Enhancing Error Detection on Medical Knowledge Graphs via Intrinsic Label.

The construction of medical knowledge graphs (MKGs) is steadily progressing from manual to automatic methods, which inevitably introduce noise, which could impair the performance of downstream healthcare applications. Existing error detection approaches depend on the topological structure and external labels of entities in MKGs to improve their quality. Nevertheless, due to the cost of manual annotation and imperfect automatic algorithms, precise entity labels in MKGs cannot be readily obtained.

GC-CDSS: Personalized gastric cancer treatment recommendations system based on knowledge graph.

Background: Gastric cancer (GC) is one of the most common malignant tumors in the world, posing a serious threat to human health. Currently, gastric cancer treatment strategies emphasize a multidisciplinary team (MDT) consultation approach. However, there are numerous treatment guidelines and insights from clinical trials.

Integration of multiple terminology bases: a multi-view alignment method using the hierarchical structure.

Motivation: In the medical field, multiple terminology bases coexist across different institutions and contexts, often resulting in the presence of redundant terms. The identification of overlapping terms among these bases holds significant potential for harmonizing multiple standards and establishing unified framework, which enhances user access to comprehensive and well-structured medical information. However, the majority of terminology bases exhibit differences not only in semantic aspects but also in the hierarchy of their classification systems.

A co-adaptive duality-aware framework for biomedical relation extraction.

Motivation: Biomedical relation extraction is a vital task for electronic health record mining and biomedical knowledge base construction. Previous work often adopts pipeline methods or joint methods to extract subject, relation, and object while ignoring the interaction of subject-object entity pair and relation within the triplet structure. However, we observe that entity pair and relation within a triplet are highly related, which motivates us to build a framework to extract triplets that can capture the rich interactions among the elements in a triplet.

Subsequence and distant supervision based active learning for relation extraction of Chinese medical texts.

In recent years, relation extraction on unstructured texts has become an important task in medical research. However, relation extraction requires a large amount of labeled corpus, manually annotating sequences is time consuming and expensive. Therefore, efficient and economical methods for annotating sequences are required to ensure the performance of relational extraction.

ST-Unet: Swin Transformer boosted U-Net with Cross-Layer Feature Enhancement for medical image segmentation.

Medical image segmentation is an essential task in clinical diagnosis and case analysis. Most of the existing methods are based on U-shaped convolutional neural networks (CNNs), and one of disadvantages is that the long-term dependencies and global contextual connections cannot be effectively established, which results in inaccuracy segmentation. For fully using low-level features to enhance global features and reduce the semantic gap between encoding and decoding stages, we propose a novel Swin Transformer boosted U-Net (ST-Unet) for medical image processing in this paper, in which Swin Transformer and CNNs are used as encoder and decoder respectively.

A combined recall and rank framework with online negative sampling for Chinese procedure terminology normalization.

Motivation: Medical terminology normalization aims to map the clinical mention to terminologies coming from a knowledge base, which plays an important role in analyzing electronic health record and many downstream tasks. In this article, we focus on Chinese procedure terminology normalization. The expressions of terminology are various and one medical mention may be linked to multiple terminologies.

Lab indicators standardization method for the regional healthcare platform: a case study on heart failure.

Background: Laboratory indicator test results in electronic health records have been applied to many clinical big data analysis. However, it is quite common that the same laboratory examination item (i.e.

Representation learning for clinical time series prediction tasks in electronic health records.

Background: Electronic health records (EHRs) provide possibilities to improve patient care and facilitate clinical research. However, there are many challenges faced by the applications of EHRs, such as temporality, high dimensionality, sparseness, noise, random error and systematic bias. In particular, temporal information is difficult to effectively use by traditional machine learning methods while the sequential information of EHRs is very useful.

Constructing Large Scale Cohort for Clinical Study on Heart Failure with Electronic Health Record in Regional Healthcare Platform: Challenges and Strategies in Data Reuse.

Regional healthcare platforms collect clinical data from hospitals in specific areas for the purpose of healthcare management. It is a common requirement to reuse the data for clinical research. However, we have to face challenges like the inconsistence of terminology in electronic health records (EHR) and the complexities in data quality and data formats in regional healthcare platform.

Chinese Clinical Named Entity Recognition Using Residual Dilated Convolutional Neural Network With Conditional Random Field.

Clinical named entity recognition (CNER) is a fundamental and crucial task for clinical and translation research. In recent years, deep learning methods have achieved significant success in CNER tasks. However, these methods depend greatly on recurrent neural networks (RNNs), which maintain a vector of hidden activations that are propagated through time, thus causing too much time to train models.

QAnalysis: a question-answer driven analytic tool on knowledge graphs for leveraging electronic medical records for clinical research.

Background: While doctors should analyze a large amount of electronic medical record (EMR) data to conduct clinical research, the analyzing process requires information technology (IT) skills, which is difficult for most doctors in China.

Methods: In this paper, we build a novel tool QAnalysis, where doctors enter their analytic requirements in their natural language and then the tool returns charts and tables to the doctors. For a given question from a user, we first segment the sentence, and then we use grammar parser to analyze the structure of the sentence.

Incorporating dictionaries into deep neural networks for the Chinese clinical named entity recognition.

Clinical named entity recognition aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other natural language processing tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets.

Mortality prediction system for heart failure with orthogonal relief and dynamic radius means.

Objective: This paper constructs a mortality prediction system based on a real-world dataset. This mortality prediction system aims to predict mortality in heart failure (HF) patients. Effective mortality prediction can improve resources allocation and clinical outcomes, avoiding inappropriate overtreatment of low-mortality patients and discharging of high-mortality patients.

An automatic approach for constructing a knowledge base of symptoms in Chinese.

Background: While a large number of well-known knowledge bases (KBs) in life science have been published as Linked Open Data, there are few KBs in Chinese. However, KBs in Chinese are necessary when we want to automatically process and analyze electronic medical records (EMRs) in Chinese. Of all, the symptom KB in Chinese is the most seriously in need, since symptoms are the starting point of clinical diagnosis.

Self-supervised Chinese ontology learning from online encyclopedias.

Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into ontological form.