The work presented here applies deep learning to the task of automated cardiac auscultation, i.e. recognizing abnormalities in heart sounds. We describe an automated heart sound classification algorithm that combines the use of time-frequency heat map representations with a deep convolutional neural network (CNN). Given the cost-sensitive nature of misclassification, our CNN architecture is trained using a modified loss function that directly optimizes the trade-off between sensitivity and specificity. We evaluated our algorithm at the 2016 PhysioNet Computing in Cardiology challenge where the objective was to accurately classify normal and abnormal heart sounds from single, short, potentially noisy recordings. Our entry to the challenge achieved a final specificity of 0.95, sensitivity of 0.73 and overall score of 0.84. We achieved the greatest specificity score out of all challenge entries and, using just a single CNN, our algorithm differed in overall score by only 0.02 compared to the top place finisher, which used an ensemble approach.
While there have been many previous efforts applied to automated heart sound analysis, gauging the success of historical approaches has been somewhat difficult, due to differences in dataset quality, number of recordings available for training and testing algorithms, recorded signal lengths and the environment in which data was collected (e.g. clinical vs. non-clinical settings). Moreover, some existing works have not performed appropriate train-test data splits and have reported results on training or validation data, which is highly likely to produce optimistic results due to overfitting @cite_27 . In this work, we report results from the 2016 PhysioNet Computing in Cardiology Challenge, which evaluated entries on a large test-set that was not made publicly available. To reduce overfitting, no recordings from the same subject were included in both the training and the test set and a variety of both and PCG recordings, which exhibited very poor signal quality, were included to encourage the development of accurate and robust algorithms.
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The clinical notes in a given patient record contain much redundancy, in large part due to clinicians’ documentation habit of copying from previous notes in the record and pasting into a new note. Previous work has shown that this redundancy has a negative impact on the quality of text mining and topic modeling in particular. In this paper we describe a novel variant of Latent Dirichlet Allocation (LDA) topic modeling, Red-LDA, which takes into account the inherent redundancy of patient records when modeling content of clinical notes. To assess the value of Red-LDA, we experiment with three baselines and our novel redundancy-aware topic modeling method: given a large collection of patient records, (i) apply vanilla LDA to all documents in all input records; (ii) identify and remove all redundancy by chosing a single representative document for each record as input to LDA; (iii) identify and remove all redundant paragraphs in each record, leaving partial, non-redundant documents as input to LDA; and (iv) apply Red-LDA to all documents in all input records. Both quantitative evaluation carried out through log-likelihood on held-out data and topic coherence of produced topics and qualitative assessement of topics carried out by physicians show that Red-LDA produces superior models to all three baseline strategies. This research contributes to the emerging field of understanding the characteristics of the electronic health record and how to account for them in the framework of data mining. The code for the two redundancy-elimination baselines and Red-LDA is made publicly available to the community. Display Omitted We present the UPhenome model, which derives phenotypes in an unsupervised manner.UPhenome scales easily to large sets of diseases and clinical observations.The learned phenotypes combine clinical text, ICD9 codes, lab tests, and medications.UPhenome learns phenotypes that can be applied to unseen patient records. We present the Unsupervised Phenome Model (UPhenome), a probabilistic graphical model for large-scale discovery of computational models of disease, or phenotypes. We tackle this challenge through the joint modeling of a large set of diseases and a large set of clinical observations. The observations are drawn directly from heterogeneous patient record data (notes, laboratory tests, medications, and diagnosis codes), and the diseases are modeled in an unsupervised fashion. We apply UPhenome to two qualitatively different mixtures of patients and diseases: records of extremely sick patients in the intensive care unit with constant monitoring, and records of outpatients regularly followed by care providers over multiple years. We demonstrate that the UPhenome model can learn from these different care settings, without any additional adaptation. Our experiments show that (i) the learned phenotypes combine the heterogeneous data types more coherently than baseline LDA-based phenotypes; (ii) they each represent single diseases rather than a mix of diseases more often than the baseline ones; and (iii) when applied to unseen patient records, they are correlated with the patients ground-truth disorders. Code for training, inference, and quantitative evaluation is made available to the research community. When a large feedforward neural network is trained on a small training set, it typically performs poorly on held-out