Designing a new clinical trial entails many decisions, such as defining a cohort and setting the study objectives to name a few, and therefore can benefit from recommendations based on exhaustive mining of past clinical trial records. Here, we propose a novel recommendation methodology, based on neural embeddings trained on a first-of-a-kind knowledge graph of clinical trials. We addressed several important research questions in this context, including designing a knowledge graph (KG) for clinical trial data, effectiveness of various KG embedding (KGE) methods for it, a novel inductive inference using KGE, and its use in generating recommendations for clinical trial design. We used publicly available data from clinicaltrials.gov for the study. Results show that our recommendations approach achieves relevance scores of 70%-83%, measured as the text similarity to actual clinical trial elements, and the most relevant recommendation can be found near the top of list. Our study also suggests potential improvement in training KGE using node semantics.

Knowledge graph completion is a task that revolves around filling in missing triples based on the information available in a knowledge graph. Among the current studies, text-based methods complete the task by utilizing textual descriptions of triples. However, this modeling approach may encounter limitations, particularly when the description fails to accurately and adequately express the intended meaning. To overcome these challenges, we propose the augmentation of data through two additional mechanisms. Firstly, we employ ChatGPT as an external knowledge base to generate coherent descriptions to bridge the semantic gap between the queries and answers. Secondly, we leverage inverse relations to create a symmetric graph, thereby creating extra labeling and providing supplementary information for link prediction. This approach offers additional insights into the relationships between entities. Through these efforts, we have observed significant improvements in knowledge graph completion, as these mechanisms enhance the richness and diversity of the available data, leading to more accurate results.

In this work, we present a web application named DBLPLink, which performs entity linking over the DBLP scholarly knowledge graph. DBLPLink uses text-to-text pre-trained language models, such as T5, to produce entity label spans from an input text question. Entity candidates are fetched from a database based on the labels, and an entity re-ranker sorts them based on entity embeddings, such as TransE, DistMult and ComplEx. The results are displayed so that users may compare and contrast the results between T5-small, T5-base and the different KG embeddings used. The demo can be accessed at https://ltdemos.informatik.uni-hamburg.de/dblplink/. Code and data shall be made available at https://github.com/uhh-lt/dblplink.

Bilinear based models are powerful and widely used approaches for Knowledge Graphs Completion (KGC). Although bilinear based models have achieved significant advances, these studies mainly concentrate on posterior properties (based on evidence, e.g. symmetry pattern) while neglecting the prior properties. In this paper, we find a prior property named "the law of identity" that cannot be captured by bilinear based models, which hinders them from comprehensively modeling the characteristics of KGs. To address this issue, we introduce a solution called Unit Ball Bilinear Model (UniBi). This model not only achieves theoretical superiority but also offers enhanced interpretability and performance by minimizing ineffective learning through minimal constraints. Experiments demonstrate that UniBi models the prior property and verify its interpretability and performance.

Adapter-style efficient transfer learning (ETL) has shown excellent performance in the tuning of vision-language models (VLMs) under the low-data regime, where only a few additional parameters are introduced to excavate the task-specific knowledge based on the general and powerful representation of VLMs. However, most adapter-style works face two limitations: (i) modeling task-specific knowledge with a single modality only; and (ii) overlooking the exploitation of the inter-class relationships in downstream tasks, thereby leading to sub-optimal solutions. To mitigate that, we propose an effective adapter-style tuning strategy, dubbed GraphAdapter, which performs the textual adapter by explicitly modeling the dual-modality structure knowledge (i.e., the correlation of different semantics/classes in textual and visual modalities) with a dual knowledge graph. In particular, the dual knowledge graph is established with two sub-graphs, i.e., a textual knowledge sub-graph, and a visual knowledge sub-graph, where the nodes and edges represent the semantics/classes and their correlations in two modalities, respectively. This enables the textual feature of each prompt to leverage the task-specific structure knowledge from both textual and visual modalities, yielding a more effective classifier for downstream tasks. Extensive experimental results on 11 benchmark datasets reveal that our GraphAdapter significantly outperforms previous adapter-based methods. The code will be released at https://github.com/lixinustc/GraphAdapter

