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Vispi: Automatic Visual Perception and Interpretation of Chest X-rays

Permalink - Posted on 2019-06-12 15:01

Medical imaging contains the essential information for rendering diagnostic and treatment decisions. Inspecting (visual perception) and interpreting image to generate a report are tedious clinical routines for a radiologist where automation is expected to greatly reduce the workload. Despite rapid development of natural image captioning, computer-aided medical image visual perception and interpretation remain a challenging task, largely due to the lack of high-quality annotated image-report pairs and tailor-made generative models for sufficient extraction and exploitation of localized semantic features, particularly those associated with abnormalities. To tackle these challenges, we present Vispi, an automatic medical image interpretation system, which first annotates an image via classifying and localizing common thoracic diseases with visual support and then followed by report generation from an attentive LSTM model. Analyzing an open IU X-ray dataset, we demonstrate a superior performance of Vispi in disease classification, localization and report generation using automatic performance evaluation metrics ROUGE and CIDEr.


MASK: A flexible framework to facilitate de-identification of clinical texts

Permalink - Posted on 2020-05-24 08:53

Medical health records and clinical summaries contain a vast amount of important information in textual form that can help advancing research on treatments, drugs and public health. However, the majority of these information is not shared because they contain private information about patients, their families, or medical staff treating them. Regulations such as HIPPA in the US, PHIPPA in Canada and GDPR regulate the protection, processing and distribution of this information. In case this information is de-identified and personal information are replaced or redacted, they could be distributed to the research community. In this paper, we present MASK, a software package that is designed to perform the de-identification task. The software is able to perform named entity recognition using some of the state-of-the-art techniques and then mask or redact recognized entities. The user is able to select named entity recognition algorithm (currently implemented are two versions of CRF-based techniques and BiLSTM-based neural network with pre-trained GLoVe and ELMo embedding) and masking algorithm (e.g. shift dates, replace names/locations, totally redact entity).


Noise Pollution in Hospital Readmission Prediction: Long Document Classification with Reinforcement Learning

Permalink - Posted on 2020-05-04 04:06

This paper presents a reinforcement learning approach to extract noise in long clinical documents for the task of readmission prediction after kidney transplant. We face the challenges of developing robust models on a small dataset where each document may consist of over 10K tokens with full of noise including tabular text and task-irrelevant sentences. We first experiment four types of encoders to empirically decide the best document representation, and then apply reinforcement learning to remove noisy text from the long documents, which models the noise extraction process as a sequential decision problem. Our results show that the old bag-of-words encoder outperforms deep learning-based encoders on this task, and reinforcement learning is able to improve upon baseline while pruning out 25% text segments. Our analysis depicts that reinforcement learning is able to identify both typical noisy tokens and task-specific noisy text.


Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction

Permalink - Posted on 2020-05-22 05:07

Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of DL-based models in scenarios with limited training data size. Recently, bidirectional encoder representations from transformers (BERT) and related models have achieved tremendous successes in the natural language processing domain. The pre-training of BERT on a very large training corpus generates contextualized embeddings that can boost the performance of models trained on smaller datasets. We propose Med-BERT, which adapts the BERT framework for pre-training contextualized embedding models on structured diagnosis data from 28,490,650 patients EHR dataset. Fine-tuning experiments are conducted on two disease-prediction tasks: (1) prediction of heart failure in patients with diabetes and (2) prediction of pancreatic cancer from two clinical databases. Med-BERT substantially improves prediction accuracy, boosting the area under receiver operating characteristics curve (AUC) by 2.02-7.12%. In particular, pre-trained Med-BERT substantially improves the performance of tasks with very small fine-tuning training sets (300-500 samples) boosting the AUC by more than 20% or equivalent to the AUC of 10 times larger training set. We believe that Med-BERT will benefit disease-prediction studies with small local training datasets, reduce data collection expenses, and accelerate the pace of artificial intelligence aided healthcare.


