scholarly journals Improving rare disease classification using imperfect knowledge graph

2019 ◽  
Vol 19 (S5) ◽  
Author(s):  
Xuedong Li ◽  
Yue Wang ◽  
Dongwu Wang ◽  
Walter Yuan ◽  
Dezhong Peng ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Medical Knowledge ◽  
Classification Algorithm ◽  
Disease Classification ◽  
Knowledge Graph ◽  
Data Set ◽  
Wide Range ◽  
Imperfect Knowledge ◽  
Knowledge Graphs

Abstract Background Accurately recognizing rare diseases based on symptom description is an important task in patient triage, early risk stratification, and target therapies. However, due to the very nature of rare diseases, the lack of historical data poses a great challenge to machine learning-based approaches. On the other hand, medical knowledge in automatically constructed knowledge graphs (KGs) has the potential to compensate the lack of labeled training examples. This work aims to develop a rare disease classification algorithm that makes effective use of a knowledge graph, even when the graph is imperfect. Method We develop a text classification algorithm that represents a document as a combination of a “bag of words” and a “bag of knowledge terms,” where a “knowledge term” is a term shared between the document and the subgraph of KG relevant to the disease classification task. We use two Chinese disease diagnosis corpora to evaluate the algorithm. The first one, HaoDaiFu, contains 51,374 chief complaints categorized into 805 diseases. The second data set, ChinaRe, contains 86,663 patient descriptions categorized into 44 disease categories. Results On the two evaluation data sets, the proposed algorithm delivers robust performance and outperforms a wide range of baselines, including resampling, deep learning, and feature selection approaches. Both classification-based metric (macro-averaged F1 score) and ranking-based metric (mean reciprocal rank) are used in evaluation. Conclusion Medical knowledge in large-scale knowledge graphs can be effectively leveraged to improve rare diseases classification models, even when the knowledge graph is incomplete.

scholarly journals Phenotypically Similar Rare Disease Identification from an Integrative Knowledge Graph for Data Harmonization: Preliminary Study

10.2196/18395 ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. e18395
Author(s):  
Qian Zhu ◽  
Dac-Trung Nguyen ◽  
Gioconda Alyea ◽  
Karen Hanson ◽  
Eric Sid ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Clinical Manifestations ◽  
Classification Systems ◽  
Disease Classification ◽  
Knowledge Graph ◽  
Data Harmonization ◽  
Disease Similarity ◽  
Similar Disease ◽  
Preliminary Study

Background Although many efforts have been made to develop comprehensive disease resources that capture rare disease information for the purpose of clinical decision making and education, there is no standardized protocol for defining and harmonizing rare diseases across multiple resources. This introduces data redundancy and inconsistency that may ultimately increase confusion and difficulty for the wide use of these resources. To overcome such encumbrances, we report our preliminary study to identify phenotypical similarity among genetic and rare diseases (GARD) that are presenting similar clinical manifestations, and support further data harmonization. Objective To support rare disease data harmonization, we aim to systematically identify phenotypically similar GARD diseases from a disease-oriented integrative knowledge graph and determine their similarity types. Methods We identified phenotypically similar GARD diseases programmatically with 2 methods: (1) We measured disease similarity by comparing disease mappings between GARD and other rare disease resources, incorporating manual assessment; 2) we derived clinical manifestations presenting among sibling diseases from disease classifications and prioritized the identified similar diseases based on their phenotypes and genotypes. Results For disease similarity comparison, approximately 87% (341/392) identified, phenotypically similar disease pairs were validated; 80% (271/392) of these disease pairs were accurately identified as phenotypically similar based on similarity score. The evaluation result shows a high precision (94%) and a satisfactory quality (86% F measure). By deriving phenotypical similarity from Monarch Disease Ontology (MONDO) and Orphanet disease classification trees, we identified a total of 360 disease pairs with at least 1 shared clinical phenotype and gene, which were applied for prioritizing clinical relevance. A total of 662 phenotypically similar disease pairs were identified and will be applied for GARD data harmonization. Conclusions We successfully identified phenotypically similar rare diseases among the GARD diseases via 2 approaches, disease mapping comparison and phenotypical similarity derivation from disease classification systems. The results will not only direct GARD data harmonization in expanding translational science research but will also accelerate data transparency and consistency across different disease resources and terminologies, helping to build a robust and up-to-date knowledge resource on rare diseases.

