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.
At least one attempt has been made to use deep learning (namely character-level recurrent neural networks) to build more general coding models, but with limited success @cite_7 . The main limitation with this method is that deep learning models require a large amount of data to train @cite_24 , but even a large clinical dataset may only contain a few examples of case files with any given ICD code. Additionally, the ICD-9 standard contains over 14,000 different codes; treating coding as a simple multi-class classification problem with 14,000 different classes is infeasible.
@cite_24 @cite_7
2950489286 2806321514 209945127 1982243179 2604685013 2786906486 2808523546 2096664202 1929903369 1838058638 2591924527 2802962644 2557074642 2787358858 2311857205 2808139377 2768948924 2530816535 2951970475 1998808035
Despite the recent advances in automatically describing image contents, their applications have been mostly limited to image caption datasets containing natural images (e.g., Flickr 30k, MSCOCO). In this paper, we present a deep learning model to efficiently detect a disease from an image and annotate its contexts (e.g., location, severity and the affected organs). We employ a publicly available radiology dataset of chest x-rays and their reports, and use its image annotations to mine disease names to train convolutional neural networks (CNNs). In doing so, we adopt various regularization techniques to circumvent the large normal-vs-diseased cases bias. Recurrent neural networks (RNNs) are then trained to describe the contexts of a detected disease, based on the deep CNN features. Moreover, we introduce a novel approach to use the weights of the already trained pair of CNN RNN on the domain-specific image text dataset, to infer the joint image text contexts for composite image labeling. Significantly improved image annotation results are demonstrated using the recurrent neural cascade model by taking the joint image text contexts into account. Deep learning algorithms require large amounts of labeled data which is difficult to attain for medical imaging. Even if a particular dataset is accessible, a learned classifier struggles to maintain the same level of performance on a different medical imaging dataset from a new or never-seen data source domain. Utilizing generative adversarial networks in a semi-supervised learning architecture, we address both problems of labeled data scarcity and data domain overfitting. For cardiac abnormality classification in chest X-rays, we demonstrate that an order of magnitude less data is required with semi-supervised learning generative adversarial networks than with conventional supervised learning convolutional neural networks. In addition, we demonstrate its robustness across different datasets for similar classification tasks. Neural network models and other machine learning methods have successfully been applied to several medical classification problems. These models can be periodically refined and retrained as new cases become available. Since training neural networks by backpropagation is time consuming, it is desirable that a minimum number of representative cases be kept in the training set (i.e., redundant cases should be removed). The removal of redundant cases should be carefully monitored so that classification performance is not significantly affected. We made experiments on data removal on a data set of 700 patients suspected of having myocardial infarction and show that there is no statistical difference in classification performance (measured by the differences in areas under the ROC curve on two previously unknown sets of 553 and 500 cases) when as many as 86 of the cases are randomly removed. A proportional reduction in the amount of time required to train the neural network model is achieved. 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. Training recurrent neural networks to model long term dependencies is difficult. Hence, we propose to use external linguistic knowledge as an explicit signal to inform the model which memories it should utilize. Specifically, external knowledge is used to augment a sequence with typed edges between arbitrarily distant elements, and the resulting graph is decomposed into directed acyclic subgraphs. We introduce a model that encodes such graphs as explicit memory in recurrent neural networks, and use it to model coreference relations in text. We apply our model to several text comprehension tasks and achieve new state-of-the-art results on all considered benchmarks, including CNN, bAbi, and LAMBADA. On the bAbi QA tasks, our model solves 15 out of the 20 tasks with only 1000 training examples per task. Analysis of the learned representations further demonstrates the ability of our model to encode fine-grained entity information across a document. Recently several different deep learning architectures have been proposed that take a string of characters as the raw input signal and automatically derive features for text classification. Little studies are available that compare the effectiveness of these approaches for character based text classification with each other. In this paper we perform such an empirical comparison for the important cybersecurity problem of DGA detection: classifying domain names as either benign vs. produced by malware (i.e., by a Domain Generation Algorithm). Training and evaluating on a dataset with 2M domain names shows that there is surprisingly little difference between various convolutional neural network (CNN) and recurrent neural network (RNN) based architectures in terms of accuracy, prompting a preference for the simpler architectures, since they are faster