Extracting Daily Dosage from Medication Instructions in EHRs: An Automated Approach and Lessons Learned

Permalink - Posted on 2020-05-21 20:55

Understanding a patient's medication history is essential for physicians to provide appropriate treatment recommendations. A medication's prescribed daily dosage is a key element of the medication history; however, it is generally not provided as a discrete quantity and needs to be derived from free text medication instructions (Sigs) in the structured electronic health record (EHR). Existing works in daily dosage extraction are narrow in scope, dealing with dosage extraction for a single drug from clinical notes. Here, we present an automated approach to calculate daily dosage for all medications in EHR structured data. We describe and characterize the variable language used in Sigs, and present our hybrid system for calculating daily dosage combining deep learning-based named entity extractor with lexicon dictionaries and regular expressions. Our system achieves 0.98 precision and 0.95 recall on an expert-generated dataset of 1000 Sigs, demonstrating its effectiveness on the general purpose daily dosage calculation task.


Trialstreamer: Mapping and Browsing Medical Evidence in Real-Time

Permalink - Posted on 2020-05-21 19:32

We introduce Trialstreamer, a living database of clinical trial reports. Here we mainly describe the evidence extraction component; this extracts from biomedical abstracts key pieces of information that clinicians need when appraising the literature, and also the relations between these. Specifically, the system extracts descriptions of trial participants, the treatments compared in each arm (the interventions), and which outcomes were measured. The system then attempts to infer which interventions were reported to work best by determining their relationship with identified trial outcome measures. In addition to summarizing individual trials, these extracted data elements allow automatic synthesis of results across many trials on the same topic. We apply the system at scale to all reports of randomized controlled trials indexed in MEDLINE, powering the automatic generation of evidence maps, which provide a global view of the efficacy of different interventions combining data from all relevant clinical trials on a topic. We make all code and models freely available alongside a demonstration of the web interface.


BlaBla: Linguistic Feature Extraction for Clinical Analysis in Multiple Languages

Permalink - Posted on 2020-05-20 17:31

We introduce BlaBla, an open-source Python library for extracting linguistic features with proven clinical relevance to neurological and psychiatric diseases across many languages. BlaBla is a unifying framework for accelerating and simplifying clinical linguistic research. The library is built on state-of-the-art NLP frameworks and supports multithreaded/GPU-enabled feature extraction via both native Python calls and a command line interface. We describe BlaBla's architecture and clinical validation of its features across 12 diseases. We further demonstrate the application of BlaBla to a task visualizing and classifying language disorders in three languages on real clinical data from the AphasiaBank dataset. We make the codebase freely available to researchers with the hope of providing a consistent, well-validated foundation for the next generation of clinical linguistic research.


Closing the Gap: Joint De-Identification and Concept Extraction in the Clinical Domain

Permalink - Posted on 2020-05-19 12:44

Exploiting natural language processing in the clinical domain requires de-identification, i.e., anonymization of personal information in texts. However, current research considers de-identification and downstream tasks, such as concept extraction, only in isolation and does not study the effects of de-identification on other tasks. In this paper, we close this gap by reporting concept extraction performance on automatically anonymized data and investigating joint models for de-identification and concept extraction. In particular, we propose a stacked model with restricted access to privacy-sensitive information and a multitask model. We set the new state of the art on benchmark datasets in English (96.1% F1 for de-identification and 88.9% F1 for concept extraction) and Spanish (91.4% F1 for concept extraction).


ISeeU2: Visually Interpretable ICU mortality prediction using deep learning and free-text medical notes

Permalink - Posted on 2020-05-19 08:30

Accurate mortality prediction allows Intensive Care Units (ICUs) to adequately benchmark clinical practice and identify patients with unexpected outcomes. Traditionally, simple statistical models have been used to assess patient death risk, many times with sub-optimal performance. On the other hand deep learning holds promise to positively impact clinical practice by leveraging medical data to assist diagnosis and prediction, including mortality prediction. However, as the question of whether powerful Deep Learning models attend correlations backed by sound medical knowledge when generating predictions remains open, additional interpretability tools are needed to foster trust and encourage the use of AI by clinicians. In this work we show a Deep Learning model trained on MIMIC-III to predict mortality using raw nursing notes, together with visual explanations for word importance. Our model reaches a ROC of 0.8629 (+/-0.0058), outperforming the traditional SAPS-II score and providing enhanced interpretability when compared with similar Deep Learning approaches.


