively overview of model-specific and model-agnostic interpretable ML methods and tools. Via several case studies covering bioimaging, cancer genomics, and biomedical text mining, we show how bioinformatics research could benefit from XAI methods and how they could help improve decision fairness.

A Machine with Short-Term, Episodic, and Semantic Memory Systems

Inspired by the cognitive science theory of the explicit human memory systems, we have modeled an agent with short-term, episodic, and semantic memory systems, each of which is modeled with a knowledge graph. To evaluate this system and analyze the behavior of this agent, we designed and released our own reinforcement learning agent environment, "the Room", where an agent has to learn how to encode, store, and retrieve memories to maximize its return by answering questions. We show that our deep Q-learning based agent successfully learns whether a short-term memory should be forgotten, or rather be stored in the episodic or semantic memory systems. Our experiments indicate that an agent with human-like memory systems can outperform an agent without this memory structure in the environment.

Prompting as Probing: Using Language Models for Knowledge Base Construction

Language Models (LMs) have proven to be useful in various downstream applications, such as summarisation, translation, question answering and text classification. LMs are becoming increasingly important tools in Artificial Intelligence, because of the vast quantity of information they can store. In this work, we present ProP (Prompting as Probing), which utilizes GPT-3, a large Language Model originally proposed by OpenAI in 2020, to perform the task of Knowledge Base Construction (KBC). ProP implements a multi-step approach that combines a variety of prompting techniques to achieve this. Our results show that manual prompt curation is essential, that the LM must be encouraged to give answer sets of variable lengths, in particular including empty answer sets, that true/false questions are a useful device to increase precision on suggestions generated by the LM, that the size of the LM is a crucial factor, and that a dictionary of entity aliases improves the LM score. Our evaluation study indicates that these proposed techniques can substantially enhance the quality of the final predictions: ProP won track 2 of the LM-KBC competition, outperforming the baseline by 36.4 percentage points. Our implementation is available on https://github.com/HEmile/iswc-challenge.