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
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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. 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. We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead, we employ unpaired segmentation images that we use to build an anatomical prior. Critically these segmentations can be derived from imaging data from a different dataset and imaging modality than the current task. We introduce a generative probabilistic model that employs the learned prior through a convolutional neural network to compute segmentations in an unsupervised setting. We conducted an empirical analysis of the proposed approach in the context of structural brain MRI segmentation, using a multi-study dataset of more than 14,000 scans. Our results show that an anatomical prior enables fast unsupervised segmentation which is typically not possible using standard convolutional networks. The integration of anatomical priors can facilitate CNN-based anatomical segmentation in a range of novel clinical problems, where few or no annotations are available and thus standard networks are not trainable. The code, model definitions and model weights are freely available at http: github.com adalca neuron. Abstract A multitude of information sources is present in the electronic health record (EHR), each of which can contain clues to automatically assign diagnosis and procedure codes. These sources however show information overlap and quality differences, which complicates the retrieval of these clues. Through feature selection, a denser representation with a consistent quality and less information overlap can be obtained. We introduce and compare coverage-based feature selection methods, based on confidence and information gain. These approaches were evaluated over a range of medical specialties, with seven different medical specialties for ICD-9-CM code prediction (six at the Antwerp University Hospital and one in the MIMIC-III dataset) and two different medical specialties for ICD-10-CM code prediction. Using confidence coverage to integrate all sources in an EHR shows a consistent improvement in F-measure (49.83 for diagnosis codes on average), both compared with the baseline (44.25 for diagnosis codes on average) and with using the best standalone source (44.41 for diagnosis codes on average). Confidence coverage creates a concise patient stay representation independent of a rigid framework such as UMLS, and contains easily interpretable features. Confidence coverage has several advantages to a baseline setup. In our baseline setup, feature selection was limited to a filter removing features with less than five total occurrences in the trainingset. Prediction results improved consistently when using multiple heterogeneous sources to predict clinical codes, while reducing the number of features and the processing time. Extreme multi-label text classification (XMTC) refers to the problem of assigning to each document its most relevant subset of class labels from an extremely large label collection, where the number of labels could reach hundreds of thousands or millions. The huge label space raises research challenges such as data sparsity and scalability. Significant progress has been made in recent years by the development of new machine learning methods, such as tree induction with large-margin partitions of the instance spaces and label-vector embedding in the target space. However, deep learning has not been explored for XMTC, despite its big successes in other related areas. This paper presents the first attempt at applying deep learning to XMTC, with a family of new Convolutional Neural Network (CNN) models which are tailored for multi-label classification in particular. With a comparative evaluation of 7 state-of-the-art methods on 6 benchmark datasets where the number of labels is up to 670,000, we show that the proposed CNN approach successfully scaled to the largest datasets, and consistently produced the best or the second best results on all the datasets. On the Wikipedia dataset with over 2 million documents and 500,000 labels in particular, it outperformed the second best method by 11.7 15.3 in precision@K and by 11.5 11.7 in NDCG@K for K = 1,3,5. Learning tasks on source code (i.e., formal languages) have been considered recently, but most work has tried to transfer natural language methods and does not capitalize on the unique opportunities offered by code's known syntax. For example, long-range dependencies induced by using the same variable or function in distant locations are often not considered. We propose to use graphs to represent both the syntactic and semantic structure of code and use graph-based deep learning methods to learn to reason over program structures. In this work, we present how to construct graphs from source code and how to scale Gated Graph Neural Networks training to such large graphs. We evaluate our method on two tasks: VarNaming, in which a network attempts to predict the name of a variable given its usage, and VarMisuse, in which the network learns to reason about selecting the correct variable that should be used at a given program location. Our comparison to methods that use less structured program representations shows the advantages of modeling known structure, and suggests that our models learn to infer meaningful names and to solve the VarMisuse task in many cases. Additionally, our testing showed that VarMisuse identifies a number of bugs in mature open-source projects. Deep supervised hashing has emerged as an influential solution to large-scale semantic image retrieval problems in computer vision. In the light of recent progress, convolutional neural network based hashing methods typically seek pair-wise or triplet labels to conduct the similarity preserving learning. However, complex semantic concepts of visual contents are hard to capture by similar dissimilar labels, which limits the retrieval performance. Generally, pair-wise or triplet losses not only suffer from expensive training costs but also lack in extracting sufficient semantic information. In this regard, we propose a novel deep supervised hashing model to learn more compact class-level similarity preserving binary codes. Our deep learning based model is motivated by deep metric learning that directly takes semantic labels as supervised information in training and generates corresponding discriminant hashing code. Specifically, a novel cubic constraint loss function based on Gaussian distribution is proposed, which preserves semantic