Assertion Detection in Multi-Label Clinical Text using Scope Localization

Permalink - Posted on 2020-05-19 06:56

Multi-label sentences (text) in the clinical domain result from the rich description of scenarios during patient care. The state-of-theart methods for assertion detection mostly address this task in the setting of a single assertion label per sentence (text). In addition, few rules based and deep learning methods perform negation/assertion scope detection on single-label text. It is a significant challenge extending these methods to address multi-label sentences without diminishing performance. Therefore, we developed a convolutional neural network (CNN) architecture to localize multiple labels and their scopes in a single stage end-to-end fashion, and demonstrate that our model performs atleast 12% better than the state-of-the-art on multi-label clinical text.


Interaction Matching for Long-Tail Multi-Label Classification

Permalink - Posted on 2020-05-18 15:27

We present an elegant and effective approach for addressing limitations in existing multi-label classification models by incorporating interaction matching, a concept shown to be useful for ad-hoc search result ranking. By performing soft n-gram interaction matching, we match labels with natural language descriptions (which are common to have in most multi-labeling tasks). Our approach can be used to enhance existing multi-label classification approaches, which are biased toward frequently-occurring labels. We evaluate our approach on two challenging tasks: automatic medical coding of clinical notes and automatic labeling of entities from software tutorial text. Our results show that our method can yield up to an 11% relative improvement in macro performance, with most of the gains stemming labels that appear infrequently in the training set (i.e., the long tail of labels).


Distilling neural networks into skipgram-level decision lists

Permalink - Posted on 2020-05-14 16:25

Several previous studies on explanation for recurrent neural networks focus on approaches that find the most important input segments for a network as its explanations. In that case, the manner in which these input segments combine with each other to form an explanatory pattern remains unknown. To overcome this, some previous work tries to find patterns (called rules) in the data that explain neural outputs. However, their explanations are often insensitive to model parameters, which limits the scalability of text explanations. To overcome these limitations, we propose a pipeline to explain RNNs by means of decision lists (also called rules) over skipgrams. For evaluation of explanations, we create a synthetic sepsis-identification dataset, as well as apply our technique on additional clinical and sentiment analysis datasets. We find that our technique persistently achieves high explanation fidelity and qualitatively interpretable rules.


Evidence Inference 2.0: More Data, Better Models

Permalink - Posted on 2020-05-08 17:16

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.


Entity-Enriched Neural Models for Clinical Question Answering

Permalink - Posted on 2020-05-13 21:04

We explore state-of-the-art neural models for question answering on electronic medical records and improve their ability to generalize better on previously unseen (paraphrased) questions at test time. We enable this by learning to predict logical forms as an auxiliary task along with the main task of answer span detection. The predicted logical forms also serve as a rationale for the answer. Further, we also incorporate medical entity information in these models via the ERNIE architecture. We train our models on the large-scale emrQA dataset and observe that our multi-task entity-enriched models generalize to paraphrased questions ~5% better than the baseline BERT model.


Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data

Permalink - Posted on 2020-01-06 22:24

Widespread adoption of electronic health records (EHRs) has fueled the development of using machine learning to build prediction models for various clinical outcomes. This process is often constrained by having a relatively small number of patient records for training the model. We demonstrate that using patient representation schemes inspired from techniques in natural language processing can increase the accuracy of clinical prediction models by transferring information learned from the entire patient population to the task of training a specific model, where only a subset of the population is relevant. Such patient representation schemes enable a 3.5% mean improvement in AUROC on five prediction tasks compared to standard baselines, with the average improvement rising to 19% when only a small number of patient records are available for training the clinical prediction model.


Comparative Analysis of Text Classification Approaches in Electronic Health Records

Permalink - Posted on 2020-05-08 14:04

Text classification tasks which aim at harvesting and/or organizing information from electronic health records are pivotal to support clinical and translational research. However these present specific challenges compared to other classification tasks, notably due to the particular nature of the medical lexicon and language used in clinical records. Recent advances in embedding methods have shown promising results for several clinical tasks, yet there is no exhaustive comparison of such approaches with other commonly used word representations and classification models. In this work, we analyse the impact of various word representations, text pre-processing and classification algorithms on the performance of four different text classification tasks. The results show that traditional approaches, when tailored to the specific language and structure of the text inherent to the classification task, can achieve or exceed the performance of more recent ones based on contextual embeddings such as BERT.


