We propose an entity-agnostic representation learning method for handling the problem of inefficient parameter storage costs brought by embedding knowledge graphs. Conventional knowledge graph embedding methods map elements in a knowledge graph, including entities and relations, into continuous vector spaces by assigning them one or multiple specific embeddings (i.e., vector representations). Thus the number of embedding parameters increases linearly as the growth of knowledge graphs. In our proposed model, Entity-Agnostic Representation Learning (EARL), we only learn the embeddings for a small set of entities and refer to them as reserved entities. To obtain the embeddings for the full set of entities, we encode their distinguishable information from their connected relations, k-nearest reserved entities, and multi-hop neighbors. We learn universal and entity-agnostic encoders for transforming distinguishable information into entity embeddings. This approach allows our proposed EARL to have a static, efficient, and lower parameter count than conventional knowledge graph embedding methods. Experimental results show that EARL uses fewer parameters and performs better on link prediction tasks than baselines, reflecting its parameter efficiency.

Developing personalized diagnostic strategies and targeted treatments requires a deep understanding of disease biology and the ability to dissect the relationship between molecular and genetic factors and their phenotypic consequences. However, such knowledge is fragmented across publications, non-standardized repositories, and evolving ontologies describing various scales of biological organization between genotypes and clinical phenotypes. Here, we present PrimeKG, a multimodal knowledge graph for precision medicine analyses. PrimeKG integrates 20 high-quality resources to describe 17,080 diseases with 4,050,249 relationships representing ten major biological scales, including disease-associated protein perturbations, biological processes and pathways, anatomical and phenotypic scales, and the entire range of approved drugs with their therapeutic action, considerably expanding previous efforts in disease-rooted knowledge graphs. PrimeKG contains an abundance of ‘indications’, ‘contradictions’, and ‘off-label use’ drug-disease edges that lack in other knowledge graphs and can support AI analyses of how drugs affect disease-associated networks. We supplement PrimeKG’s graph structure with language descriptions of clinical guidelines to enable multimodal analyses and provide instructions for continual updates of PrimeKG as new data become available.

Reasoning over Temporal Knowledge Graphs (TKGs) aims to predict future facts based on given history. One of the key challenges for prediction is to learn the evolution of facts. Most existing works focus on exploring evolutionary information in history to obtain effective temporal embeddings for entities and relations, but they ignore the variation in evolution patterns of facts, which makes them struggle to adapt to future data with different evolution patterns. Moreover, new entities continue to emerge along with the evolution of facts over time. Since existing models highly rely on historical information to learn embeddings for entities, they perform poorly on such entities with little historical information. To tackle these issues, we propose a novel Temporal Meta-learning framework for TKG reasoning, MetaTKG for brevity. Specifically, our method regards TKG prediction as many temporal meta-tasks, and utilizes the designed Temporal Meta-learner to learn evolutionary meta-knowledge from these meta-tasks. The proposed method aims to guide the backbones to learn to adapt quickly to future data and deal with entities with little historical information by the learned meta-knowledge. Specially, in temporal meta-learner, we design a Gating Integration module to adaptively establish temporal correlations between meta-tasks. Extensive experiments on four widely-used datasets and three backbones demonstrate that our method can greatly improve the performance.

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of knowledge graphs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of knowledge graphs. Features include a simple, modular extract-transform-load (ETL) pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate knowledge graphs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph machine learning, including node embeddings and training of models for link prediction and node classification.

In this paper we present a novel method, $\textit{Knowledge Persistence}$ ($\mathcal{KP}$), for faster evaluation of Knowledge Graph (KG) completion approaches. Current ranking-based evaluation is quadratic in the size of the KG, leading to long evaluation times and consequently a high carbon footprint. $\mathcal{KP}$ addresses this by representing the topology of the KG completion methods through the lens of topological data analysis, concretely using persistent homology. The characteristics of persistent homology allow $\mathcal{KP}$ to evaluate the quality of the KG completion looking only at a fraction of the data. Experimental results on standard datasets show that the proposed metric is highly correlated with ranking metrics (Hits@N, MR, MRR). Performance evaluation shows that $\mathcal{KP}$ is computationally efficient: In some cases, the evaluation time (validation+test) of a KG completion method has been reduced from 18 hours (using Hits@10) to 27 seconds (using $\mathcal{KP}$), and on average (across methods & data) reduces the evaluation time (validation+test) by $\approx$ $\textbf{99.96}\%$.

