Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug discovery rely on incorporating information from different biomedical databases. These databases contain various biological entities and relations such as proteins (PDB), genes (Gene Ontology), drugs (DrugBank), diseases (DDB), and protein-protein interactions (BioGRID). The process of semantically integrating heterogeneous biomedical databases is often riddled with imperfections. The quality of data-driven drug discovery relies on the accuracy of the mining methods used and the data's quality as well. Thus, having complete and refined biomedical knowledge graphs is central to achieving more accurate drug discovery outcomes. Here we propose using the latest graph representation learning and embedding models to refine and complete biomedical knowledge graphs. This preliminary work demonstrates learning discrete representations of the integrated biomedical knowledge graph Chem2Bio2RD [3]. We perform a knowledge graph completion and refinement task using a simple top-K cosine similarity measure between the learned embedding vectors to predict missing links between drugs and targets present in the data. We show that this simple procedure can be used alternatively to binary classifiers in link prediction.
Harbin Institute of Technology（哈尔滨工业大学）；Cornell University（康奈尔大学）
Currently, there is a rapidly increasing need for high-quality biomedical knowledge graphs (BioKG) that provide direct and precise biomedical knowledge. In the context of COVID-19, this issue is even more necessary to be highlighted. However, most BioKG construction inevitably includes numerous conflicts and noises deriving from incorrect knowledge descriptions in literature and defective information extraction techniques. Many studies have demonstrated that reasoning upon the knowledge graph is effective in eliminating such conflicts and noises. This paper proposes a method BioGRER to improve…
Knowledge Graph (KG) completion is an important task that greatly benefits knowledge discovery in many fields (e.g. biomedical research). In recent years, learning KG embeddings to perform this task has received considerable attention. Despite the success of KG embedding methods, they predominantly use negative sampling, resulting in increased computational complexity as well as biased predictions due to the closed world assumption. To overcome these limitations, we propose \textbf{KG-NSF}, a negative sampling-free framework for learning KG embeddings based on the cross-correlation matrices of…
Knowledge graph (KG) refinement mainly aims at KG completion and correction (i.e., error detection). However, most conventional KG embedding models only focus on KG completion with an unreasonable assumption that all facts in KG hold without noises, ignoring error detection which also should be significant and essential for KG refinement.In this paper, we propose a novel support-confidence-aware KG embedding framework (SCEF), which implements KG completion and correction simultaneously by learning knowledge representations with both triple support and triple confidence. Specifically, we build …
Knowledge Graph Embeddings (KGE) have become a quite popular class of models specifically devised to deal with ontologies and graph structure data, as they can implicitly encode statistical dependencies between entities and relations in a latent space. KGE techniques are particularly effective for the biomedical domain, where it is quite common to deal with large knowledge graphs underlying complex interactions between biological and chemical objects. Recently in the literature, the PharmKG dataset has been proposed as one of the most challenging knowledge graph biomedical benchmark, with hund…
Knowledge Graph Completion for Action Prediction on Situational Graphs -- A Case Study on Household Tasks
University of Stavanger, Information Access（斯塔万格大学信息访问与人工智能研究所）；Honday Research Institute Europe, Germany（霍恩戴欧洲研究 institute）；University of Mannheim, Data（曼海姆大学数据与网络科学研究所）
Recent advances in the healthcare industry have led to an abundance of unstructured data, making it challenging to perform tasks such as efficient and accurate information retrieval at scale. Our work offers an all-in-one scalable solution for extracting and exploring complex information from large-scale research documents, which would otherwise be tedious. First, we briefly explain our knowledge synthesis process to extract helpful information from unstructured text data of research documents. Then, on top of the knowledge extracted from the documents, we perform complex information retrieval…
Reasoning over paths in large scale knowledge graphs is an important problem for many applications. In this paper we discuss a simple approach to automatically build and rank paths between a source and target entity pair with learned embeddings using a knowledge base completion model (KBC). We assembled a knowledge graph by mining the available biomedical scientific literature and extracted a set of high frequency paths to use for validation. We demonstrate that our method is able to effectively rank a list of known paths between a pair of entities and also come up with plausible paths that ar…
University of Washington（华盛顿大学）；Allen Institute for Artificial Intelligence (AI2)（艾伦人工智能研究所）
Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes. Predicting missing links in these graphs can boost many important applications, such as drug design and repurposing. Recent work has shown that general-domain language models (LMs) can serve as "soft" KGs, and that they can be fine-tuned for the task of KG completion. In this work, we study scientific LMs for KG completion, exploring whether we can tap into their latent knowledge to enhance biomedical link prediction. We evaluate several domain-specific LMs, fine-tuning them on datasets cent…
Knowledge Graphs (KG) constitute a flexible representation of complex relationships between entities particularly useful for biomedical data. These KG, however, are very sparse with many missing edges (facts) and the visualisation of the mesh of interactions nontrivial. Here we apply a compositional model to embed nodes and relationships into a vectorised semantic space to perform graph completion. A visualisation tool based on Convolutional Neural Networks and Self-Organised Maps (SOM) is proposed to extract high-level insights from the KG. We apply this technique to a subset of CTD, containi…