test data. This "overfitting" is greatly reduced by randomly omitting half of the feature detectors on each training case. This prevents complex co-adaptations in which a feature detector is only helpful in the context of several other specific feature detectors. Instead, each neuron learns to detect a feature that is generally helpful for producing the correct answer given the combinatorially large variety of internal contexts in which it must operate. Random "dropout" gives big improvements on many benchmark tasks and sets new records for speech and object recognition. Physiological signals, including heart rate (HR), heart rate variability (HRV), and respiratory frequency (RF) are important indicators of our health, which are usually measured in clinical examinations. Traditional physiological signal measurement often involves contact sensors, which may be inconvenient or cause discomfort in long-term monitoring sessions. Recently, there were studies exploring remote HR measurement from facial videos, and several methods have been proposed. However, previous methods cannot be fairly compared, since they mostly used private, self-collected small datasets as there has been no public benchmark database for the evaluation. Besides, we haven't found any study that validates such methods for clinical applications yet, e.g., diagnosing cardiac arrhythmias disease, which could be one major goal of this technology. In this paper, we introduce the Oulu Bio-Face (OBF) database as a benchmark set to fill in the blank. The OBF database includes large number of facial videos with simultaneously recorded reference physiological signals. The data were recorded both from healthy subjects and from patients with atrial fibrillation (AF), which is the most common sustained and widespread cardiac arrhythmia encountered in clinical practice. Accuracy of HR, HRV and RF measured from OBF videos are provided as the baseline results for future evaluation. We also demonstrated that the video-extracted HRV features can achieve promising performance for AF detection, which has never been studied before. From a wider outlook, the remote technology may lead to convenient self-examination in mobile condition for earlier diagnosis of the arrhythmia. This study proposes a methodology to support coding professionals in assigning ICD-9-CM codes to inpatient episodes. This subject has been predominantly addressed through the use of natural language processing methods, which show limited generalizability. To surpass this issue, this paper proposes a methodology entailing an adaptive data processing method based on structured electronic health record data, whereby raw clinical data is mapped into a feature set, and based on which supervised learning algorithms are trained. After applying a filter method for feature selection, support vector machine (SVM) classifiers are trained to obtain predictions for assigning codes to each episode. This approach is tested using a dataset of inpatient episodes from a department of Internal Medicine. Classifiers exhibited F1-measure values around 52 . Recall was generally higher than precision, which is considered valuable for coding support purposes. Analyzing results on an individual code basis sheds light on some key-issues regarding the use of structured electronic health record data in supporting clinical coding. With the increasing prevalence of Alzheimer's disease, research focuses on the early computer-aided diagnosis of dementia with the goal to understand the disease process, determine risk and preserving factors, and explore preventive therapies. By now, large amounts of data from multi-site studies have been made available for developing, training, and evaluating automated classifiers. Yet, their translation to the clinic remains challenging, in part due to their limited generalizability across different datasets. In this work, we describe a compact classification approach that mitigates overfitting by regularizing the multinomial regression with the mixed l1 l2 norm. We combine volume, thickness, and anatomical shape features from MRI scans to characterize neuroanatomy for the three-class classification of Alzheimer's disease, mild cognitive impairment and healthy controls. We demonstrate high classification accuracy via independent evaluation within the scope of the CADDementia challenge. We, furthermore, demonstrate that variations between source and target datasets can substantially influence classification accuracy. The main contribution of this work addresses this problem by proposing an approach for supervised domain adaptation based on instance weighting. Integration of this method into our classifier allows us to assess different strategies for domain adaptation. Our results demonstrate (i) that training on only the target training set yields better results than the naive combination (union) of source and target training sets, and (ii) that domain adaptation with instance weighting yields the best classification results, especially if only a small training component of the target dataset is available. These insights imply that successful deployment of systems for computer-aided diagnostics to the clinic depends not only on accurate classifiers that avoid overfitting, but also on a dedicated domain adaptation strategy. In the scenario of real-time monitoring of hospital patients, high-quality inference of patients' health status using all information available from clinical covariates and lab tests is essential to enable