to train and less prone to overfitting. This paper proposes an effective segmentation-free approach using a hybrid neural network hidden Markov model (NN-HMM) for offline handwritten Chinese text recognition (HCTR). In the general Bayesian framework, the handwritten Chinese text line is sequentially modeled by HMMs with each representing one character class, while the NN-based classifier is adopted to calculate the posterior probability of all HMM states. The key issues in feature extraction, character modeling, and language modeling are comprehensively investigated to show the effectiveness of NN-HMM framework for offline HCTR. First, a conventional deep neural network (DNN) architecture is studied with a well-designed feature extractor. As for the training procedure, the label refinement using forced alignment and the sequence training can yield significant gains on top of the frame-level cross-entropy criterion. Second, a deep convolutional neural network (DCNN) with automatically learned discriminative features demonstrates its superiority to DNN in the HMM framework. Moreover, to solve the challenging problem of distinguishing quite confusing classes due to the large vocabulary of Chinese characters, NN-based classifier should output 19900 HMM states as the classification units via a high-resolution modeling within each character. On the ICDAR 2013 competition task of CASIA-HWDB database, DNN-HMM yields a promising character error rate (CER) of 5.24 by making a good trade-off between the computational complexity and recognition accuracy. To the best of our knowledge, DCNN-HMM can achieve a best published CER of 3.53 . Background and objective The volume of healthcare data is growing rapidly with the adoption of health information technology. We focus on automated ICD9 code assignment from discharge summary content and methods for evaluating such assignments. Methods We study ICD9 diagnosis codes and discharge summaries from the publicly available Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC II) repository. We experiment with two coding approaches: one that treats each ICD9 code independently of each other (flat classifier), and one that leverages the hierarchical nature of ICD9 codes into its modeling (hierarchy-based classifier). We propose novel evaluation metrics, which reflect the distances among gold-standard and predicted codes and their locations in the ICD9 tree. Experimental setup, code for modeling, and evaluation scripts are made available to the research community. Results The hierarchy-based classifier outperforms the flat classifier with F-measures of 39.5 and 27.6 , respectively, when trained on 20 533 documents and tested on 2282 documents. While recall is improved at the expense of precision, our novel evaluation metrics show a more refined assessment: for instance, the hierarchy-based classifier identifies the correct sub-tree of gold-standard codes more often than the flat classifier. Error analysis reveals that gold-standard codes are not perfect, and as such the recall and precision are likely underestimated. Conclusions Hierarchy-based classification yields better ICD9 coding than flat classification for MIMIC patients. Automated ICD9 coding is an example of a task for which data and tools can be shared and for which the research community can work together to build on shared models and advance the state of the art. Deep convolutional neural networks (CNN) have seen tremendous success in large-scale generic object recognition. In comparison with generic object recognition, fine-grained image classification (FGIC) is much more challenging because (i) fine-grained labeled data is much more expensive to acquire (usually requiring domain expertise); (ii) there exists large intra-class and small inter-class variance. Most recent work exploiting deep CNN for image recognition with small training data adopts a simple strategy: pre-train a deep CNN on a large-scale external dataset (e.g., ImageNet) and fine-tune on the small-scale target data to fit the specific classification task. In this paper, beyond the fine-tuning strategy, we propose a systematic framework of learning a deep CNN that addresses the challenges from two new perspectives: (i) identifying easily annotated hyper-classes inherent in the fine-grained data and acquiring a large number of hyper-class-labeled images from readily available external sources (e.g., image search engines), and formulating the problem into multitask learning; (ii) a novel learning model by exploiting a regularization between the fine-grained recognition model and the hyper-class recognition model. We demonstrate the success of the proposed framework on two small-scale fine-grained datasets (Stanford Dogs and Stanford Cars) and on a large-scale car dataset that we collected. Deep learning has gained much success in sentence-level relation classification. For example, convolutional neural networks (CNN) have delivered competitive performance without much effort on feature engineering as the conventional pattern-based methods. Thus a lot of works have been produced based on CNN structures. However, a key issue that has not been well addressed by the CNN-based method is the lack of capability to learn temporal features, especially long-distance dependency between nominal pairs. In this paper, we propose a simple framework based on recurrent neural networks (RNN) and compare it with CNN-based model. To show the limitation of popular used SemEval-2010 Task 8 dataset, we introduce another dataset refined from MIMLRE(, 2014). Experiments on two different datasets strongly indicates that the RNN-based model can deliver better performance on relation classification, and it is