LISN, CNRS (UMR 9015), Paris Saclay University（巴黎萨克雷大学、法国国家科学研究中心LISN实验室（UMR 9015））；LIPN, CNRS (UMR 7030), University Sorbonne Paris Nord（索邦巴黎北大学、法国国家科学研究中心LIPN实验室（UMR 7030））
Knowledge graph embedding techniques are widely used for knowledge graph refinement tasks such as graph completion and triple classification. These techniques aim at embedding the entities and relations of a Knowledge Graph (KG) in a low dimensional continuous feature space. This paper adopts a transformer-based triplet network creating an embedding space that clusters the information about an entity or relation in the KG. It creates textual sequences from facts and fine-tunes a triplet network of pre-trained transformer-based language models. It adheres to an evaluation paradigm that relies o…
The Ohio State University（俄亥俄州立大学）；National Institutes of Health（美国国立卫生研究院）；Washington University in St. Louis（圣路易斯华盛顿大学）
Learning representations for knowledge base entities and concepts is becoming increasingly important for NLP applications. However, recent entity embedding methods have relied on structured resources that are expensive to create for new domains and corpora. We present a distantly-supervised method for jointly learning embeddings of entities and text from an unnanotated corpus, using only a list of mappings between entities and surface forms. We learn embeddings from open-domain and biomedical corpora, and compare against prior methods that rely on human-annotated text or large knowledge graph …
University of Texas Health Science Center at Houston（休斯顿德克萨斯大学健康科学中心）；University of Minnesota（明尼苏达大学）；University of Pennsylvania（宾夕法尼亚大学）；University of Maryland School of Medicine（马里兰大学医学院）
To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep vi…
German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心）
Fact triples are a common form of structured knowledge used within the biomedical domain. As the amount of unstructured scientific texts continues to grow, manual annotation of these texts for the task of relation extraction becomes increasingly expensive. Distant supervision offers a viable approach to combat this by quickly producing large amounts of labeled, but considerably noisy, data. We aim to reduce such noise by extending an entity-enriched relation classification BERT model to the problem of multiple instance learning, and defining a simple data encoding scheme that significantly red…
Carnegie Mellon University（卡内基梅隆大学）；University of Pittsburgh（匹兹堡大学）；Microsoft Research（微软研究院）
Knowledge Graph (KG) completion research usually focuses on densely connected benchmark datasets that are not representative of real KGs. We curate two KG datasets that include biomedical and encyclopedic knowledge and use an existing commonsense KG dataset to explore KG completion in the more realistic setting where dense connectivity is not guaranteed. We develop a deep convolutional network that utilizes textual entity representations and demonstrate that our model outperforms recent KG completion methods in this challenging setting. We find that our model's performance improvements stem pr…
University of California, Davis（加利福尼亚大学戴维斯分校）；Harvard T.H. Chan School of Public Health（哈佛陈曾熙公共卫生学院）
Matrix completion has attracted attention in many fields, including statistics, applied mathematics, and electrical engineering. Most of the works focus on the independent sampling models under which the observed entries are sampled independently. Motivated by applications in the integration of knowledge graphs derived from multi-source biomedical data such as those from Electronic Health Records (EHR) and biomedical text, we propose the {\bf B}lock-wise {\bf O}verlapping {\bf N}oisy {\bf M}atrix {\bf I}ntegration (BONMI) to treat blockwise missingness of symmetric matrices representing relate…
Coupled Tensor-Tensor Completion Method with Applications in Drug Repurposing
Idaho State University（爱达荷州立大学）；Massachusetts Institute of Technology（麻省理工学院）；University of Michigan（密歇根大学）；Statistics Online Computational Resource (SOCR)（统计在线计算资源（SOCR））
Tensor completion is the problem of estimating the missing values of high-order data from partially observed entries. Data corruption due to prevailing outliers poses major challenges to traditional tensor completion algorithms, which catalyzed the development of robust algorithms that alleviate the effect of outliers. However, existing robust methods largely presume that the corruption is sparse, which may not hold in practice. In this paper, we develop a two-stage robust tensor completion approach to deal with tensor completion of visual data with a large amount of gross corruption. A novel …
National University of Singapore（新加坡国立大学）；KAIST（韩国科学技术院）
In this paper, we design and analyze MC2G (Matrix Completion with 2 Graphs), an algorithm that performs matrix completion in the presence of social and item similarity graphs. MC2G runs in quasilinear time and is parameter free. It is based on spectral clustering and local refinement steps. The expected number of sampled entries required for MC2G to succeed (i.e., recover the clusters in the graphs and complete the matrix) matches an information-theoretic lower bound up to a constant factor for a wide range of parameters. We show via extensive experiments on both synthetic and real datasets th…
In clinical practice and biomedical research, measurements are often collected sparsely and irregularly in time while the data acquisition is expensive and inconvenient. Examples include measurements of spine bone mineral density, cancer growth through mammography or biopsy, a progression of defective vision, or assessment of gait in patients with neurological disorders. Since the data collection is often costly and inconvenient, estimation of progression from sparse observations is of great interest for practitioners. From the statistical standpoint, such data is often analyzed in the context…
Department of Computer Science, UC Santa Barbara（计算机科学系，加州大学圣芭芭拉分校）；Center for Control, Dynamical Systems, and Computation, UC Santa Barbara（控制、动态系统与计算中心，加州大学圣芭芭拉分校）；U.S. Army DEVCOM Research Laboratory（美国陆军 DEVCOM 研究实验室）