Language models are trained on large volumes of text, and as a result their parameters might contain a significant body of factual knowledge. Any downstream task performed by these models implicitly builds on these facts, and thus it is highly desirable to have means for representing this body of knowledge in an interpretable way. However, there is currently no mechanism for such a representation. Here, we propose to address this goal by extracting a knowledge-graph of facts from a given language model. We describe a procedure for ``crawling'' the internal knowledge-base of a language model. Specifically, given a seed entity, we expand a knowledge-graph around it. The crawling procedure is decomposed into sub-tasks, realized through specially designed prompts that control for both precision (i.e., that no wrong facts are generated) and recall (i.e., the number of facts generated). We evaluate our approach on graphs crawled starting from dozens of seed entities, and show it yields high precision graphs (82-92%), while emitting a reasonable number of facts per entity.

In this study, the authors propose a computational cognitive model for sign language (SL) perception and comprehension with detailed algorithmic descriptions based on cognitive functionalities in human language processing. The semantic network model (SNM) that represents semantic relations between concepts, it is used as a form of knowledge representation. The proposed model is applied in the comprehension of sign language for classifier predicates. The spreading activation search method is initiated by labeling a set of source nodes (e.g. concepts in the semantic network) with weights or "activation" and then iteratively propagating or "spreading" that activation out to other nodes linked to the source nodes. The results demonstrate that the proposed search method improves the performance of sign language comprehension in the SNM.

Language models (LMs) pretrained on large corpora of text from the web have been observed to contain large amounts of various types of knowledge about the world. This observation has led to a new and exciting paradigm in knowledge graph construction where, instead of manual curation or text mining, one extracts knowledge from the parameters of an LM. Recently, it has been shown that finetuning LMs on a set of factual knowledge makes them produce better answers to queries from a different set, thus making finetuned LMs a good candidate for knowledge extraction and, consequently, knowledge graph construction. In this paper, we analyze finetuned LMs for factual knowledge extraction. We show that along with its previously known positive effects, finetuning also leads to a (potentially harmful) phenomenon which we call Frequency Shock, where at the test time the model over-predicts rare entities that appear in the training set and under-predicts common entities that do not appear in the training set enough times. We show that Frequency Shock leads to a degradation in the predictions of the model and beyond a point, the harm from Frequency Shock can even outweigh the positive effects of finetuning, making finetuning harmful overall. We then consider two solutions to remedy the identified negative effect: 1- model mixing and 2- mixture finetuning with the LM's pre-training task. The two solutions combined lead to significant improvements compared to vanilla finetuning.

Modelling taxonomic and thematic relatedness is important for building AI with comprehensive natural language understanding. The goal of this paper is to learn more about how taxonomic information is structurally encoded in embeddings. To do this, we design a new hypernym-hyponym probing task and perform a comparative probing study of taxonomic and thematic SGNS and GloVe embeddings. Our experiments indicate that both types of embeddings encode some taxonomic information, but the amount, as well as the geometric properties of the encodings, are independently related to both the encoder architecture, as well as the embedding training data. Specifically, we find that only taxonomic embeddings carry taxonomic information in their norm, which is determined by the underlying distribution in the data.

In today's multilingual lexical databases, the majority of the world's languages are under-represented. Beyond a mere issue of resource incompleteness, we show that existing lexical databases have structural limitations that result in a reduced expressivity on culturally-specific words and in mapping them across languages. In particular, the lexical meaning space of dominant languages, such as English, is represented more accurately while linguistically or culturally diverse languages are mapped in an approximate manner. Our paper assesses state-of-the-art multilingual lexical databases and evaluates their strengths and limitations with respect to their expressivity on lexical phenomena of linguistic diversity.