Towards Using Word Embedding Vector Space for Better Cohort Analysis

On websites like Reddit, users join communities where they discuss specific topics which cluster them into possible cohorts. The authors within these cohorts have the opportunity to post more openly under the blanket of anonymity, and such openness provides a more accurate signal on the real issues individuals are facing. Some communities contain discussions about mental health struggles such as depression and suicidal ideation. To better understand and analyse these individuals, we propose to exploit properties of word embeddings that group related concepts close to each other in the embeddings space. For the posts from each topically situated sub-community, we build a word embeddings model and use handcrafted lexicons to identify emotions, values and psycholinguistically relevant concepts. We then extract insights into ways users perceive these concepts by measuring distances between them and references made by users either to themselves, others or other things around them. We show how our proposed approach can extract meaningful signals that go beyond the kinds of analyses performed at the individual word level

Classification of Radiology Reports Using Neural Attention Models

The electronic health record (EHR) contains a large amount of multi-dimensional and unstructured clinical data of significant operational and research value. Distinguished from previous studies, our approach embraces a double-annotated dataset and strays away from obscure "black-box" models to comprehensive deep learning models. In this paper, we present a novel neural attention mechanism that not only classifies clinically important findings. Specifically, convolutional neural networks (CNN) with attention analysis are used to classify radiology head computed tomography reports based on five categories that radiologists would account for in assessing acute and communicable findings in daily practice. The experiments show that our CNN attention models outperform non-neural models, especially when trained on a larger dataset. Our attention analysis demonstrates the intuition behind the classifier's decision by generating a heatmap that highlights attended terms used by the CNN model; this is valuable when potential downstream medical decisions are to be performed by human experts or the classifier information is to be used in cohort construction such as for epidemiological studies

DeepCare: A Deep Dynamic Memory Model for Predictive Medicine

Personalized predictive medicine necessitates the modeling of patient illness and care processes, which inherently have long-term temporal dependencies. Healthcare observations, recorded in electronic medical records, are episodic and irregular in time. We introduce DeepCare, an end-to-end deep dynamic neural network that reads medical records, stores previous illness history, infers current illness states and predicts future medical outcomes. At the data level, DeepCare represents care episodes as vectors in space, models patient health state trajectories through explicit memory of historical records. Built on Long Short-Term Memory (LSTM), DeepCare introduces time parameterizations to handle irregular timed events by moderating the forgetting and consolidation of memory cells. DeepCare also incorporates medical interventions that change the course of illness and shape future medical risk. Moving up to the health state level, historical and present health states are then aggregated through multiscale temporal pooling, before passing through a neural network that estimates future outcomes. We demonstrate the efficacy of DeepCare for disease progression modeling, intervention recommendation, and future risk prediction. On two important cohorts with heavy social and economic burden -- diabetes and mental health -- the results show improved modeling and risk prediction accuracy.Comment: Accepted at JBI under the new name: "Predicting healthcare trajectories from medical records: A deep learning approach

SimLex-999: Evaluating Semantic Models with (Genuine) Similarity Estimation

We present SimLex-999, a gold standard resource for evaluating distributional semantic models that improves on existing resources in several important ways. First, in contrast to gold standards such as WordSim-353 and MEN, it explicitly quantifies similarity rather than association or relatedness, so that pairs of entities that are associated but not actually similar [Freud, psychology] have a low rating. We show that, via this focus on similarity, SimLex-999 incentivizes the development of models with a different, and arguably wider range of applications than those which reflect conceptual association. Second, SimLex-999 contains a range of concrete and abstract adjective, noun and verb pairs, together with an independent rating of concreteness and (free) association strength for each pair. This diversity enables fine-grained analyses of the performance of models on concepts of different types, and consequently greater insight into how architectures can be improved. Further, unlike existing gold standard evaluations, for which automatic approaches have reached or surpassed the inter-annotator agreement ceiling, state-of-the-art models perform well below this ceiling on SimLex-999. There is therefore plenty of scope for SimLex-999 to quantify future improvements to distributional semantic models, guiding the development of the next generation of representation-learning architectures

Attend and Diagnose: Clinical Time Series Analysis using Attention Models

With widespread adoption of electronic health records, there is an increased emphasis for predictive models that can effectively deal with clinical time-series data. Powered by Recurrent Neural Network (RNN) architectures with Long Short-Term Memory (LSTM) units, deep neural networks have achieved state-of-the-art results in several clinical prediction tasks. Despite the success of RNNs, its sequential nature prohibits parallelized computing, thus making it inefficient particularly when processing long sequences. Recently, architectures which are based solely on attention mechanisms have shown remarkable success in transduction tasks in NLP, while being computationally superior. In this paper, for the first time, we utilize attention models for clinical time-series modeling, thereby dispensing recurrence entirely. We develop the \textit{SAnD} (Simply Attend and Diagnose) architecture, which employs a masked, self-attention mechanism, and uses positional encoding and dense interpolation strategies for incorporating temporal order. Furthermore, we develop a multi-task variant of \textit{SAnD} to jointly infer models with multiple diagnosis tasks. Using the recent MIMIC-III benchmark datasets, we demonstrate that the proposed approach achieves state-of-the-art performance in all tasks, outperforming LSTM models and classical baselines with hand-engineered features.Comment: AAAI 201

Named Entity Recognition in Electronic Health Records Using Transfer Learning Bootstrapped Neural Networks

Neural networks (NNs) have become the state of the art in many machine learning applications, especially in image and sound processing [1]. The same, although to a lesser extent [2,3], could be said in natural language processing (NLP) tasks, such as named entity recognition. However, the success of NNs remains dependent on the availability of large labelled datasets, which is a significant hurdle in many important applications. One such case are electronic health records (EHRs), which are arguably the largest source of medical data, most of which lies hidden in natural text [4,5]. Data access is difficult due to data privacy concerns, and therefore annotated datasets are scarce. With scarce data, NNs will likely not be able to extract this hidden information with practical accuracy. In our study, we develop an approach that solves these problems for named entity recognition, obtaining 94.6 F1 score in I2B2 2009 Medical Extraction Challenge [6], 4.3 above the architecture that won the competition. Beyond the official I2B2 challenge, we further achieve 82.4 F1 on extracting relationships between medical terms. To reach this state-of-the-art accuracy, our approach applies transfer learning to leverage on datasets annotated for other I2B2 tasks, and designs and trains embeddings that specially benefit from such transfer.Comment: 11 pages, 4 figures, 8 table