Personalized Early Stage Alzheimer's Disease Detection: A Case Study of President Reagan's Speeches

Permalink - Posted on 2020-05-08 13:26

Alzheimer`s disease (AD)-related global healthcare cost is estimated to be $1 trillion by 2050. Currently, there is no cure for this disease; however, clinical studies show that early diagnosis and intervention helps to extend the quality of life and inform technologies for personalized mental healthcare. Clinical research indicates that the onset and progression of Alzheimer`s disease lead to dementia and other mental health issues. As a result, the language capabilities of patient start to decline. In this paper, we show that machine learning-based unsupervised clustering of and anomaly detection with linguistic biomarkers are promising approaches for intuitive visualization and personalized early stage detection of Alzheimer`s disease. We demonstrate this approach on 10 year`s (1980 to 1989) of President Ronald Reagan`s speech data set. Key linguistic biomarkers that indicate early-stage AD are identified. Experimental results show that Reagan had early onset of Alzheimer`s sometime between 1983 and 1987. This finding is corroborated by prior work that analyzed his interviews using a statistical technique. The proposed technique also identifies the exact speeches that reflect linguistic biomarkers for early stage AD.


An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining

Permalink - Posted on 2020-05-06 13:25

Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language processing tasks such as text similarity, relation extraction, named entity recognition, and text inference. Our empirical results demonstrate that the MTL fine-tuned models outperform state-of-the-art transformer models (e.g., BERT and its variants) by 2.0% and 1.3% in biomedical and clinical domains, respectively. Pairwise MTL further demonstrates more details about which tasks can improve or decrease others. This is particularly helpful in the context that researchers are in the hassle of choosing a suitable model for new problems. The code and models are publicly available at https://github.com/ncbi-nlp/bluebert


Generating SOAP Notes from Doctor-Patient Conversations

Permalink - Posted on 2020-05-04 19:10

Following each patient visit, physicians must draft detailed clinical summaries called SOAP notes. Moreover, with electronic health records, these notes must be digitized. For all the benefits of this documentation the process remains onerous, contributing to increasing physician burnout. In a parallel development, patients increasingly record audio from their visits (with consent), often through dedicated apps. In this paper, we present the first study to evaluate complete pipelines for leveraging these transcripts to train machine learning model to generate these notes. We first describe a unique dataset of patient visit records, consisting of transcripts, paired SOAP notes, and annotations marking noteworthy utterances that support each summary sentence. We decompose the problem into extractive and abstractive subtasks, exploring a spectrum of approaches according to how much they demand from each component. Our best performing method first (i) extracts noteworthy utterances via multi-label classification assigns them to summary section(s); (ii) clusters noteworthy utterances on a per-section basis; and (iii) generates the summary sentences by conditioning on the corresponding cluster and the subsection of the SOAP sentence to be generated. Compared to an end-to-end approach that generates the full SOAP note from the full conversation, our approach improves by 7 ROUGE-1 points. Oracle experiments indicate that fixing our generative capabilities, improvements in extraction alone could provide (up to) a further 9 ROUGE point gain.


Rationalizing Medical Relation Prediction from Corpus-level Statistics

Permalink - Posted on 2020-05-02 17:39

Nowadays, the interpretability of machine learning models is becoming increasingly important, especially in the medical domain. Aiming to shed some light on how to rationalize medical relation prediction, we present a new interpretable framework inspired by existing theories on how human memory works, e.g., theories of recall and recognition. Given the corpus-level statistics, i.e., a global co-occurrence graph of a clinical text corpus, to predict the relations between two entities, we first recall rich contexts associated with the target entities, and then recognize relational interactions between these contexts to form model rationales, which will contribute to the final prediction. We conduct experiments on a real-world public clinical dataset and show that our framework can not only achieve competitive predictive performance against a comprehensive list of neural baseline models, but also present rationales to justify its prediction. We further collaborate with medical experts deeply to verify the usefulness of our model rationales for clinical decision making.