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Pre-trained models such as BERT are widely used in NLP tasks and are fine-tuned to improve the performance of various NLP tasks consistently. Nevertheless, the fine-tuned BERT model trained on our protocol corpus still has a weak…

Embedding models have become essential for retrieval-augmented generation (RAG) tasks, semantic clustering, and text re-ranking. But despite their growing use, many of these come with notable limitations. For example, Jina fails to capture…

Electronic Health Records (EHRs) offer considerable potential for clinical prediction, but their complexity and heterogeneity challenge traditional machine learning. Domain-specific EHR foundation models trained on unlabeled EHR data have…

Robust machine learning relies on access to data that can be used with standardized frameworks in important tasks and the ability to develop models whose performance can be reasonably reproduced. In machine learning for healthcare, the…

Multimodal electronic health record (EHR) data can offer a holistic assessment of a patient's health status, supporting various predictive healthcare tasks. Recently, several studies have embraced the multitask learning approach in the…

Electronic Health Records (EHRs) provide vital contextual information to radiologists and other physicians when making a diagnosis. Unfortunately, because a given patient's record may contain hundreds of notes and reports, identifying…

In recent years, we have witnessed an increased interest in temporal modeling of patient records from large scale Electronic Health Records (EHR). While simpler RNN models have been used for such problems, memory networks, which in other…

Clinical event sequences consist of hundreds of clinical events that represent records of patient care in time. Developing accurate predictive models of such sequences is of a great importance for supporting a variety of models for…

Clinical prediction from structured electronic health records (EHRs) is challenging due to high dimensionality, heterogeneity, class imbalance, and distribution shift. While tabular in-context learning (TICL) and retrieval-augmented methods…

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even…

Biomedical documents such as Electronic Health Records (EHRs) contain a large amount of information in an unstructured format. The data in EHRs is a hugely valuable resource documenting clinical narratives and decisions, but whilst the text…

EHR systems lack a unified code system forrepresenting medical concepts, which acts asa barrier for the deployment of deep learningmodels in large scale to multiple clinics and hos-pitals. To overcome this problem, we…

Embedding algorithms are increasingly used to represent clinical concepts in healthcare for improving machine learning tasks such as clinical phenotyping and disease prediction. Recent studies have adapted state-of-the-art bidirectional…

Domain shift presents a significant challenge in applying Deep Learning to the segmentation of 3D medical images from sources like Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Although numerous Domain Adaptation methods…

Neural network representation learning frameworks have recently shown to be highly effective at a wide range of tasks ranging from radiography interpretation via data-driven diagnostics to clinical decision support. This often superior…

While electronic health records (EHRs) are widely used across various applications in healthcare, most applications use the EHRs in their raw (tabular) format. Relying on raw or simple data pre-processing can greatly limit the performance…

We present a self-supervised, time-to-event (TTE) foundation model called MOTOR (Many Outcome Time Oriented Representations) which is pretrained on timestamped sequences of events in electronic health records (EHR) and health insurance…

Inspired by the success of the General Language Understanding Evaluation benchmark, we introduce the Biomedical Language Understanding Evaluation (BLUE) benchmark to facilitate research in the development of pre-training language…

Electronic Health Record (EHR) data can be represented as discrete counts over a high dimensional set of possible procedures, diagnoses, and medications. Supervised topic models present an attractive option for incorporating EHR data as…

Biomedical Named Entity Recognition (NER) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health…