particularly capable of learning long-distance relation patterns. This makes it suitable for real-world applications where complicated expressions are often involved. Deep neural networks require a large amount of labeled training data during supervised learning. However, collecting and labeling so much data might be infeasible in many cases. In this paper, we introduce a deep transfer learning scheme, called selective joint fine-tuning, for improving the performance of deep learning tasks with insufficient training data. In this scheme, a target learning task with insufficient training data is carried out simultaneously with another source learning task with abundant training data. However, the source learning task does not use all existing training data. Our core idea is to identify and use a subset of training images from the original source learning task whose low-level characteristics are similar to those from the target learning task, and jointly fine-tune shared convolutional layers for both tasks. Specifically, we compute descriptors from linear or nonlinear filter bank responses on training images from both tasks, and use such descriptors to search for a desired subset of training samples for the source learning task. Experiments demonstrate that our deep transfer learning scheme achieves state-of-the-art performance on multiple visual classification tasks with insufficient training data for deep learning. Such tasks include Caltech 256, MIT Indoor 67, and fine-grained classification problems (Oxford Flowers 102 and Stanford Dogs 120). In comparison to fine-tuning without a source domain, the proposed method can improve the classification accuracy by 2 - 10 using a single model. Codes and models are available at https: github.com ZYYSzj Selective-Joint-Fine-tuning. With the development of Fully Convolutional Neural Network (FCN), there have been progressive advances in the field of semantic segmentation in recent years. The FCN-based solutions are able to summarize features across training images and generate matching templates for the desired object classes, yet they overlook intra-class difference (ICD) among multiple instances in the same class. In this work, we present a novel fine-to-coarse learning (FCL) procedure, which first guides the network with designed 'finer' sub-class labels, whose decisions are mapped to the original 'coarse' object category through end-to-end learning. A sub-class labeling strategy is designed with unsupervised clustering upon deep convolutional features, and the proposed FCL procedure enables a balance between the fine-scale (i.e. sub-class) and the coarse-scale (i.e. class) knowledge. We conduct extensive experiments on several popular datasets, including PASCAL VOC, Context, Person-Part and NYUDepth-v2 to demonstrate the advantage of learning finer sub-classes and the potential to guide the learning of deep networks with unsupervised clustering. Deep learning methods exhibit promising performance for predictive modeling in healthcare, but two important challenges remain: - Data insufficiency: Often in healthcare predictive modeling, the sample size is insufficient for deep learning methods to achieve satisfactory results. Interpretation: The representations learned by deep learning methods should align with medical knowledge. To address these challenges, we propose GRaph-based Attention Model (GRAM) that supplements electronic health records (EHR) with hierarchical information inherent to medical ontologies. Based on the data volume and the ontology structure, GRAM represents a medical concept as a combination of its ancestors in the ontology via an attention mechanism. We compared predictive performance (i.e. accuracy, data needs, interpretability) of GRAM to various methods including the recurrent neural network (RNN) in two sequential diagnoses prediction tasks and one heart failure prediction task. Compared to the basic RNN, GRAM achieved 10 higher accuracy for predicting diseases rarely observed in the training data and 3 improved area under the ROC curve for predicting heart failure using an order of magnitude less training data. Additionally, unlike other methods, the medical concept representations learned by GRAM are well aligned with the medical ontology. Finally, GRAM exhibits intuitive attention behaviors by adaptively generalizing to higher level concepts when facing data insufficiency at the lower level concepts. In recent years, Convolutional Neural Networks (CNNs) have shown remarkable performance in many computer vision tasks such as object recognition and detection. However, complex training issues, such as "catastrophic forgetting" and hyper-parameter tuning, make incremental learning in CNNs a difficult challenge. In this paper, we propose a hierarchical deep neural network, with CNNs at multiple levels, and a corresponding training method for lifelong learning. The network grows in a tree-like manner to accommodate the new classes of data without losing the ability to identify the previously trained classes. The proposed network was tested on CIFAR-10 and CIFAR-100 datasets, and compared against the method of fine tuning specific layers of a conventional CNN. We obtained comparable accuracies and achieved 40 and 20 reduction in training effort in CIFAR-10 and CIFAR 100 respectively. The network was able to organize the incoming classes of data into feature-driven super-classes. Our model improves upon existing hierarchical CNN models by adding the capability of self-growth and also yields important observations on feature selective classification. Deep learning is considered as a popular and powerful method in pattern recognition and classification. However, there are not