scholarly journals Phenotypically Similar Rare Disease Identification from an Integrative Knowledge Graph for Data Harmonization: Preliminary Study (Preprint)

2020 ◽  
Author(s):  
Qian Zhu ◽  
Dac-Trung Nguyen ◽  
Gioconda Alyea ◽  
Karen Hanson ◽  
Eric Sid ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Clinical Manifestations ◽  
Classification Systems ◽  
Disease Classification ◽  
Knowledge Graph ◽  
Data Harmonization ◽  
Disease Similarity ◽  
Similar Disease ◽  
Preliminary Study

BACKGROUND Although many efforts have been made to develop comprehensive disease resources that capture rare disease information for the purpose of clinical decision making and education, there is no standardized protocol for defining and harmonizing rare diseases across multiple resources. This introduces data redundancy and inconsistency that may ultimately increase confusion and difficulty for the wide use of these resources. To overcome such encumbrances, we report our preliminary study to identify phenotypical similarity among genetic and rare diseases (GARD) that are presenting similar clinical manifestations, and support further data harmonization. OBJECTIVE To support rare disease data harmonization, we aim to systematically identify phenotypically similar GARD diseases from a disease-oriented integrative knowledge graph and determine their similarity types. METHODS We identified phenotypically similar GARD diseases programmatically with 2 methods: (1) We measured disease similarity by comparing disease mappings between GARD and other rare disease resources, incorporating manual assessment; 2) we derived clinical manifestations presenting among sibling diseases from disease classifications and prioritized the identified similar diseases based on their phenotypes and genotypes. RESULTS For disease similarity comparison, approximately 87% (341/392) identified, phenotypically similar disease pairs were validated; 80% (271/392) of these disease pairs were accurately identified as phenotypically similar based on similarity score. The evaluation result shows a high precision (94%) and a satisfactory quality (86% F measure). By deriving phenotypical similarity from Monarch Disease Ontology (MONDO) and Orphanet disease classification trees, we identified a total of 360 disease pairs with at least 1 shared clinical phenotype and gene, which were applied for prioritizing clinical relevance. A total of 662 phenotypically similar disease pairs were identified and will be applied for GARD data harmonization. CONCLUSIONS We successfully identified phenotypically similar rare diseases among the GARD diseases via 2 approaches, disease mapping comparison and phenotypical similarity derivation from disease classification systems. The results will not only direct GARD data harmonization in expanding translational science research but will also accelerate data transparency and consistency across different disease resources and terminologies, helping to build a robust and up-to-date knowledge resource on rare diseases.

scholarly journals Research of Personalized Recommendation Technology Based on Knowledge Graphs

2021 ◽  
Vol 11 (15) ◽  
pp. 7104
Author(s):  
Xu Yang ◽  
Ziyi Huan ◽  
Yisong Zhai ◽  
Ting Lin
Keyword(s):  
Neural Network ◽  
Hot Spot ◽  
Experimental Results ◽  
Graph Representation ◽  
Personalized Recommendation ◽  
Knowledge Graph ◽  
Learning Technology ◽  
Data Set ◽  
Model Based ◽  
Knowledge Graphs

Nowadays, personalized recommendation based on knowledge graphs has become a hot spot for researchers due to its good recommendation effect. In this paper, we researched personalized recommendation based on knowledge graphs. First of all, we study the knowledge graphs’ construction method and complete the construction of the movie knowledge graphs. Furthermore, we use Neo4j graph database to store the movie data and vividly display it. Then, the classical translation model TransE algorithm in knowledge graph representation learning technology is studied in this paper, and we improved the algorithm through a cross-training method by using the information of the neighboring feature structures of the entities in the knowledge graph. Furthermore, the negative sampling process of TransE algorithm is improved. The experimental results show that the improved TransE model can more accurately vectorize entities and relations. Finally, this paper constructs a recommendation model by combining knowledge graphs with ranking learning and neural network. We propose the Bayesian personalized recommendation model based on knowledge graphs (KG-BPR) and the neural network recommendation model based on knowledge graphs(KG-NN). The semantic information of entities and relations in knowledge graphs is embedded into vector space by using improved TransE method, and we compare the results. The item entity vectors containing external knowledge information are integrated into the BPR model and neural network, respectively, which make up for the lack of knowledge information of the item itself. Finally, the experimental analysis is carried out on MovieLens-1M data set. The experimental results show that the two recommendation models proposed in this paper can effectively improve the accuracy, recall, F1 value and MAP value of recommendation.

