Making the most use of abundant information in electronic health records (EHR) is rapidly becoming an important topic in the medical domain. Recent work presented a promising framework that embeds entire features in raw EHR data regardless of its form and medical code standards. The framework, however, only focuses on encoding EHR with minimal preprocessing and fails to consider how to learn efficient EHR representation in terms of computation and memory usage. In this paper, we search for a versatile encoder not only reducing the large data into a manageable size but also well preserving the core information of patients to perform diverse clinical tasks. We found that hierarchically structured Convolutional Neural Network (CNN) often outperforms the state-of-the-art model on diverse tasks such as reconstruction, prediction, and generation, even with fewer parameters and less training time. Moreover, it turns out that making use of the inherent hierarchy of EHR data can boost the performance of any kind of backbone models and clinical tasks performed. Through extensive experiments, we present concrete evidence to generalize our research findings into real-world practice. We give a clear guideline on building the encoder based on the research findings captured while exploring numerous settings.
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Variational Autoencoders and their many variants have displayed impressive ability to perform dimensionality reduction, often achieving state-of-the-art performance. Many current methods however, struggle to learn good representations in High Dimensional, Low Sample Size (HDLSS) tasks, which is an inherently challenging setting. We address this challenge by using an ensemble of lightweight VAEs to learn posteriors over subsets of the feature-space, which get aggregated into a joint posterior in a novel divide-and-conquer approach. Specifically, we present an alternative factorisation of the joint posterior that induces a form of implicit data augmentation that yields greater sample efficiency. Through a series of experiments on eight real-world datasets, we show that our method learns better latent representations in HDLSS settings, which leads to higher accuracy in a downstream classification task. Furthermore, we verify that our approach has a positive effect on disentanglement and achieves a lower estimated Total Correlation on learnt representations. Finally, we show that our approach is robust to partial features at inference, exhibiting little performance degradation even with most features missing.
Deep learning-based super-resolution models have the potential to revolutionize biomedical imaging and diagnoses by effectively tackling various challenges associated with early detection, personalized medicine, and clinical automation. However, the requirement of an extensive collection of high-resolution images presents limitations for widespread adoption in clinical practice. In our experiment, we proposed an approach to effectively train the deep learning-based super-resolution models using only one real image by leveraging self-generated high-resolution images. We employed a mixed metric of image screening to automatically select images with a distribution similar to ground truth, creating an incrementally curated training data set that encourages the model to generate improved images over time. After five training iterations, the proposed deep learning-based super-resolution model experienced a 7.5\% and 5.49\% improvement in structural similarity and peak-signal-to-noise ratio, respectively. Significantly, the model consistently produces visually enhanced results for training, improving its performance while preserving the characteristics of original biomedical images. These findings indicate a potential way to train a deep neural network in a self-revolution manner independent of real-world human data.
Electronic health records (EHRs), which contain patients' medical histories, tend to be written in freely formatted (unstructured) text because they are complicated by their nature. Quickly understanding a patient's history is challenging and critical because writing styles vary among doctors, which may even cause clinical incidents. This paper proposes a Health Record Timeliner system (HeaRT), which visualises patients' clinical histories directly from natural language text in EHRs. Unlike only a few previous attempts, our system achieved feasible and practical performance for the first time, by integrating a state-of-the-art language model that recognises clinical entities (e.g. diseases, medicines, and time expressions) and their temporal relations from the raw text in EHRs and radiology reports. By chronologically aligning the clinical entities to the clinical events extracted from a medical report, this web-based system visualises them in a Gantt chart-like format. Our novel evaluation method showed that the proposed system successfully generated coherent timelines from the two sets of radiology reports describing the same CT scan but written by different radiologists. Real-world assessments are planned to improve the remaining issues.
Time-to-event (TTE) models are used in medicine and other fields for estimating the probability distribution of the time until a specific event occurs. TTE models provide many advantages over classification using fixed time horizons, including naturally handling censored observations, but require more parameters and are challenging to train in settings with limited labeled data. Existing approaches, e.g. proportional hazards or accelerated failure time, employ distributional assumptions to reduce parameters but are vulnerable to model misspecification. In this work, we address these challenges with MOTOR (Many Outcome Time Oriented Representations), a self-supervised model that leverages temporal structure found in collections of timestamped events in electronic health records (EHR) and health insurance claims. MOTOR uses a TTE pretraining objective that predicts the probability distribution of times when events occur, making it well-suited to transfer learning for medical prediction tasks. Having pretrained on EHR and claims data of up to 55M patient records (9B clinical events), we evaluate performance after finetuning for 19 tasks across two datasets. Task-specific models built using MOTOR improve time-dependent C statistics by 4.6% over state-of-the-art while greatly improving sample efficiency, achieving comparable performance to existing methods using only 5% of available task data.