many deep structured applications used in medical imaging diagnosis area, because large dataset is not always available for medical images. In this study we tested the feasibility of using deep learning algorithms for lung cancer diagnosis with the cases from Lung Image Database Consortium (LIDC) database. The nodules on each computed tomography (CT) slice were segmented according to marks provided by the radiologists. After down sampling and rotating we acquired 174412 samples with 52 by 52 pixel each and the corresponding truth files. Three deep learning algorithms were designed and implemented, including Convolutional Neural Network (CNN), Deep Belief Networks (DBNs), Stacked Denoising Autoencoder (SDAE). To compare the performance of deep learning algorithms with traditional computer aided diagnosis (CADx) system, we designed a scheme with 28 image features and support vector machine. The accuracies of CNN, DBNs, and SDAE are 0.7976, 0.8119, and 0.7929, respectively; the accuracy of our designed traditional CADx is 0.7940, which is slightly lower than CNN and DBNs. We also noticed that the mislabeled nodules using DBNs are 4 larger than using traditional CADx, this might be resulting from down sampling process lost some size information of the nodules. Deep neural networks have witnessed great successes in various real applications, but it requires a large number of labeled data for training. In this paper, we propose tri-net, a deep neural network which is able to use massive unlabeled data to help learning with limited labeled data. We consider model initialization, diversity augmentation and pseudo-label editing simultaneously. In our work, we utilize output smearing to initialize modules, use fine-tuning on labeled data to augment diversity and eliminate unstable pseudo-labels to alleviate the influence of suspicious pseudolabeled data. Experiments show that our method achieves the best performance in comparison with state-of-the-art semi-supervised deep learning methods. In particular, it achieves 8:30 error rate on CIFAR- 10 by using only 4000 labeled examples. 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. In this paper, we present a simple and efficient method for training deep neural networks in a semi-supervised setting where only a small portion of training data is labeled. We introduce self-ensembling, where we form a consensus prediction of the unknown labels using the outputs of the network-in-training on different epochs, and most importantly, under different regularization and input augmentation conditions. This ensemble prediction can be expected to be a better predictor for the unknown labels than the output of the network at the most recent training epoch, and can thus be used as a target for training. Using our method, we set new records for two standard semi-supervised learning benchmarks, reducing the (non-augmented) classification error rate from 18.44 to 7.05 in SVHN with 500 labels and from 18.63 to 16.55 in CIFAR-10 with 4000 labels, and further to 5.12 and 12.16 by enabling the standard augmentations. We additionally obtain a clear improvement in CIFAR-100 classification accuracy by using random images from the Tiny Images dataset as unlabeled extra inputs during training. Finally, we demonstrate good tolerance to incorrect labels. In this paper, we present a simple and efficient method for training deep neural networks in a semi-supervised setting where only a small portion of training data is labeled. We introduce self-ensembling, where we form a consensus prediction of the unknown labels using the outputs of the network-in-training on different epochs, and most importantly, under different regularization and input augmentation conditions. This ensemble prediction can be expected to be a better predictor for the unknown labels than the output of the network at the most recent training epoch, and can thus be used as a target for training. Using our method, we set new records for two standard semi-supervised learning benchmarks, reducing the (non-augmented) classification error rate from 18.44 to 7.05 in SVHN with 500 labels and from 18.63 to 16.55 in CIFAR-10 with 4000 labels, and further to 5.12 and 12.16 by enabling the standard augmentations. We additionally obtain a clear improvement in CIFAR-100 classification accuracy by using random images from the Tiny Images dataset as unlabeled extra inputs during training. Finally, we demonstrate good tolerance to incorrect labels. This paper proposes to learn a set of high-level feature representations through deep learning, referred to as Deep hidden IDentity features (DeepID), for face verification. We argue that DeepID can be effectively learned through challenging multi-class face identification tasks, whilst they can be generalized to other tasks (such as verification) and new identities unseen in the training set. Moreover, the generalization capability of DeepID increases as more face classes are to be predicted at training. DeepID features are taken from the last hidden layer neuron activations of deep convolutional networks (ConvNets). When learned as classifiers to recognize about 10, 000 face identities in the training set and configured to keep reducing the neuron numbers along the feature extraction hierarchy, these deep ConvNets gradually form compact identity-related features in the top layers with only a small number of hidden neurons. The proposed features are extracted from various face regions to form complementary and over-complete representations. Any state-of-the-art classifiers can be learned based on these high-level representations for face verification. 97:45 verification accuracy on LFW is achieved with only weakly aligned faces.