scholarly journals Virtual Knowledge Graphs: An Overview of Systems and Use Cases

2019 ◽  
Vol 1 (3) ◽  
pp. 201-223 ◽  
Author(s):  
Guohui Xiao ◽  
Linfang Ding ◽  
Benjamin Cogrel ◽  
Diego Calvanese
Keyword(s):  
Data Integration ◽  
Domain Knowledge ◽  
Data Access ◽  
Use Cases ◽  
Future Research ◽  
Knowledge Graph ◽  
Research Directions ◽  
Wide Range ◽  
Future Research Directions ◽  
Knowledge Graphs

In this paper, we present the virtual knowledge graph (VKG) paradigm for data integration and access, also known in the literature as Ontology-based Data Access. Instead of structuring the integration layer as a collection of relational tables, the VKG paradigm replaces the rigid structure of tables with the flexibility of graphs that are kept virtual and embed domain knowledge. We explain the main notions of this paradigm, its tooling ecosystem and significant use cases in a wide range of applications. Finally, we discuss future research directions.

scholarly journals The use of machine learning in rare diseases: a scoping review

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Julia Schaefer ◽  
Moritz Lehne ◽  
Josef Schepers ◽  
Fabian Prasser ◽  
Sylvia Thun
Keyword(s):  
Machine Learning ◽  
Rare Disease ◽  
Rare Diseases ◽  
Scoping Review ◽  
Input Data ◽  
Skin Diseases ◽  
Demographic Data ◽  
Support Vector ◽  
Research Activity ◽  
Data Set

Abstract Background Emerging machine learning technologies are beginning to transform medicine and healthcare and could also improve the diagnosis and treatment of rare diseases. Currently, there are no systematic reviews that investigate, from a general perspective, how machine learning is used in a rare disease context. This scoping review aims to address this gap and explores the use of machine learning in rare diseases, investigating, for example, in which rare diseases machine learning is applied, which types of algorithms and input data are used or which medical applications (e.g., diagnosis, prognosis or treatment) are studied. Methods Using a complex search string including generic search terms and 381 individual disease names, studies from the past 10 years (2010–2019) that applied machine learning in a rare disease context were identified on PubMed. To systematically map the research activity, eligible studies were categorized along different dimensions (e.g., rare disease group, type of algorithm, input data), and the number of studies within these categories was analyzed. Results Two hundred eleven studies from 32 countries investigating 74 different rare diseases were identified. Diseases with a higher prevalence appeared more often in the studies than diseases with a lower prevalence. Moreover, some rare disease groups were investigated more frequently than to be expected (e.g., rare neurologic diseases and rare systemic or rheumatologic diseases), others less frequently (e.g., rare inborn errors of metabolism and rare skin diseases). Ensemble methods (36.0%), support vector machines (32.2%) and artificial neural networks (31.8%) were the algorithms most commonly applied in the studies. Only a small proportion of studies evaluated their algorithms on an external data set (11.8%) or against a human expert (2.4%). As input data, images (32.2%), demographic data (27.0%) and “omics” data (26.5%) were used most frequently. Most studies used machine learning for diagnosis (40.8%) or prognosis (38.4%) whereas studies aiming to improve treatment were relatively scarce (4.7%). Patient numbers in the studies were small, typically ranging from 20 to 99 (35.5%). Conclusion Our review provides an overview of the use of machine learning in rare diseases. Mapping the current research activity, it can guide future work and help to facilitate the successful application of machine learning in rare diseases.