The common standard for quality evaluation of automatic speech recognition (ASR) systems is reference-based metrics such as the Word Error Rate (WER), computed using manual ground-truth transcriptions that are time-consuming and expensive to obtain. This work proposes a multi-language referenceless quality metric, which allows comparing the performance of different ASR models on a speech dataset without ground truth transcriptions. To estimate the quality of ASR hypotheses, a pre-trained language model (LM) is fine-tuned with contrastive learning in a self-supervised learning manner. In experiments conducted on several unseen test datasets consisting of outputs from top commercial ASR engines in various languages, the proposed referenceless metric obtains a much higher correlation with WER scores and their ranks than the perplexity metric from the state-of-art multi-lingual LM in all experiments, and also reduces WER by more than $7\%$ when used for ensembling hypotheses. The fine-tuned model and experiments are made available for the reproducibility: //github.com/aixplain/NoRefER
The remarkable success of deep learning has prompted interest in its application to medical diagnosis. Even tough state-of-the-art deep learning models have achieved human-level accuracy on the classification of different types of medical data, these models are hardly adopted in clinical workflows, mainly due to their lack of interpretability. The black-box-ness of deep learning models has raised the need for devising strategies to explain the decision process of these models, leading to the creation of the topic of eXplainable Artificial Intelligence (XAI). In this context, we provide a thorough survey of XAI applied to medical diagnosis, including visual, textual, and example-based explanation methods. Moreover, this work reviews the existing medical imaging datasets and the existing metrics for evaluating the quality of the explanations . Complementary to most existing surveys, we include a performance comparison among a set of report generation-based methods. Finally, the major challenges in applying XAI to medical imaging are also discussed.
Named entity recognition (NER) is the task to identify text spans that mention named entities, and to classify them into predefined categories such as person, location, organization etc. NER serves as the basis for a variety of natural language applications such as question answering, text summarization, and machine translation. Although early NER systems are successful in producing decent recognition accuracy, they often require much human effort in carefully designing rules or features. In recent years, deep learning, empowered by continuous real-valued vector representations and semantic composition through nonlinear processing, has been employed in NER systems, yielding stat-of-the-art performance. In this paper, we provide a comprehensive review on existing deep learning techniques for NER. We first introduce NER resources, including tagged NER corpora and off-the-shelf NER tools. Then, we systematically categorize existing works based on a taxonomy along three axes: distributed representations for input, context encoder, and tag decoder. Next, we survey the most representative methods for recent applied techniques of deep learning in new NER problem settings and applications. Finally, we present readers with the challenges faced by NER systems and outline future directions in this area.
The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-Net'), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.
Image captioning is a challenging task that combines the field of computer vision and natural language processing. A variety of approaches have been proposed to achieve the goal of automatically describing an image, and recurrent neural network (RNN) or long-short term memory (LSTM) based models dominate this field. However, RNNs or LSTMs cannot be calculated in parallel and ignore the underlying hierarchical structure of a sentence. In this paper, we propose a framework that only employs convolutional neural networks (CNNs) to generate captions. Owing to parallel computing, our basic model is around 3 times faster than NIC (an LSTM-based model) during training time, while also providing better results. We conduct extensive experiments on MSCOCO and investigate the influence of the model width and depth. Compared with LSTM-based models that apply similar attention mechanisms, our proposed models achieves comparable scores of BLEU-1,2,3,4 and METEOR, and higher scores of CIDEr. We also test our model on the paragraph annotation dataset, and get higher CIDEr score compared with hierarchical LSTMs
We study the problem of named entity recognition (NER) from electronic medical records, which is one of the most fundamental and critical problems for medical text mining. Medical records which are written by clinicians from different specialties usually contain quite different terminologies and writing styles. The difference of specialties and the cost of human annotation makes it particularly difficult to train a universal medical NER system. In this paper, we propose a label-aware double transfer learning framework (La-DTL) for cross-specialty NER, so that a medical NER system designed for one specialty could be conveniently applied to another one with minimal annotation efforts. The transferability is guaranteed by two components: (i) we propose label-aware MMD for feature representation transfer, and (ii) we perform parameter transfer with a theoretical upper bound which is also label aware. We conduct extensive experiments on 12 cross-specialty NER tasks. The experimental results demonstrate that La-DTL provides consistent accuracy improvement over strong baselines. Besides, the promising experimental results on non-medical NER scenarios indicate that La-DTL is potential to be seamlessly adapted to a wide range of NER tasks.
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