Search

Acute respiratory distress syndrome (ARDS) is a fulminant inflammatory lung injury that develops in patients with critical illnesses, affecting 200,000 patients in the United States annually. However, a recent study suggests that most patients with ARDS are diagnosed late or missed completely and fail to receive life-saving treatments. This is primarily due to the dependency of current diagnosis criteria on chest x-ray, which is not necessarily available at the time of diagnosis. In machine learning, such an information is known as Privileged Information - information that is available at training but not at testing. However, in diagnosing ARDS, privileged information (chest x-rays) are sometimes only available for a portion of the training data. To address this issue, the Learning Using Partially Available Privileged Information (LUPAPI) paradigm is proposed. As there are multiple ways to incorporate partially available privileged information, three models built on classical SVM are described. Another complexity of diagnosing ARDS is the uncertainty in clinical interpretation of chest x-rays. To address this, the LUPAPI framework is then extended to incorporate label uncertainty, resulting in a novel and comprehensive machine learning paradigm - Learning Using Label Uncertainty and Partially Available Privileged Information (LULUPAPI). The proposed frameworks use Electronic Health Record (EHR) data as regular information, chest x-rays as partially available privileged information, and clinicians’ confidence levels in ARDS diagnosis as a measure of label uncertainty. Experiments on an ARDS dataset demonstrate that both the LUPAPI and LULUPAPI models outperform SVM, with LULUPAPI performing better than LUPAPI.

The task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. There is a need to develop novel and efficient prediction approaches in order to avoid costly and laborious yet not-always-deterministic experiments to determine drug–target interactions (DTIs) by experiments alone. These approaches should be capable of identifying the potential DTIs in a timely manner. In this article, we describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, which have been proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also briefly discussed. Lastly, the challenges one may face in prediction of DTI using machine learning approaches are highlighted and we conclude by shedding some lights on important future research directions.

While Internet of Things (IoT) devices and sensors create continuous streams of information, Big Data infrastructures are deemed to handle the influx of data in real-time. One type of such a continuous stream of information is time series data. Due to the richness of information in time series and inadequacy of summary statistics to encapsulate structures and patterns in such data, development of new approaches to learn time series is of interest. In this paper, we propose a novel method, called pattern tree, to learn patterns in the times-series using a binary-structured tree. While a pattern tree can be used for many purposes such as lossless compression, prediction and anomaly detection, in this paper we focus on its application in time series estimation and forecasting. In comparison to other methods, our proposed pattern tree method improves the mean squared error of estimation.

BackgroundThis study outlines an image processing algorithm for accurate and consistent lung segmentation in chest radiographs of critically ill adults and children typically obscured by medical equipment. In particular, this work focuses on applications in analysis of acute respiratory distress syndrome – a critical illness with a mortality rate of 40% that affects 200,000 patients in the United States and 3 million globally each year.MethodsChest radiographs were obtained from critically ill adults (n = 100), adults diagnosed with acute respiratory distress syndrome (ARDS) (n = 25), and children (n = 100) hospitalized at Michigan Medicine. Physicians annotated the lung field of each radiograph to establish the ground truth. A Total Variation-based Active Contour (TVAC) lung segmentation algorithm was developed and compared to multiple state-of-the-art methods including a deep learning model (U-Net), a random walker algorithm, and an active spline model, using the Sørensen–Dice coefficient to measure segmentation accuracy.ResultsThe TVAC algorithm accurately segmented lung fields in all patients in the study. For the adult cohort, an averaged Dice coefficient of 0.86 ±0.04 (min: 0.76) was reported for TVAC, 0.89 ±0.12 (min: 0.01) for U-Net, 0.74 ±0.19 (min: 0.15) for the random walker algorithm, and 0.64 ±0.17 (min: 0.20) for the active spline model. For the pediatric cohort, a Dice coefficient of 0.85 ±0.04 (min: 0.75) was reported for TVAC, 0.87 ±0.09 (min: 0.56) for U-Net, 0.67 ±0.18 (min: 0.18) for the random walker algorithm, and 0.61 ±0.18 (min: 0.18) for the active spline model.ConclusionThe proposed algorithm demonstrates the most consistent performance of all segmentation methods tested. These results suggest that TVAC can accurately identify lung fields in chest radiographs in critically ill adults and children.