successful medical interventions and improve patient outcomes. Developing a computational framework that can learn from observational large-scale electronic health records (EHRs) and make accurate real-time predictions is a critical step. In this work, we develop and explore a Bayesian nonparametric model based on Gaussian process (GP) regression for hospital patient monitoring. We propose MedGP, a statistical framework that incorporates 24 clinical and lab covariates and supports a rich reference data set from which relationships between observed covariates may be inferred and exploited for high-quality inference of patient state over time. To do this, we develop a highly structured sparse GP kernel to enable tractable computation over tens of thousands of time points while estimating correlations among clinical covariates, patients, and periodicity in patient observations. MedGP has a number of benefits over current methods, including (i) not requiring an alignment of the time series data, (ii) quantifying confidence regions in the predictions, (iii) exploiting a vast and rich database of patients, and (iv) inferring interpretable relationships among clinical covariates. We evaluate and compare results from MedGP on the task of online prediction for three patient subgroups from two medical data sets across 8,043 patients. We found MedGP improves online prediction over baseline methods for nearly all covariates across different disease subgroups and studies. The publicly available code is at this https URL. Clinical medical data, especially in the intensive care unit (ICU), consist of multivariate time series of observations. For each patient visit (or episode), sensor data and lab test results are recorded in the patient's Electronic Health Record (EHR). While potentially containing a wealth of insights, the data is difficult to mine effectively, owing to varying length, irregular sampling and missing data. Recurrent Neural Networks (RNNs), particularly those using Long Short-Term Memory (LSTM) hidden units, are powerful and increasingly popular models for learning from sequence data. They effectively model varying length sequences and capture long range dependencies. We present the first study to empirically evaluate the ability of LSTMs to recognize patterns in multivariate time series of clinical measurements. Specifically, we consider multilabel classification of diagnoses, training a model to classify 128 diagnoses given 13 frequently but irregularly sampled clinical measurements. First, we establish the effectiveness of a simple LSTM network for modeling clinical data. Then we demonstrate a straightforward and effective training strategy in which we replicate targets at each sequence step. Trained only on raw time series, our models outperform several strong baselines, including a multilayer perceptron trained on hand-engineered features. Abstract: Clinical medical data, especially in the intensive care unit (ICU), consist of multivariate time series of observations. For each patient visit (or episode), sensor data and lab test results are recorded in the patient's Electronic Health Record (EHR). While potentially containing a wealth of insights, the data is difficult to mine effectively, owing to varying length, irregular sampling and missing data. Recurrent Neural Networks (RNNs), particularly those using Long Short-Term Memory (LSTM) hidden units, are powerful and increasingly popular models for learning from sequence data. They effectively model varying length sequences and capture long range dependencies. We present the first study to empirically evaluate the ability of LSTMs to recognize patterns in multivariate time series of clinical measurements. Specifically, we consider multilabel classification of diagnoses, training a model to classify 128 diagnoses given 13 frequently but irregularly sampled clinical measurements. First, we establish the effectiveness of a simple LSTM network for modeling clinical data. Then we demonstrate a straightforward and effective training strategy in which we replicate targets at each sequence step. Trained only on raw time series, our models outperform several strong baselines, including a multilayer perceptron trained on hand-engineered features. Misdosing medications with sensitive therapeutic windows, such as heparin, can place patients at unnecessary risk, increase length of hospital stay, and lead to wasted hospital resources. In this work, we present a clinician-in-the-loop sequential decision making framework, which provides an individualized dosing policy adapted to each patient's evolving clinical phenotype. We employed retrospective data from the publicly available MIMIC II intensive care unit database, and developed a deep reinforcement learning algorithm that learns an optimal heparin dosing policy from sample dosing trails and their associated outcomes in large electronic medical records. Using separate training and testing datasets, our model was observed to be effective in proposing heparin doses that resulted in better expected outcomes than the clinical guidelines. Our results demonstrate that a sequential modeling approach, learned from retrospective data, could potentially be used at the bedside to derive individualized patient dosing policies. In this article, we present an account of the state of the art in acoustic scene classification (ASC), the task of classifying environments from the sounds they produce. Starting from a historical review of previous research in this area, we