This study explores the creation of a machine learning model to automatically identify whether a Neonatal Intensive Care Unit (NICU) patient was diagnosed with neonatal jaundice during a particular hospitalization based on their associated clinical notes. We develop a number of techniques for text preprocessing and feature selection and compare the effectiveness of different classification models. We show that using ensemble decision tree classification, both with AdaBoost and with bagging, outperforms support vector machines (SVM), the current state-of-the-art technique for neonatal jaundice coding.
More successful automated coding models have utilized non-deep machine learning techniques such as support vector machines (SVMs) @cite_15 and focus on training a model to detect the presence of a single ICD code or class of related codes. Some of these methods also leverage structured data stored in health records in addition to free-text narratives @cite_22 .
@cite_15 @cite_22
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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. International Classification of Diseases(ICD) is an authoritative health care classification system of different diseases and conditions for clinical and management purposes. Considering the complicated and dedicated process to assign correct codes to each patient admission based on overall diagnosis, we propose a hierarchical deep learning model with attention mechanism which can automatically assign ICD diagnostic codes given written diagnosis. We utilize character-aware neural language models to generate hidden representations of written diagnosis descriptions and ICD codes, and design an attention mechanism to address the mismatch between the numbers of descriptions and corresponding codes. Our experimental results show the strong potential of automated ICD coding from diagnosis descriptions. Our best model achieves 0.53 and 0.90 of F1 score and area under curve of receiver operating characteristic respectively. The result outperforms those achieved using character-unaware encoding method or without attention mechanism. It indicates that our proposed deep learning model can code automatically in a reasonable way and provide a framework for computer-auxiliary ICD coding. Background: Electronic medical records (EMRs) are revolutionizing health-related research. One key issue for study quality is the accurate identification of patients with the condition of interest. Information in EMRs can be entered as structured codes or unstructured free text. The majority of research studies have used only coded parts of EMRs for case-detection, which may bias findings, miss cases, and reduce study quality. This review examines whether incorporating information from text into case-detection algorithms can improve research quality. Methods: A systematic search returned 9659 papers, 67 of which reported on the extraction of information from free text of EMRs with the stated purpose of detecting cases of a named clinical condition. Methods for extracting information from text and the technical accuracy of case-detection algorithms were reviewed. Results: Studies mainly used US hospital-based EMRs, and extracted information from text for 41 conditions using keyword searches, rule-based algorithms, and machine learning methods. There was no clear difference in case-detection algorithm accuracy between rule-based and machine learning methods of extraction. Inclusion of information from text resulted in a significant improvement in algorithm sensitivity and area under the receiver operating characteristic in comparison to codes alone (median sensitivity 78 (codes + text) vs 62 (codes), P = .03; median area under the receiver operating characteristic 95 (codes + text) vs 88 (codes), P = .025). Conclusions: Text in EMRs is accessible, especially with open source information extraction algorithms, and significantly improves case detection when combined with codes. More harmonization of reporting within EMR studies is needed, particularly standardized reporting of algorithm accuracy metrics like positive predictive value (precision) and sensitivity (recall). Large amount of electronic clinical data encompass important information in free text format. To be able to help guide medical decision-making, text needs to be efficiently processed and coded. In this research, we investigate techniques to improve classification of Emergency Department computed topography (CT) reports. The proposed system uses Natural Language Processing (NLP) to generate structured output from patient reports and then applies machine learning techniques to code for the presence of clinically important injuries for traumatic orbital fracture victims. Topic modeling of the corpora is also utilized as an alternative representation of the patient reports. Our results show that both NLP and topic modeling improve raw text classification results. Within NLP features, filtering the codes using modifiers produces the best performance. Topic modeling, on the other hand, shows mixed results. Topic vectors provide good dimensionality reduction and get comparable classification results as with NLP features. However, binary topic classification fails to improve upon raw text classification. High-dimensional problem domains pose significant challenges for anomaly detection. The presence of irrelevant features can conceal the presence of anomalies. This problem, known as the 'curse of dimensionality', is an obstacle for many anomaly detection techniques. Building a robust anomaly detection model for use in high-dimensional spaces requires the combination of an unsupervised feature extractor and an anomaly detector. While one-class support vector machines are effective at producing decision surfaces from well-behaved feature vectors, they can be inefficient at modelling the variation in large, high-dimensional datasets. Architectures such as deep belief networks (DBNs) are a promising technique for learning robust features. We present a hybrid model where an unsupervised DBN is trained to extract generic underlying features, and a one-class SVM is trained from the features learned by the DBN. Since a linear kernel can be substituted for nonlinear ones in our hybrid model