The data available in Electronic Health Records (EHRs) provides the opportunity to transform care, and the best way to provide better care for one patient is through learning from the data available on all other patients. Temporal modelling of a patient's medical history, which takes into account the sequence of past events, can be used to predict future events such as a diagnosis of a new disorder or complication of a previous or existing disorder. While most prediction approaches use mostly the structured data in EHRs or a subset of single-domain predictions and outcomes, we present MedGPT a novel transformer-based pipeline that uses Named Entity Recognition and Linking tools (i.e. MedCAT) to structure and organize the free text portion of EHRs and anticipate a range of future medical events (initially disorders). Since a large portion of EHR data is in text form, such an approach benefits from a granular and detailed view of a patient while introducing modest additional noise. MedGPT effectively deals with the noise and the added granularity, and achieves a precision of 0.344, 0.552 and 0.640 (vs LSTM 0.329, 0.538 and 0.633) when predicting the top 1, 3 and 5 candidate future disorders on real world hospital data from King's College Hospital, London, UK (\textasciitilde600k patients). We also show that our model captures medical knowledge by testing it on an experimental medical multiple choice question answering task, and by examining the attentional focus of the model using gradient-based saliency methods.
相關內容
Deep learning has the potential to augment many components of the clinical workflow, such as medical image interpretation. However, the translation of these black box algorithms into clinical practice has been marred by the relative lack of transparency compared to conventional machine learning methods, hindering in clinician trust in the systems for critical medical decision-making. Specifically, common deep learning approaches do not have intuitive ways of expressing uncertainty with respect to cases that might require further human review. Furthermore, the possibility of algorithmic bias has caused hesitancy regarding the use of developed algorithms in clinical settings. To these ends, we explore how conformal methods can complement deep learning models by providing both clinically intuitive way (by means of confidence prediction sets) of expressing model uncertainty as well as facilitating model transparency in clinical workflows. In this paper, we conduct a field survey with clinicians to assess clinical use-cases of conformal predictions. Next, we conduct experiments with a mammographic breast density and dermatology photography datasets to demonstrate the utility of conformal predictions in "rule-in" and "rule-out" disease scenarios. Further, we show that conformal predictors can be used to equalize coverage with respect to patient demographics such as race and skin tone. We find that a conformal predictions to be a promising framework with potential to increase clinical usability and transparency for better collaboration between deep learning algorithms and clinicians.
Uncertainty quantification is a fundamental problem in the analysis and interpretation of synthetic control (SC) methods. We develop conditional prediction intervals in the SC framework, and provide conditions under which these intervals offer finite-sample probability guarantees. Our method allows for covariate adjustment and non-stationary data. The construction begins by noting that the statistical uncertainty of the SC prediction is governed by two distinct sources of randomness: one coming from the construction of the (likely misspecified) SC weights in the pre-treatment period, and the other coming from the unobservable stochastic error in the post-treatment period when the treatment effect is analyzed. Accordingly, our proposed prediction intervals are constructed taking into account both sources of randomness. For implementation, we propose a simulation-based approach along with finite-sample-based probability bound arguments, naturally leading to principled sensitivity analysis methods. We illustrate the numerical performance of our methods using empirical applications and a small simulation study. \texttt{Python}, \texttt{R} and \texttt{Stata} software packages implementing our methodology are available.
Algorithmic fairness has emphasized the role of biased data in automated decision outcomes. Recently, there has been a shift in attention to sources of bias that implicate fairness in other stages in the ML pipeline. We contend that one source of such bias, human preferences in model selection, remains under-explored in terms of its role in disparate impact across demographic groups. Using a deep learning model trained on real-world medical imaging data, we verify our claim empirically and argue that choice of metric for model comparison, especially those that do not take variability into account, can significantly bias model selection outcomes.
Sequential diagnosis prediction on the Electronic Health Record (EHR) has been proven crucial for predictive analytics in the medical domain. EHR data, sequential records of a patient's interactions with healthcare systems, has numerous inherent characteristics of temporality, irregularity and data insufficiency. Some recent works train healthcare predictive models by making use of sequential information in EHR data, but they are vulnerable to irregular, temporal EHR data with the states of admission/discharge from hospital, and insufficient data. To mitigate this, we propose an end-to-end robust transformer-based model called SETOR, which exploits neural ordinary differential equation to handle both irregular intervals between a patient's visits with admitted timestamps and length of stay in each visit, to alleviate the limitation of insufficient data by integrating medical ontology, and to capture the dependencies between the patient's visits by employing multi-layer transformer blocks. Experiments conducted on two real-world healthcare datasets show that, our sequential diagnoses prediction model SETOR not only achieves better predictive results than previous state-of-the-art approaches, irrespective of sufficient or insufficient training data, but also derives more interpretable embeddings of medical codes. The experimental codes are available at the GitHub repository (//github.com/Xueping/SETOR).
External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
This paper strives to find amidst a set of sentences the one best describing the content of a given image or video. Different from existing works, which rely on a joint subspace for their image and video caption retrieval, we propose to do so in a visual space exclusively. Apart from this conceptual novelty, we contribute \emph{Word2VisualVec}, a deep neural network architecture that learns to predict a visual feature representation from textual input. Example captions are encoded into a textual embedding based on multi-scale sentence vectorization and further transferred into a deep visual feature of choice via a simple multi-layer perceptron. We further generalize Word2VisualVec for video caption retrieval, by predicting from text both 3-D convolutional neural network features as well as a visual-audio representation. Experiments on Flickr8k, Flickr30k, the Microsoft Video Description dataset and the very recent NIST TrecVid challenge for video caption retrieval detail Word2VisualVec's properties, its benefit over textual embeddings, the potential for multimodal query composition and its state-of-the-art results.
Multi-source translation is an approach to exploit multiple inputs (e.g. in two different languages) to increase translation accuracy. In this paper, we examine approaches for multi-source neural machine translation (NMT) using an incomplete multilingual corpus in which some translations are missing. In practice, many multilingual corpora are not complete due to the difficulty to provide translations in all of the relevant languages (for example, in TED talks, most English talks only have subtitles for a small portion of the languages that TED supports). Existing studies on multi-source translation did not explicitly handle such situations. This study focuses on the use of incomplete multilingual corpora in multi-encoder NMT and mixture of NMT experts and examines a very simple implementation where missing source translations are replaced by a special symbol <NULL>. These methods allow us to use incomplete corpora both at training time and test time. In experiments with real incomplete multilingual corpora of TED Talks, the multi-source NMT with the <NULL> tokens achieved higher translation accuracies measured by BLEU than those by any one-to-one NMT systems.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
Tumor growth is associated with cell invasion and mass-effect, which are traditionally formulated by mathematical models, namely reaction-diffusion equations and biomechanics. Such models can be personalized based on clinical measurements to build the predictive models for tumor growth. In this paper, we investigate the possibility of using deep convolutional neural networks (ConvNets) to directly represent and learn the cell invasion and mass-effect, and to predict the subsequent involvement regions of a tumor. The invasion network learns the cell invasion from information related to metabolic rate, cell density and tumor boundary derived from multimodal imaging data. The expansion network models the mass-effect from the growing motion of tumor mass. We also study different architectures that fuse the invasion and expansion networks, in order to exploit the inherent correlations among them. Our network can easily be trained on population data and personalized to a target patient, unlike most previous mathematical modeling methods that fail to incorporate population data. Quantitative experiments on a pancreatic tumor data set show that the proposed method substantially outperforms a state-of-the-art mathematical model-based approach in both accuracy and efficiency, and that the information captured by each of the two subnetworks are complementary.
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191