scholarly journals Path-based knowledge reasoning with textual semantic information for medical knowledge graph completion

2021 ◽  
Vol 21 (S9) ◽  
Author(s):  
Yinyu Lan ◽  
Shizhu He ◽  
Kang Liu ◽  
Xiangrong Zeng ◽  
Shengping Liu ◽  
...  
Keyword(s):  
Semantic Information ◽  
State Of The Art ◽  
Semantic Representation ◽  
Medical Knowledge ◽  
The State ◽  
Language Models ◽  
Knowledge Graph ◽  
Knowledge Reasoning ◽  
Numerical Computing ◽  
Knowledge Graphs

Abstract Background Knowledge graphs (KGs), especially medical knowledge graphs, are often significantly incomplete, so it necessitating a demand for medical knowledge graph completion (MedKGC). MedKGC can find new facts based on the existed knowledge in the KGs. The path-based knowledge reasoning algorithm is one of the most important approaches to this task. This type of method has received great attention in recent years because of its high performance and interpretability. In fact, traditional methods such as path ranking algorithm take the paths between an entity pair as atomic features. However, the medical KGs are very sparse, which makes it difficult to model effective semantic representation for extremely sparse path features. The sparsity in the medical KGs is mainly reflected in the long-tailed distribution of entities and paths. Previous methods merely consider the context structure in the paths of knowledge graph and ignore the textual semantics of the symbols in the path. Therefore, their performance cannot be further improved due to the two aspects of entity sparseness and path sparseness. Methods To address the above issues, this paper proposes two novel path-based reasoning methods to solve the sparsity issues of entity and path respectively, which adopts the textual semantic information of entities and paths for MedKGC. By using the pre-trained model BERT, combining the textual semantic representations of the entities and the relationships, we model the task of symbolic reasoning in the medical KG as a numerical computing issue in textual semantic representation. Results Experiments results on the publicly authoritative Chinese symptom knowledge graph demonstrated that the proposed method is significantly better than the state-of-the-art path-based knowledge graph reasoning methods, and the average performance is improved by 5.83% for all relations. Conclusions In this paper, we propose two new knowledge graph reasoning algorithms, which adopt textual semantic information of entities and paths and can effectively alleviate the sparsity problem of entities and paths in the MedKGC. As far as we know, it is the first method to use pre-trained language models and text path representations for medical knowledge reasoning. Our method can complete the impaired symptom knowledge graph in an interpretable way, and it outperforms the state-of-the-art path-based reasoning methods.

scholarly journals A Method to Learn Embedding of a Probabilistic Medical Knowledge Graph: Algorithm Development (Preprint)

2019 ◽  
Author(s):  
Linfeng Li ◽  
Peng Wang ◽  
Yao Wang ◽  
Shenghui Wang ◽  
Jun Yan ◽  
...  
Keyword(s):  
Medical Records ◽  
Large Scale ◽  
Semantic Representation ◽  
Medical Knowledge ◽  
Mapping Function ◽  
Graph Algorithm ◽  
Knowledge Graph ◽  
Knowledge Graphs ◽  
Representation Method ◽  
Better Than

BACKGROUND Knowledge graph embedding is an effective semantic representation method for entities and relations in knowledge graphs. Several translation-based algorithms, including TransE, TransH, TransR, TransD, and TranSparse, have been proposed to learn effective embedding vectors from typical knowledge graphs in which the relations between head and tail entities are deterministic. However, in medical knowledge graphs, the relations between head and tail entities are inherently probabilistic. This difference introduces a challenge in embedding medical knowledge graphs. OBJECTIVE We aimed to address the challenge of how to learn the probability values of triplets into representation vectors by making enhancements to existing TransX (where X is E, H, R, D, or Sparse) algorithms, including the following: (1) constructing a mapping function between the score value and the probability, and (2) introducing probability-based loss of triplets into the original margin-based loss function. METHODS We performed the proposed PrTransX algorithm on a medical knowledge graph that we built from large-scale real-world electronic medical records data. We evaluated the embeddings using link prediction task. RESULTS Compared with the corresponding TransX algorithms, the proposed PrTransX performed better than the TransX model in all evaluation indicators, achieving a higher proportion of corrected entities ranked in the top 10 and normalized discounted cumulative gain of the top 10 predicted tail entities, and lower mean rank. CONCLUSIONS The proposed PrTransX successfully incorporated the uncertainty of the knowledge triplets into the embedding vectors.