without loss of accuracy, our model is scalable and computationally efficient. The experimental results show that our proposed model yields comparable anomaly detection performance with a deep autoencoder, while reducing its training and testing time by a factor of 3 and 1000, respectively. HighlightsWe use a combination of a one-class SVM and deep learning.In our model linear kernels can be used rather than nonlinear ones.Our model delivers a comparable accuracy with a deep autoencoder.Our model executes 3times faster in training and 1000 faster than a deep autoencoder. The promise of unsupervised learning methods lies in their potential to use vast amounts of unlabeled data to learn complex, highly nonlinear models with millions of free parameters. We consider two well-known unsupervised learning models, deep belief networks (DBNs) and sparse coding, that have recently been applied to a flurry of machine learning applications (Hinton & Salakhutdinov, 2006; , 2007). Unfortunately, current learning algorithms for both models are too slow for large-scale applications, forcing researchers to focus on smaller-scale models, or to use fewer training examples. In this paper, we suggest massively parallel methods to help resolve these problems. We argue that modern graphics processors far surpass the computational capabilities of multicore CPUs, and have the potential to revolutionize the applicability of deep unsupervised learning methods. We develop general principles for massively parallelizing unsupervised learning tasks using graphics processors. We show that these principles can be applied to successfully scaling up learning algorithms for both DBNs and sparse coding. Our implementation of DBN learning is up to 70 times faster than a dual-core CPU implementation for large models. For example, we are able to reduce the time required to learn a four-layer DBN with 100 million free parameters from several weeks to around a single day. For sparse coding, we develop a simple, inherently parallel algorithm, that leads to a 5 to 15-fold speedup over previous methods. Spam is a key problem in electronic communication, including large-scale email systems and the growing number of blogs. Content-based filtering is one reliable method of combating this threat in its various forms, but some academic researchers and industrial practitioners disagree on how best to filter spam. The former have advocated the use of Support Vector Machines (SVMs) for content-based filtering, as this machine learning methodology gives state-of-the-art performance for text classification. However, similar performance gains have yet to be demonstrated for online spam filtering. Additionally, practitioners cite the high cost of SVMs as reason to prefer faster (if less statistically robust) Bayesian methods. In this paper, we offer a resolution to this controversy. First, we show that online SVMs indeed give state-of-the-art classification performance on online spam filtering on large benchmark data sets. Second, we show that nearly equivalent performance may be achieved by a Relaxed Online SVM (ROSVM) at greatly reduced computational cost. Our results are experimentally verified on email spam, blog spam, and splog detection tasks. Based on ideas from Support Vector Machines (SVMs), Learning To Classify Text Using Support Vector Machines presents a new approach to generating text classifiers from examples. The approach combines high performance and efficiency with theoretical understanding and improved robustness. In particular, it is highly effective without greedy heuristic components. The SVM approach is computationally efficient in training and classification, and it comes with a learning theory that can guide real-world applications. Learning To Classify Text Using Support Vector Machines gives a complete and detailed description of the SVM approach to learning text classifiers, including training algorithms, transductive text classification, efficient performance estimation, and a statistical learning model of text classification. In addition, it includes an overview of the field of text classification, making it self-contained even for newcomers to the field. This book gives a concise introduction to SVMs for pattern recognition, and it includes a detailed description of how to formulate text-classification tasks for machine learning. Radiological reporting has generated large quantities of digital content within the electronic health record, which is potentially a valuable source of information for improving clinical care and supporting research. Although radiology reports are stored for communication and documentation of diagnostic imaging, harnessing their potential requires efficient and automated information extraction: they exist mainly as free-text clinical narrative, from which it is a major challenge to obtain structured data. Natural language processing (NLP) provides techniques that aid the conversion of text into a structured representation, and thus enables computers to derive meaning from human (ie, natural language) input. Used on radiology reports, NLP techniques enable automatic identification and extraction of information. By exploring the various purposes for their use, this review examines how radiology benefits from NLP. A systematic literature search identified 67 relevant publications describing NLP methods that support practical applications in radiology. This review takes a close look at the individual studies in terms of tasks (ie, the extracted information), the NLP methodology and tools used, and their application purpose and performance results. Additionally, limitations, future challenges, and requirements for advancing NLP in radiology will be discussed. The ability of fast similarity search at large scale is of great importance to many Information Retrieval (IR) applications. A promising way to accelerate similarity search is semantic hashing which designs compact binary codes for a large number of documents so that semantically similar documents are mapped to similar codes (within a short Hamming distance). Although some recently proposed techniques are able to generate high-quality codes for documents known in advance, obtaining the codes for previously unseen documents remains to