Related papers: ClinicalBERT: Modeling Clinical Notes and Predicti…

Reliable biomedical and clinical retrieval requires more than strong ranking performance: it requires a practical way to find systematic model failures and curate the training evidence needed to correct them. Late-interaction models such as…

$\textbf{Objective}$ Develop an automatic diagnostic system which only uses textual admission information from Electronic Health Records (EHRs) and assist clinicians with a timely and statistically proved decision tool. The hope is that the…

The rapid growth of biomedical literature poses a significant challenge for curation and interpretation. This has become more evident during the COVID-19 pandemic. LitCovid, a literature database of COVID-19 related papers in PubMed, has…

The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain,…

In the past decade, there has been much discussion about the issue of biased reporting in clinical research. Despite this attention, there have been limited tools developed for the systematic assessment of qualitative statements made in…

A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical…

Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of…

Utilizing clinical texts in survival analysis is difficult because they are largely unstructured. Current automatic extraction models fail to capture textual information comprehensively since their labels are limited in scope. Furthermore,…

We present a Three-level Hierarchical Transformer Network (3-level-HTN) for modeling long-term dependencies across clinical notes for the purpose of patient-level prediction. The network is equipped with three levels of Transformer-based…

Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult…

In this study, we introduce ExBEHRT, an extended version of BEHRT (BERT applied to electronic health records), and apply different algorithms to interpret its results. While BEHRT considers only diagnoses and patient age, we extend the…

International Classification of Diseases (ICD) coding plays an important role in systematically classifying morbidity and mortality data. In this study, we propose a hierarchical label-wise attention Transformer model (HiLAT) for the…

Representations derived from models such as BERT (Bidirectional Encoder Representations from Transformers) and HuBERT (Hidden units BERT), have helped to achieve state-of-the-art performance in dimensional speech emotion recognition.…

Modern computational organic chemistry is becoming increasingly data-driven. There remain a large number of important unsolved problems in this area such as product prediction given reactants, drug discovery, and metric-optimized molecule…

The clinical notes are usually typed into the system by physicians. They are typically required to be marked by standard medical codes, and each code represents a diagnosis or medical treatment procedure. Annotating these notes is time…

Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved…

The field of natural language processing (NLP) has made significant progress with the rapid development of deep learning technologies. One of the research directions in text sentiment analysis is sentiment analysis of medical texts, which…

Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to…

Clinical information extraction, which involves structuring clinical concepts from unstructured medical text, remains a challenging problem that could benefit from the inclusion of tabular background information available in electronic…

Prediction of medical codes from clinical notes is a practical and essential need for every healthcare delivery organization within current medical systems. Automating annotation will save significant time and excessive effort that human…