scholarly journals How to design a registry for undiagnosed patients in the framework of rare disease diagnosis – suggestions on software, data set and coding system

2021 ◽  
Author(s):  
Alexandra Berger ◽  
Anne-Kathrin Rustemeier ◽  
Jens Göbel ◽  
Dennis Kadioglu ◽  
Vanessa Britz ◽  
...  
Keyword(s):  
Open Source ◽  
Rare Disease ◽  
Rare Diseases ◽  
Action Plan ◽  
Correct Diagnosis ◽  
Disease Patient ◽  
Disease Diagnosis ◽  
Clinical Findings ◽  
Snomed Ct ◽  
Data Set

Abstract Background: About 30 million people in the EU and USA, respectively, suffer from a rare disease. Driven by European legislative requirements, national strategies for the improvement of care in rare diseases are being developed. To improve timely and correct diagnosis for patients with rare diseases, the development of a registry for undiagnosed patients was recommended by the German National Action Plan. In this paper we focus on the question on how such a registry for undiagnosed patients can be built and which information it should contain.Results: To develop a registry for undiagnosed patients, a software for data acquisition and storage, an appropriate data set and an applicable terminology/classification system for the data collected are needed. We have used the open-source software OSSE (Open-Source Registry System for Rare Diseases) to build the registry for undiagnosed patients. Our data set is based on the minimal data set for rare disease patient registries recommended by the European Rare Disease Registries Platform. We extended this Common Data Set to also include symptoms, clinical findings and other diagnoses. In order to ensure findability, comparability and statistical analysis, symptoms, clinical findings and diagnoses have to be encoded. We evaluated three medical ontologies (SNOMED CT, HPO and LOINC) for their usefulness. With exact matches of 98% of tested medical terms, a mean number of five deposited synonyms, SNOMED CT seemed to fit our needs best. HPO and LOINC provided 73% and 31% of exacts matches of clinical terms respectively. Allowing more generic codes for a defined symptom, with SNOMED CT 99%, with HPO 89% and with LOINC 39% of terms could be encoded.Conclusions: With the use of the OSSE software and a data set, which, in addition to the Common Data Set, focuses on symptoms and clinical findings, a functioning and meaningful registry for undiagnosed patients can be implemented. The next step is the implementation of the registry in centres for rare diseases. With the help of medical informatics and big data analysis, case similarity analyses could be realized and aid as a decision-support tool enabling diagnosis of some patients.

scholarly journals Research on Medical Knowledge Graph for Stroke

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Binjie Cheng ◽  
Jin Zhang ◽  
Hong Liu ◽  
Meiling Cai ◽  
Ying Wang
Keyword(s):  
Medical Knowledge ◽  
Similarity Measures ◽  
Graph Model ◽  
Knowledge Graph ◽  
Medical Field ◽  
Graph Models ◽  
Experimental Part ◽  
External Data ◽  
Embedded Model ◽  
Knowledge Graphs

Knowledge graph can effectively analyze and construct the essential characteristics of data. At present, scholars have proposed many knowledge graph models from different perspectives, especially in the medical field, but there are still relatively few studies on stroke diseases using medical knowledge graphs. Therefore, this paper will build a medical knowledge graph model for stroke. Firstly, a stroke disease dictionary and an ontology database are built through the international standard medical term sets and semiautomatic extraction-based crowdsourcing website data. Secondly, the external data are linked to the nodes of the existing knowledge graph via the entity similarity measures and the knowledge representation is performed by the knowledge graph embedded model. Thirdly, the structure of the established knowledge graph is modified continuously through iterative updating. Finally, in the experimental part, the proposed stroke medical knowledge graph is applied to the real stroke data and the performance of the proposed knowledge graph approach on the series of Trans ∗ models is compared.

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