Biomedical event extraction is critical in understanding biomolecular interactions described in scientific corpus. One of the main challenges is to identify nested structured events that are associated with non-indicative trigger words. We propose to incorporate domain knowledge from Unified Medical Language System (UMLS) to a pre-trained language model via Graph Edge-conditioned Attention Networks (GEANet) and hierarchical graph representation. To better recognize the trigger words, each sentence is first grounded to a sentence graph based on a jointly modeled hierarchical knowledge graph from UMLS. The grounded graphs are then propagated by GEANet, a novel graph neural networks for enhanced capabilities in inferring complex events. On BioNLP 2011 GENIA Event Extraction task, our approach achieved 1.41% F1 and 3.19% F1 improvements on all events and complex events, respectively. Ablation studies confirm the importance of GEANet and hierarchical KG.

Hyper-relational knowledge graphs (KGs) (e.g., Wikidata) enable associating additional key-value pairs along with the main triple to disambiguate, or restrict the validity of a fact. In this work, we propose a message passing based graph encoder - StarE capable of modeling such hyper-relational KGs. Unlike existing approaches, StarE can encode an arbitrary number of additional information (qualifiers) along with the main triple while keeping the semantic roles of qualifiers and triples intact. We also demonstrate that existing benchmarks for evaluating link prediction (LP) performance on hyper-relational KGs suffer from fundamental flaws and thus develop a new Wikidata-based dataset - WD50K. Our experiments demonstrate that StarE based LP model outperforms existing approaches across multiple benchmarks. We also confirm that leveraging qualifiers is vital for link prediction with gains up to 25 MRR points compared to triple-based representations.

Commonsense knowledge graph (CKG) is a special type of knowledge graph (KG), where entities are composed of free-form text. However, most existing CKG completion methods focus on the setting where all the entities are presented at training time. Although this setting is standard for conventional KG completion, it has limitations for CKG completion. At test time, entities in CKGs can be unseen because they may have unseen text/names and entities may be disconnected from the training graph, since CKGs are generally very sparse. Here, we propose to study the inductive learning setting for CKG completion where unseen entities may present at test time. We develop a novel learning framework named InductivE. Different from previous approaches, InductiveE ensures the inductive learning capability by directly computing entity embeddings from raw entity attributes/text. InductiveE consists of a free-text encoder, a graph encoder, and a KG completion decoder. Specifically, the free-text encoder first extracts the textual representation of each entity based on the pre-trained language model and word embedding. The graph encoder is a gated relational graph convolutional neural network that learns from a densified graph for more informative entity representation learning. We develop a method that densifies CKGs by adding edges among semantic-related entities and provide more supportive information for unseen entities, leading to better generalization ability of entity embedding for unseen entities. Finally, inductiveE employs Conv-TransE as the CKG completion decoder. Experimental results show that InductiveE significantly outperforms state-of-the-art baselines in both standard and inductive settings on ATOMIC and ConceptNet benchmarks. InductivE performs especially well on inductive scenarios where it achieves above 48% improvement over present methods.

Clinicians face several significant barriers to search and synthesize accurate, succinct, updated, and trustworthy medical information from several literature sources during the practice of medicine and patient care. In this talk, we will be presenting our research behind the development of a Focused Clinical Search Service, powered by a Healthcare Knowledge Graph, to interpret the query intent behind clinical search queries and retrieve relevant medical snippets from a diverse corpus of medical literature.

Knowledge graph embedding approaches represent nodes and edges of graphs as mathematical vectors. Current approaches focus on embedding complete knowledge graphs, i.e. all nodes and edges. This leads to very high computational requirements on large graphs such as DBpedia or Wikidata. However, for most downstream application scenarios, only a small subset of concepts is of actual interest. In this paper, we present RDF2Vec Light, a lightweight embedding approach based on RDF2Vec which generates vectors for only a subset of entities. To that end, RDF2Vec Light only traverses and processes a subgraph of the knowledge graph. Our method allows the application of embeddings of very large knowledge graphs in scenarios where such embeddings were not possible before due to a significantly lower runtime and significantly reduced hardware requirements.

Knowledge graphs (KGs) are of great importance to many real world applications, but they generally suffer from incomplete information in the form of missing relations between entities. Knowledge graph completion (also known as relation prediction) is the task of inferring missing facts given existing ones. Most of the existing work is proposed by maximizing the likelihood of observed instance-level triples. Not much attention, however, is paid to the ontological information, such as type information of entities and relations. In this work, we propose a type-augmented relation prediction (TaRP) method, where we apply both the type information and instance-level information for relation prediction. In particular, type information and instance-level information are encoded as prior probabilities and likelihoods of relations respectively, and are combined by following Bayes' rule. Our proposed TaRP method achieves significantly better performance than state-of-the-art methods on three benchmark datasets: FB15K, YAGO26K-906, and DB111K-174. In addition, we show that TaRP achieves significantly improved data efficiency. More importantly, the type information extracted from a specific dataset can generalize well to other datasets through the proposed TaRP model.

As a novel contribution to the problem of semantifying biological assays, in this paper, we propose a neural-network-based approach to automatically semantify, thereby structure, unstructured bioassay text descriptions. Experimental evaluations, to this end, show promise as the neural-based semantification significantly outperforms a naive frequency-based baseline approach. Specifically, the neural method attains 72% F1 versus 47% F1 from the frequency-based method.

We present CoDEx, a set of knowledge graph Completion Datasets Extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from a popular link prediction benchmark by showing that CoDEx covers more diverse and interpretable content, and contains fewer relation patterns that can be covered by trivial frequency-based rules. Data, code, and pretrained models are available at https://github.com/tsafavi/codex.

Knowledge Graph Embedding (KGE) is a popular method for KG reasoning and usually a higher dimensional one ensures better reasoning capability. However, high-dimensional KGEs pose huge challenges to storage and computing resources and are not suitable for resource-limited or time-constrained applications, for which faster and cheaper reasoning is necessary. To address this problem, we propose DistilE, a knowledge distillation method to build low-dimensional student KGE from pre-trained high-dimensional teacher KGE. We take the original KGE loss as hard label loss and design specific soft label loss for different KGEs in DistilE. We also propose a two-stage distillation approach to make the student and teacher adapt to each other and further improve the reasoning capability of the student. Our DistilE is general enough to be applied to various KGEs. Experimental results of link prediction show that our method successfully distills a good student which performs better than a same dimensional one directly trained, and sometimes even better than the teacher, and it can achieve 2 times - 8 times embedding compression rate and more than 10 times faster inference speed than the teacher with a small performance loss. We also experimentally prove the effectiveness of our two-stage training proposal via ablation study.

Most knowledge graph use cases are data-centric, focusing on representing data entities and their semantic relationships. There are no published success stories to represent large-scale complicated business logic with knowledge graph technologies. In this paper, we will share our innovative and practical approach to representing complicated U.S. and Canadian income tax compliance logic (calculations and rules) via a large-scale knowledge graph. We will cover how the Tax Knowledge Graph is constructed and automated, how it is used to calculate tax refunds, reasoned to find missing info, and navigated to explain the calculated results. The Tax Knowledge Graph has helped transform Intuit's flagship TurboTax product into a smart and personalized experience, accelerating and automating the tax preparation process while instilling confidence for millions of customers.