Nowadays, increasingly more data are available as knowledge graphs (KGs). While this data model supports advanced reasoning and querying, they remain difficult to mine due to their size and complexity. Graph mining approaches can be used to extract patterns from KGs. However this presents two main issues. First, graph mining approaches tend to extract too many patterns for a human analyst to interpret (pattern explosion). Second, real-life KGs tend to differ from the graphs usually treated in graph mining: they are multigraphs, their vertex degrees tend to follow a power-law, and the way in which they model knowledge can produce spurious patterns. Recently, a graph mining approach named GraphMDL+ has been proposed to tackle the problem of pattern explosion, using the Minimum Description Length (MDL) principle. However, GraphMDL+, like other graph mining approaches, is not suited for KGs without adaptations. In this paper we propose KG-MDL, a graph pattern mining approach based on the MDL principle that, given a KG, generates a human-sized and descriptive set of graph patterns, and so in a parameter-less and anytime way. We report on experiments on medium-sized KGs showing that our approach generates sets of patterns that are both small enough to be interpreted by humans and descriptive of the KG. We show that the extracted patterns highlight relevant characteristics of the data: both of the schema used to create the data, and of the concrete facts it contains. We also discuss the issues related to mining graph patterns on knowledge graphs, as opposed to other types of graph data.

Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.

Datasets that pair Knowledge Graphs (KG) and text together (KG-T) can be used to train forward and reverse neural models that generate text from KG and vice versa. However models trained on datasets where KG and text pairs are not equivalent can suffer from more hallucination and poorer recall. In this paper, we verify this empirically by generating datasets with different levels of noise and find that noisier datasets do indeed lead to more hallucination. We argue that the ability of forward and reverse models trained on a dataset to cyclically regenerate source KG or text is a proxy for the equivalence between the KG and the text in the dataset. Using cyclic evaluation we find that manually created WebNLG is much better than automatically created TeKGen and T-REx. Guided by these observations, we construct a new, improved dataset called LAGRANGE using heuristics meant to improve equivalence between KG and text and show the impact of each of the heuristics on cyclic evaluation. We also construct two synthetic datasets using large language models (LLMs), and observe that these are conducive to models that perform significantly well on cyclic generation of text, but less so on cyclic generation of KGs, probably because of a lack of a consistent underlying ontology.

We present a comprehensive benchmark dataset for Knowledge Graph Question Answering in Materials Science (KGQA4MAT), with a focus on metal-organic frameworks (MOFs). A knowledge graph for metal-organic frameworks (MOF-KG) has been constructed by integrating structured databases and knowledge extracted from the literature. To enhance MOF-KG accessibility for domain experts, we aim to develop a natural language interface for querying the knowledge graph. We have developed a benchmark comprised of 161 complex questions involving comparison, aggregation, and complicated graph structures. Each question is rephrased in three additional variations, resulting in 644 questions and 161 KG queries. To evaluate the benchmark, we have developed a systematic approach for utilizing ChatGPT to translate natural language questions into formal KG queries. We also apply the approach to the well-known QALD-9 dataset, demonstrating ChatGPT's potential in addressing KGQA issues for different platforms and query languages. The benchmark and the proposed approach aim to stimulate further research and development of user-friendly and efficient interfaces for querying domain-specific materials science knowledge graphs, thereby accelerating the discovery of novel materials.

Self-supervised knowledge-graph completion (KGC) relies on estimating a scoring model over (entity, relation, entity)-tuples, for example, by embedding an initial knowledge graph. Prediction quality can be improved by calibrating the scoring model, typically by adjusting the prediction thresholds using manually annotated examples. In this paper, we attempt for the first time cold-start calibration for KGC, where no annotated examples exist initially for calibration, and only a limited number of tuples can be selected for annotation. Our new method ACTC finds good per-relation thresholds efficiently based on a limited set of annotated tuples. Additionally to a few annotated tuples, ACTC also leverages unlabeled tuples by estimating their correctness with Logistic Regression or Gaussian Process classifiers. We also experiment with different methods for selecting candidate tuples for annotation: density-based and random selection. Experiments with five scoring models and an oracle annotator show an improvement of 7% points when using ACTC in the challenging setting with an annotation budget of only 10 tuples, and an average improvement of 4% points over different budgets.