Acute respiratory distress syndrome (ARDS) is a fulminant inflammatory lung injury that develops in patients with critical illnesses including sepsis, pneumonia, and trauma. However, many patients with ARDS are not recognized when they develop this syndrome nor given outcome-improving treatments. Because ARDS is a clinical syndrome, physicians may not be certain about a patient’s diagnosis (label uncertainty). In addition, the diagnosis requires a chest x-ray, which may not be always be available in a clinical setting (privileged information). For this paper, we implemented the Learning Using Label Uncertainty and Partially Available Privileged Information (LULUPAPI) paradigm, built on classical SVM, to detect ARDS using Electronic Health Record (EHR) data and chest radiography. In comparison to SVM, this resulted in a 3.55 percent improvement of test AUC.

The aim of using atypicality is to extract small, rare, unusual and interesting pieces out of big data. This complements statistics about typical data to give insight into data. In order to find such &ldquo, interesting&rdquo, parts of data, universal approaches are required, since it is not known in advance what we are looking for. We therefore base the atypicality criterion on codelength. In a prior paper we developed the methodology for discrete-valued data, and the current paper extends this to real-valued data. This is done by using minimum description length (MDL). We develop the information-theoretic methodology for a number of &ldquo, universal&rdquo, signal processing models, and finally apply them to recorded hydrophone data and heart rate variability (HRV) signal.

Pulse oximetry is a noninvasive and low-cost physiological monitor that measures blood oxygen levels. While the noninvasive nature of pulse oximetry is advantageous, the estimates of oxygen saturation generated by these devices are prone to motion artifacts and ambient noise, reducing the reliability of such estimations. Clinicians combat this by assessing the quality of oxygen saturation estimation by visual inspection of the photoplethysmograph (PPG), which represents changes in pulsatile blood volume and is also generated by the pulse oximeter. In this paper, we propose six morphological features that can be used to determine the quality of the PPG signal and generate a signal quality index. Unlike many similar studies, this approach uses machine learning and does not require a separate signal, such as ECG, for reference. Multiple algorithms were tested against 46 30-min PPG segments of patients with cardiovascular and respiratory conditions, including atrial fibrillation, hypoxia, acute heart failure, pneumonia, ARDS, and pulmonary embolism. These signals were independently annotated for signal quality by two clinicians, with the union of their annotations used as the ground-truth. Similar to any physiological signal recorded in a clinical setting, the utilized dataset is also unbalanced in favor of good quality segments. The experiments showed that a cost-sensitive Support Vector Machine (SVM) outperformed other tested methods and was robust to the unbalanced nature of the data. Though the proposed algorithm was tested on PPG signals, the methodology remains agnostic to the dataset used, and may be applied to any type of pulsatile physiological signal. Keywords: Pulsatile physiological signal, Signal quality index, Pulse oximetry, PPG, Cost-sensitive SVM, Decision tree ensemble, ARDS

Automating classification and segmentation process of abnormal regions in different body organs has a crucial role in most of medical imaging applications such as funduscopy, endoscopy, and dermoscopy. Detecting multiple abnormalities in each type of images is necessary for better and more accurate diagnosis procedure and medical decisions. In recent years portable medical imaging devices such as capsule endoscopy and digital dermatoscope have been introduced and made the diagnosis procedure easier and more efficient. However, these portable devices have constrained power resources and limited computational capability. To address this problem, we propose a bifurcated structure for convolutional neural networks performing both classification and segmentation of multiple abnormalities simultaneously. The proposed network is first trained by each abnormality separately. Then the network is trained using all abnormalities. In order to reduce the computational complexity, the network is redesigned to share some features which are common among all abnormalities. Later, these shared features are used in different settings (directions) to segment and classify the abnormal region of the image. Finally, results of the classification and segmentation directions are fused to obtain the classified segmentation map. Proposed framework is simulated using four frequent gastrointestinal abnormalities as well as three dermoscopic lesions and for evaluation of the proposed framework the results are compared with the corresponding ground truth map. Properties of the bifurcated network like low complexity and resource sharing make it suitable to be implemented as a part of portable medical imaging devices.