define a general framework for ASC and present different implementations of its components. We then describe a range of different algorithms submitted for a data challenge that was held to provide a general and fair benchmark for ASC techniques. The data set recorded for this purpose is presented along with the performance metrics that are used to evaluate the algorithms and statistical significance tests to compare the submitted methods. In this paper we present an approach to polyphonic sound event detection in real life recordings based on bi-directional long short term memory (BLSTM) recurrent neural networks (RNNs). A single multilabel BLSTM RNN is trained to map acoustic features of a mixture signal consisting of sounds from multiple classes, to binary activity indicators of each event class. Our method is tested on a large database of real-life recordings, with 61 classes (e.g. music, car, speech) from 10 different everyday contexts. The proposed method outperforms previous approaches by a large margin, and the results are further improved using data augmentation techniques. Overall, our system reports an average F 1-score of 65.5 on 1 second blocks and 64.7 on single frames, a relative improvement over previous state-of-the-art approach of 6.8 and 15.1 respectively. Epilepsy is a chronic neurological condition that affects approximately 70 million people worldwide. Characterised by sudden bursts of excess electricity in the brain, manifesting as seizures, epilepsy is still not well understood when compared with other neurological disorders. Seizures often happen unexpectedly and attempting to predict them has been a research topic for the last 30 years. Electroencephalograms have been integral to these studies, as the recordings that they produce can capture the brain’s electrical signals. The diagnosis of epilepsy is usually made by a neurologist, but can be difficult to make in the early stages. Supporting para-clinical evidence obtained from magnetic resonance imaging and electroencephalography may enable clinicians to make a diagnosis of epilepsy and instigate treatment earlier. However, electroencephalogram capture and interpretation is time consuming and can be expensive due to the need for trained specialists to perform the interpretation. Automated detection of correlates of seizure activity generalised across different regions of the brain and across multiple subjects may be a solution. This paper explores this idea further and presents a supervised machine learning approach that classifies seizure and non-seizure records using an open dataset containing 342 records (171 seizures and 171 non-seizures). Our approach posits a new method for generalising seizure detection across different subjects without prior knowledge about the focal point of seizures. Our results show an improvement on existing studies with 88 for sensitivity, 88 for specificity and 93 for the area under the curve, with a 12 global error, using the k-NN classifier. Quality data recorded in varied realistic environments is vital for effective human face related research. Currently available datasets for human facial expression analysis have been generated in highly controlled lab environments. We present a new static facial expression database Static Facial Expressions in the Wild (SFEW) extracted from a temporal facial expressions database Acted Facial Expressions in the Wild (AFEW) [9], which we have extracted from movies. In the past, many robust methods have been reported in the literature. However, these methods have been experimented on different databases or using different protocols within the same databases. The lack of a standard protocol makes it difficult to compare systems and acts as a hindrance in the progress of the field. Therefore, we propose a person independent training and testing protocol for expression recognition as part of the BEFIT workshop. Further, we compare our dataset with the JAFFE and Multi-PIE datasets and provide baseline results. This paper presents a novel generalized computational framework for quantitative kinematic evaluation of movement in a rehabilitation clinic setting. The framework integrates clinical knowledge and computational data‐driven analysis together in a systematic manner. The framework provides three key benefits to rehabilitation: (a) the resulting continuous normalized measure allows the clinician to monitor movement quality on a fine scale and easily compare impairments across participants, (b) the framework reveals the effect of individual movement components on the composite movement performance helping the clinician decide the training foci, and (c) the evaluation runs in real‐time, which allows the clinician to constantly track a patient’s progress and make appropriate adaptations to the therapy protocol. The creation of such an evaluation is difficult because of the sparse amount of recorded clinical observations, the high dimensionality of movement and high variations in subject’s performance. We addres... Scenario-based testing for the safety validation of highly automated vehicles is a promising approach that is being examined in research and industry. This approach heavily relies on data from real-world scenarios to derive the necessary scenario information for testing. Measurement data should be collected at a reasonable effort, contain naturalistic behavior of road users and include all data relevant for a description of the identified scenarios in sufficient quality. However, the current measurement