Using Clinical Notes with Time Series Data for ICU Management

Monitoring patients in ICU is a challenging and high-cost task. Hence, predicting the condition of patients during their ICU stay can help provide better acute care and plan the hospital's resources. There has been continuous progress in machine learning research for ICU management, and most of this work has focused on using time series signals recorded by ICU instruments. In our work, we show that adding clinical notes as another modality improves the performance of the model for three benchmark tasks: in-hospital mortality prediction, modeling decompensation, and length of stay forecasting that play an important role in ICU management. While the time-series data is measured at regular intervals, doctor notes are charted at irregular times, making it challenging to model them together. We propose a method to model them jointly, achieving considerable improvement across benchmark tasks over baseline time-series model. Our implementation can be found at \url{https://github.com/kaggarwal/ClinicalNotesICU}.Comment: Accepted at EMNLP 201

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Artificial Intelligence for In Silico Clinical Trials: A Review

A clinical trial is an essential step in drug development, which is often costly and time-consuming. In silico trials are clinical trials conducted digitally through simulation and modeling as an alternative to traditional clinical trials. AI-enabled in silico trials can increase the case group size by creating virtual cohorts as controls. In addition, it also enables automation and optimization of trial design and predicts the trial success rate. This article systematically reviews papers under three main topics: clinical simulation, individualized predictive modeling, and computer-aided trial design. We focus on how machine learning (ML) may be applied in these applications. In particular, we present the machine learning problem formulation and available data sources for each task. We end with discussing the challenges and opportunities of AI for in silico trials in real-world applications

DuETT: Dual Event Time Transformer for Electronic Health Records

Electronic health records (EHRs) recorded in hospital settings typically contain a wide range of numeric time series data that is characterized by high sparsity and irregular observations. Effective modelling for such data must exploit its time series nature, the semantic relationship between different types of observations, and information in the sparsity structure of the data. Self-supervised Transformers have shown outstanding performance in a variety of structured tasks in NLP and computer vision. But multivariate time series data contains structured relationships over two dimensions: time and recorded event type, and straightforward applications of Transformers to time series data do not leverage this distinct structure. The quadratic scaling of self-attention layers can also significantly limit the input sequence length without appropriate input engineering. We introduce the DuETT architecture, an extension of Transformers designed to attend over both time and event type dimensions, yielding robust representations from EHR data. DuETT uses an aggregated input where sparse time series are transformed into a regular sequence with fixed length; this lowers the computational complexity relative to previous EHR Transformer models and, more importantly, enables the use of larger and deeper neural networks. When trained with self-supervised prediction tasks, that provide rich and informative signals for model pre-training, our model outperforms state-of-the-art deep learning models on multiple downstream tasks from the MIMIC-IV and PhysioNet-2012 EHR datasets.Comment: Accepted at MLHC 2023, camera-ready versio

Attentive Dual Embedding for Understanding Medical Concept in Electronic Health Record

Electronic health records contain a wealth of information on a patient’s healthcare over many visits, such as diagnoses, treatments, drugs administered, and so on. The untapped potential of these data in healthcare analytics is vast. However, given that much of medical information is a cause and effect science, new embedding methods are required to ensure the learning representations reflect the comprehensive interplays between medical concepts and their relationships over time. Unlike one-hot encoding, a distributed representation should preserve these complex interactions as high-quality inputs for machine learning-based healthcare analytics tasks. Therefore, we propose a novel attentive dual embedding method called MC2Vec. MC2Vec captures the proximity relationships between medical concepts through a two-step optimization framework that recursively refines the embedding for superior output. The framework comprises a Skip-gram model to generate the initial embedding and an attentive CBOW model to fine-tune the embedding with temporal information gleaned from sequences of patient visits. Experiments with two public datasets demonstrate that MC2Vec’s produces embeddings of higher quality than five state-of-the-art methods

Preserving the knowledge of long clinical texts using aggregated ensembles of large language models

Clinical texts, such as admission notes, discharge summaries, and progress notes, contain rich and valuable information that can be used for various clinical outcome prediction tasks. However, applying large language models, such as BERT-based models, to clinical texts poses two major challenges: the limitation of input length and the diversity of data sources. This paper proposes a novel method to preserve the knowledge of long clinical texts using aggregated ensembles of large language models. Unlike previous studies which use model ensembling or text aggregation methods separately, we combine ensemble learning with text aggregation and train multiple large language models on two clinical outcome tasks: mortality prediction and length of stay prediction. We show that our method can achieve better results than baselines, ensembling, and aggregation individually, and can improve the performance of large language models while handling long inputs and diverse datasets. We conduct extensive experiments on the admission notes from the MIMIC-III clinical database by combining multiple unstructured and high-dimensional datasets, demonstrating our method's effectiveness and superiority over existing approaches. We also provide a comprehensive analysis and discussion of our results, highlighting our method's applications and limitations for future research in the domain of clinical healthcare. The results and analysis of this study is supportive of our method assisting in clinical healthcare systems by enabling clinical decision-making with robust performance overcoming the challenges of long text inputs and varied datasets.Comment: 17 pages, 4 figures, 4 tables, 9 equations and 1 algorith

Is attention all you need in medical image analysis? A review

Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated

Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions

Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in the deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. In this paper, we provide an extensive survey of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods, publicly available datasets, and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are described in detail. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.Comment: Survey, 41 page