A central question in the era of 'big data' is what to do with the enormous amount of information. One possibility is to characterize it through statistics, e.g., averages, or classify it using machine learning, in order to understand the general structure of the overall data. The perspective in this paper is the opposite, namely that most of the value in the information in some applications is in the parts that deviate from the average, that are unusual, atypical. We define what we mean by 'atypical' in an axiomatic way as data that can be encoded with fewer bits in itself rather than using the code for the typical data. We show that this definition has good theoretical properties. We then develop an implementation based on universal source coding, and apply this to a number of real world data sets., 40 pages

With the enormous amount of data generated through the internet and sensors, Internet of Things, it becomes too overwhelming for humans to examine it all. One solution is to reduce the data to a set of statistics. The perspective in this paper is the opposite, namely that most of this data is just background noise, and the interesting parts are those that deviate from background noise, the parts that are atypical. In order to find such “interesting” parts of data, universal approaches are required, since it is not known in advance what we are looking for. The paper develops new algorithms for detecting atypical data based on information theory concepts. These are applied to a number of real-world data.

Fibromyalgia is a medical condition characterized by widespread muscle pain and tenderness and is often accompanied by fatigue and alteration in sleep, mood, and memory. Poor sleep quality and fatigue, as prominent characteristics of fibromyalgia, have a direct impact on patient behavior and quality of life. As such, the detection of extreme cases of sleep quality and fatigue level is a prerequisite for any intervention that can improve sleep quality and reduce fatigue level for people with fibromyalgia and enhance their daytime functionality. In this study, we propose a new supervised machine learning method called Learning Using Concave and Convex Kernels (LUCCK). This method employs similarity functions whose convexity or concavity can be configured so as to determine a model for each feature separately, and then uses this information to reweight the importance of each feature proportionally during classification. The data used for this study was collected from patients with fibromyalgia and consisted of blood volume pulse (BVP), 3-axis accelerometer, temperature, and electrodermal activity (EDA), recorded by an Empatica E4 wristband over the courses of several days, as well as a self-reported survey. Experiments on this dataset demonstrate that the proposed machine learning method outperforms conventional machine learning approaches in detecting extreme cases of poor sleep and fatigue in people with fibromyalgia.

Atypical sequences are subsequences of long sequences that deviates from the ‘normal’ data. In a previous paper we have developed an information theory approach to such sequences for discrete data. In the current paper we extend this principle to real-valued data, whereby it is possible to use signal processing tools to search for atypical data. The application of this principle is to extract a few interesting sets of information from ‘big data’ sets. We include a simple application to stock market data.

One characteristic of the information age is the exponential growth of information, and the ready availability of this information through networks, including the internet — “Big Data.” The question is what to do with this enormous amount of information. One possibility is to characterize it through statistics — think averages. The perspective in this paper is the opposite, namely that most of the value in the information is in the parts that deviate from the average, that are unusual, atypical. Think of art: the valuable paintings or writings are those that deviate from the norms, that are atypical. The same could be true for venture development and scientific research. The paper first discusses what exactly should be understood by “atypical.” This is by no means straightforward. It has to be a well defined theoretical concept corresponding to some intuitive idea of atypicality, which when applied gives useful results. This is followed by a simple example of iid binary sequences. This example is simple enough that complete algorithms can be developed and analyzed, which give insights into atypicality. We finally develop a more general algorithm based on the Context Tree Weighing algorithm and apply that to heart rate variability.

In this work, a novel local spline smoothing-based approach is proposed in order to despeckling medical ultrasound images. For better comparison, firstly nine conventional statistical spatial filters were applied on the ultrasound images and the results evaluated by quantitative indices of contrast to noise ratio (CNR) and speckle signal to noise ratio (SSNR). Secondly, one-dimensional cubic spline smoothing (1DCSS) function was applied on the whole speckled image as the first proposed approach. Finally, as the second proposed approach, 1DCSS was applied locally on the sliding windows of the ultrasound image then conventional statistical spatial filters were applied. The results indicate that the proposed approaches outperform the existing conventional ones.

In this paper, we proposed a method based on time-frequency dependent features extracted from Intrinsic Mode Functions (IMFs) and physiological feature such as the number of premature beats (PBs) to predict the onset of Paroxysmal Atrial Fibrillation (PAF) by using electrocardiogram (ECG) signal. To extract IMFs, we used Empirical Mode Decomposition (EMD). In order to predict PAF, we used variance of IMFs of signals, the area under the absolute of IMF curves and the number of PBs, since increasing of all of these parameters are a clear sign of PAF occurrence. We used clinical database which was provided for the 2001 Computer in Cardiology Challenge (CinC). The test set of this database consist of 28 pairs of 30-minute ECG segments that may or may not directly precede an episode of PAF. We used the training set of this database to optimize our algorithm. By applying our method on test set, we manage to predict 25 out of 28 pairs correctly which is 11 percent better than the challenge winner result.