methods fail to meet at least one of the requirements. Thus, we propose a novel method to measure data from an aerial perspective for scenario-based validation fulfilling the mentioned requirements. Furthermore, we provide a large-scale naturalistic vehicle trajectory dataset from German highways called highD. We evaluate the data in terms of quantity, variety and contained scenarios. Our dataset consists of 16.5 hours of measurements from six locations with 110 000 vehicles, a total driven distance of 45 000 km and 5600 recorded complete lane changes. The highD dataset is available online at: http: www.highD-dataset.com Abstract We introduce a new methodology that combines deep learning and level set for the automated segmentation of the left ventricle of the heart from cardiac cine magnetic resonance (MR) data. This combination is relevant for segmentation problems, where the visual object of interest presents large shape and appearance variations, but the annotated training set is small, which is the case for various medical image analysis applications, including the one considered in this paper. In particular, level set methods are based on shape and appearance terms that use small training sets, but present limitations for modelling the visual object variations. Deep learning methods can model such variations using relatively small amounts of annotated training, but they often need to be regularised to produce good generalisation. Therefore, the combination of these methods brings together the advantages of both approaches, producing a methodology that needs small training sets and produces accurate segmentation results. We test our methodology on the MICCAI 2009 left ventricle segmentation challenge database (containing 15 sequences for training, 15 for validation and 15 for testing), where our approach achieves the most accurate results in the semi-automated problem and state-of-the-art results for the fully automated challenge. A novel approach is developed for predicting body trajectories for cancer progression, where conditional probabilities of clinical data are modeled using Hidden Markov Model techniques. Basically, each potential body site is encoded by an N-letter code, and a disease trajectory is described in terms of a string of letters. Patient data base records are then represented by such strings with different lengths, start points and end points. The approach is explored using pathology data for non-Hodgkin lymphoma augmented with an artificial data base generated according to observed distributions in the clinical data. For the Hidden Markov Models a Bayesian approach is taken using the Hybrid Monte Carlo method, producing an ensemble of models rather than a single one. Using a test set consisting of both real and random trajectories, we estimate the performance of our Hidden Markov Model models and also extract most probable profiles. Given the limited data set size the results are very encouraging. Heart rate is an important indicator of people's physiological state. Recently, several papers reported methods to measure heart rate remotely from face videos. Those methods work well on stationary subjects under well controlled conditions, but their performance significantly degrades if the videos are recorded under more challenging conditions, specifically when subjects' motions and illumination variations are involved. We propose a framework which utilizes face tracking and Normalized Least Mean Square adaptive filtering methods to counter their influences. We test our framework on a large difficult and public database MAHNOB-HCI and demonstrate that our method substantially outperforms all previous methods. We also use our method for long term heart rate monitoring in a game evaluation scenario and achieve promising results. When integrating computational tools, such as automatic segmentation, into clinical practice, it is of utmost importance to be able to assess the level of accuracy on new data and, in particular, to detect when an automatic method fails. However, this is difficult to achieve due to the absence of ground truth. Segmentation accuracy on clinical data might be different from what is found through cross validation, because validation data are often used during incremental method development, which can lead to overfitting and unrealistic performance expectations. Before deployment, performance is quantified using different metrics, for which the predicted segmentation is compared with a reference segmentation, often obtained manually by an expert. But little is known about the real performance after deployment when a reference is unavailable. In this paper, we introduce the concept of reverse classification accuracy (RCA) as a framework for predicting the performance of a segmentation method on new data. In RCA, we take the predicted segmentation from a new image to train a reverse classifier, which is evaluated on a set of reference images with available ground truth. The hypothesis is that if the predicted segmentation is of good quality, then the reverse classifier will perform well on at least some of the reference images. We validate our approach on multi-organ segmentation with different classifiers and segmentation methods. Our results indicate that it is indeed possible to predict the quality of individual segmentations, in the absence of ground truth. Thus, RCA is ideal for integration into automatic processing pipelines in clinical routine and as a part of large-scale image analysis studies.