be a very challenging problem. In this paper, we emphasise this issue and propose a novel Self-Taught Hashing (STH) approach to semantic hashing: we first find the optimal l-bit binary codes for all documents in the given corpus via unsupervised learning, and then train l classifiers via supervised learning to predict the l-bit code for any query document unseen before. Our experiments on three real-world text datasets show that the proposed approach using binarised Laplacian Eigenmap (LapEig) and linear Support Vector Machine (SVM) outperforms state-of-the-art techniques significantly. Use of machine learning techniques for educational proposes (or educational data mining) is an emerging field aimed at developing methods of exploring data from computational educational settings and discovering meaningful patterns. The stored data (virtual courses, e-learning log file, demographic and academic data of students, admissions registration info, and so on) can be useful for machine learning algorithms. In this article, we cite the most current articles that use machine learning techniques for educational proposes and we present a case study for predicting students' marks. Students' key demographic characteristics and their marks in a small number of written assignments can constitute the training set for a regression method in order to predict the student's performance. Finally, a prototype version of software support tool for tutors has been constructed. In many problems of machine learning, the data are distributed nonlinearly. One way to address this kind of data is training a nonlinear classifier such as kernel support vector machine (kernel SVM). However, the computational burden of kernel SVM limits its application to large scale datasets. In this paper, we propose a Clustered Support Vector Machine (CSVM), which tackles the data in a divide and conquer manner. More specifically, CSVM groups the data into several clusters, followed which it trains a linear support vector machine in each cluster to separate the data locally. Meanwhile, CSVM has an additional global regularization, which requires the weight vector of each local linear SVM aligning with a global weight vector. The global regularization leverages the information from one cluster to another, and avoids over-fitting in each cluster. We derive a data-dependent generalization error bound for CSVM, which explains the advantage of CSVM over linear SVM. Experiments on several benchmark datasets show that the proposed method outperforms linear SVM and some other related locally linear classifiers. It is also comparable to a fine-tuned kernel SVM in terms of prediction performance, while it is more efficient than kernel SVM. The ubiquitous need for analyzing privacy-sensitive information—including health records, personal communications, product ratings and social network data—is driving significant interest in privacy-preserving data analysis across several research communities. This paper explores the release of Support Vector Machine (SVM) classifiers while preserving the privacy of training data. The SVM is a popular machine learning method that maps data to a high-dimensional feature space before learning a linear decision boundary. We present efficient mechanisms for finite-dimensional feature mappings and for (potentially infinite-dimensional) mappings with translation-invariant kernels. In the latter case, our mechanism borrows a technique from large-scale learning to learn in a finite-dimensional feature space whose inner-product uniformly approximates the desired feature space inner-product (the desired kernel) with high probability. Differential privacy is established using algorithmic stability, a property used in learning theory to bound generalization error. Utility—when the private classifier is pointwise close to the non-private classifier with high probability—is proven using smoothness of regularized empirical risk minimization with respect to small perturbations to the feature mapping. Finally we conclude with lower bounds on the differential privacy of any mechanism approximating the SVM. We propose a pre-selection method for training support vector machines (SVM) with a large-scale dataset. Specifically, the proposed method selects patterns around the class boundary and the selected data is fed to train an SVM. For the selection, that is, searching for boundary patterns, we utilize a relative neighborhood graph (RNG). An RNG has an edge for each pair of neighboring patterns and thus, we can find boundary patterns by looking for edges connecting patterns from different classes. Through large-scale handwritten digit pattern recognition experiments, we show that the proposed pre-selection method accelerates SVM training process 5–15 times faster without degrading recognition accuracy. To ensure code readability and facilitate software maintenance, program methods must be named properly. In particular, method names must be consistent with the corresponding method implementations. Debugging method names remains an important topic in the literature, where various approaches analyze commonalities among method names in a large dataset to detect inconsistent method names and suggest better ones. We note that the state-of-the-art does not analyze the implemented code itself to assess consistency. We thus propose a novel automated approach to debugging method names based on the analysis of consistency between method names and method code. The approach leverages deep feature representation techniques adapted to the nature of each artifact. Experimental results on over 2.1 million Java methods show that we can achieve up to 15 percentage points improvement over the state-of-the-art, establishing a record performance of 67.9 F1- measure in identifying inconsistent method names. We further demonstrate that our approach yields up to 25 accuracy in suggesting full names, while the state-of-the-art lags far behind at 1.1 accuracy. Finally, we report on our success in fixing 66 inconsistent method names in a live study on projects in the wild. Display Omitted First de-identification shared task on clinical narratives.10 teams participated, submitting 22 system output.Top-performing system achieved micro-averaged F1 measure of .936 using strictest evaluation metric. The 2014 i2b2 UTHealth Natural Language Processing (NLP) shared task featured four tracks. The first of these was the de-identification track focused on identifying protected health information (PHI) in longitudinal clinical narratives. The longitudinal nature of clinical narratives calls particular attention to details of information that, while benign on their own in separate records, can lead to identification of patients in combination in longitudinal records. Accordingly, the 2014 de-identification track addressed a broader set of entities and PHI than covered by the Health Insurance Portability and Accountability Act - the focus of the de-identification shared task that was organized in 2006. Ten teams tackled the 2014 de-identification task and submitted 22 system outputs for evaluation. Each team was evaluated on their best performing system output. Three of the 10 systems achieved F1 scores over .90, and seven of the top 10 scored over .75. The most successful systems combined conditional random fields and hand-written rules. Our findings indicate that automated systems can be very effective for this task, but that de-identification is not yet a solved problem. Suitable shape representations as well as their temporal evolution, termed trajectories, often lie to non-linear manifolds. This puts an additional constraint (i.e., non-linearity) in using conventional machine learning techniques for the purpose of classification, event detection, prediction, etc. This paper accommodates the well-known Sparse Coding and Dictionary Learning to the Kendall's shape space and illustrates effective coding of 3D skelet al sequences for action recognition. Grounding on the Riemannian geometry of the shape space, an intrinsic sparse coding and dictionary learning formulation is proposed for static skelet al shapes to overcome the inherent non-linearity of the manifold. As a main result, initial trajectories give rise to sparse code functions with suitable computational properties, including sparsity and vector space representation. To achieve action recognition, two different classification schemes were adopted. A bi-directional LSTM is directly performed on sparse code functions, while a linear SVM is applied after representing sparse code functions using Fourier temporal pyramid. Experiments conducted on three publicly available datasets show the superiority of the proposed approach compared to existing Riemannian representations and its competitiveness with respect to other recently-proposed approaches. When the benefits of invariance are maintained from the Kendall's shape representation, our approach not only overcomes the problem of non-linearity but also yields to discriminative sparse code functions. The processing of ECG signal provides a wealth of information on cardiac function and overall cardiovascular health. While multi-lead ECG recordings are often necessary for a proper assessment of cardiac rhythms, they are not always available or practical, for example in fet al ECG applications. Moreover, a wide range of small non-obtrusive single-lead ECG ambulatory monitoring devices are now available, from which heart rate variability (HRV) and other health-related metrics are derived. Proper beat detection and classification of abnormal rhythms is important for reliable HRV assessment and can be challenging in single-lead ECG monitoring devices. In this manuscript, we modelled the heart rate signal as an adaptive non-harmonic model and used the newly developed synchrosqueezing transform (SST) to characterize ECG patterns. We show how the proposed model can be used to enhance heart beat detection and classification between normal and abnormal rhythms. In particular, using the Massachusetts Institute of Technology-Beth Israel Hospital (MIT-BIH) arrhythmia database and the Association for the Advancement of Medical Instrumentation (AAMI) beat classes, we trained and validated a support vector machine (SVM) classifier on a portion of the annotated beat database using the SST-derived instantaneous phase, the R-peak amplitudes and R-peak to R-peak interval durations, based on a single ECG lead. We obtained sentivities and positive predictive values comparable to other published algorithms using multiple leads and many more features. In this paper we present the application of ensemble learning to epileptic seizure detection problem. We propose a robust learning framework to mitigate class imbalance in large CHB-MIT (982 hrs) scalp EEG dataset. The algorithm being used is RUSBoost which is a hybrid data sampling and boosting technique designed especially for skewed classes. The data that is being used in this study has severe class imbalance, with average representation of 0.38 of seizure class to that of 99.62 of non-seizure class. The proposed approach shows the power of RUSBoost in terms of robustness and generalization. We compared our method with the most successful Support Vector Machine (SVM) based approach and report competitive results of 97 seizure detection accuracy, mean detection delay of 2.7s and false detection rate of 0.08 seizure hr. We also report fast training times of just under three minutes on average for average training data of 21 hrs. In this paper, we propose and evaluate the application of unsupervised machine learning to anomaly detection for a Cyber-Physical System (CPS). We compare two methods: Deep Neural Networks (DNN) adapted to time series data generated by a CPS, and one-class Support Vector Machines (SVM). These methods are evaluated against data from the Secure Water Treatment (SWaT) testbed, a scaled-down but fully operational raw water purification plant. For both methods, we first train detectors using a log generated by SWaT operating under normal conditions. Then, we evaluate the performance of both methods using a log generated by SWaT operating under 36 different attack scenarios. We find that our DNN generates fewer false positives than our one-class SVM while our SVM detects slightly more anomalies. Overall, our DNN has a slightly better F measure than our SVM. We discuss the characteristics of the DNN and one-class SVM used in this experiment, and compare the advantages and disadvantages of the two methods.