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Conventional machine learning models, particularly tree-based approaches, have demonstrated promising performance across various clinical prediction tasks using electronic health record (EHR) data. Despite their strengths, these models…

Effective biomedical literature retrieval (BLR) plays a central role in precision medicine informatics. In this paper, we propose GRAPHENE, which is a deep learning based framework for precise BLR. GRAPHENE consists of three main different…

This article reviews recent advances in applying natural language processing (NLP) to Electronic Health Records (EHRs) for computational phenotyping. NLP-based computational phenotyping has numerous applications including diagnosis…

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…

This study proposes a Transformer-based longitudinal modeling method to address challenges in clinical risk classification with heterogeneous Electronic Health Record (EHR) data, including irregular temporal patterns, large modality…

Retrieval augmentation is critical when Language Models (LMs) exploit non-parametric knowledge related to the query through external knowledge bases before reasoning. The retrieved information is incorporated into LMs as context alongside…

Electronic health records (EHRs) are long, noisy, and often redundant, posing a major challenge for the clinicians who must navigate them. Large language models (LLMs) offer a promising solution for extracting and reasoning over this…

Deep Learning based models are currently dominating most state-of-the-art solutions for disease prediction. Existing works employ RNNs along with multiple levels of attention mechanisms to provide interpretability. These deep learning…

In recent years, Deep Learning (DL) models are becoming important due to their demonstrated success at overcoming complex learning problems. DL models have been applied effectively for different Natural Language Processing (NLP) tasks such…

The increasing complexity of clinical decision-making, alongside the rapid expansion of electronic health records (EHR), presents both opportunities and challenges for delivering data-informed care. This paper proposes a clinical decision…

Mining relationships between treatment(s) and medical problem(s) is vital in the biomedical domain. This helps in various applications, such as decision support system, safety surveillance, and new treatment discovery. We propose a deep…

With over 200 million published academic documents and millions of new documents being written each year, academic researchers face the challenge of searching for information within this vast corpus. However, existing retrieval systems…

As an essential task for the architecture, engineering, and construction (AEC) industry, information retrieval (IR) from unstructured textual data based on natural language processing (NLP) is gaining increasing attention. Although various…

While deep learning techniques have shown promising results in many natural language processing (NLP) tasks, it has not been widely applied to the clinical domain. The lack of large datasets and the pervasive use of domain-specific language…

Relation extraction (RE) is one of the most important tasks in information extraction, as it provides essential information for many NLP applications. In this paper, we propose a cross-lingual RE approach that does not require any human…

Large Language Models (LLMs) have achieved impressive progress in natural language processing, but their limited ability to retain long-term context constrains performance on document-level or multi-turn tasks. Retrieval-Augmented…

Dense retrieval (DR) approaches based on powerful pre-trained language models (PLMs) achieved significant advances and have become a key component for modern open-domain question-answering systems. However, they require large amounts of…

Identifying patient cohorts from clinical notes in secondary electronic health records is a fundamental task in clinical information management. However, with the growing number of clinical notes, it becomes challenging to analyze the data…

Cohort studies are of significant importance in the field of healthcare analysis. However, existing methods typically involve manual, labor-intensive, and expert-driven pattern definitions or rely on simplistic clustering techniques that…

Contextual Relation Extraction (CRE) is mainly used for constructing a knowledge graph with a help of ontology. It performs various tasks such as semantic search, query answering, and textual entailment. Relation extraction identifies the…