variations while penalizes the overlap part of different classes in the embedding space. To address the discrete optimization problem introduced by binary codes, a two-step optimization strategy is proposed to provide efficient training and avoid the problem of gradient vanishing. Extensive experiments on four large-scale benchmark databases show that our model can achieve the state-of-the-art retrieval performance. Moreover, when training samples are limited, our method surpasses other supervised deep hashing methods with non-negligible margins. Software developers often duplicate source code to replicate functionality. This practice can hinder the maintenance of a software project: bugs may arise when two identical code segments are edited inconsistently. This paper presents DejaVu, a highly scalable system for detecting these general syntactic inconsistency bugs. DejaVu operates in two phases. Given a target code base, a parallel inconsistent clone analysis first enumerates all groups of source code fragments that are similar but not identical. Next, an extensible buggy change analysis framework refines these results, separating each group of inconsistent fragments into a fine-grained set of inconsistent changes and classifying each as benign or buggy. On a 75+ million line pre-production commercial code base, DejaVu executed in under five hours and produced a report of over 8,000 potential bugs. Our analysis of a sizable random sample suggests with high likelihood that at this report contains at least 2,000 true bugs and 1,000 code smells. These bugs draw from a diverse class of software defects and are often simple to correct: syntactic inconsistencies both indicate problems and suggest solutions. Identifying historical records of patients who are similar to the new patient could help to retrieve similar reference cases for predicting the clinical outcome of the new patient. Amongst different potential applications, this study illustrates use of patient similarity in predicting survival of patients suffering from hepatocellular carcinoma (HCC) treated with locoregional chemotherapy. This study used 14 similarity measures derived from relevant clinical and imaging parameters to classify the HCC patient pairs into two classes, namely the difference between their survival time being longer or no longer than 12 months. Furthermore, this paper proposes and presents a patient similarity algorithm for the classification, named SimSVM. With the 14 similarity measures as input, SimSVM outputs the predicted class and the degree of similarity or dissimilarity. A dataset was collected from 30 patients, forming 300 and 135 patient pairs as training and test datasets respectively. The trained SimSVM with linear kernel gave the best accuracy (66.7 ), sensitivity (64.8 ) and specificity (67.9 ) on the test dataset. Descriptive names are a vital part of readable, and hence maintainable, code. Recent progress on automatically suggesting names for local variables tantalizes with the prospect of replicating that success with method and class names. However, suggesting names for methods and classes is much more difficult. This is because good method and class names need to be functionally descriptive, but suggesting such names requires that the model goes beyond local context. We introduce a neural probabilistic language model for source code that is specifically designed for the method naming problem. Our model learns which names are semantically similar by assigning them to locations, called embeddings, in a high-dimensional continuous space, in such a way that names with similar embeddings tend to be used in similar contexts. These embeddings seem to contain semantic information about tokens, even though they are learned only from statistical co-occurrences of tokens. Furthermore, we introduce a variant of our model that is, to our knowledge, the first that can propose neologisms, names that have not appeared in the training corpus. We obtain state of the art results on the method, class, and even the simpler variable naming tasks. More broadly, the continuous embeddings that are learned by our model have the potential for wide application within software engineering. We consider the problem of building high- level, class-specific feature detectors from only unlabeled data. For example, is it possible to learn a face detector using only unlabeled images? To answer this, we train a 9-layered locally connected sparse autoencoder with pooling and local contrast normalization on a large dataset of images (the model has 1 bil- lion connections, the dataset has 10 million 200x200 pixel images downloaded from the Internet). We train this network using model parallelism and asynchronous SGD on a clus- ter with 1,000 machines (16,000 cores) for three days. Contrary to what appears to be a widely-held intuition, our experimental re- sults reveal that it is possible to train a face detector without having to label images as containing a face or not. Control experiments show that this feature detector is robust not only to translation but also to scaling and out-of-plane rotation. We also find that the same network is sensitive to other high-level concepts such as cat faces and human bod- ies. Starting with these learned features, we trained our network to obtain 15.8 accu- racy in recognizing 20,000 object categories from ImageNet, a leap of 70 relative im- provement over the previous state-of-the-art. Convolutional neural networks (CNNs) perform well on problems such as handwriting recognition and image classification. However, the performance of the networks is often limited by budget and time constraints, particularly when trying to train deep networks. Motivated by the problem of online handwriting recognition, we developed a CNN for processing spatially-sparse inputs; a character drawn with a one-pixel wide pen on a high resolution grid looks like a sparse matrix. Taking advantage of the sparsity allowed us more efficiently to train and test large, deep CNNs. On the CASIA-OLHWDB1.1 dataset containing 3755 character classes we get a test error of 3.82 . Although pictures are not sparse, they can be thought of as sparse by adding padding. Applying a deep convolutional network using sparsity has resulted in a substantial reduction in test error on the CIFAR small picture datasets: 6.28 on CIFAR-10 and 24.30 for CIFAR-100. With the increasing performance of machine learning techniques in the last few years, the computer vision and robotics communities have created a large number of datasets for benchmarking object recognition tasks. These datasets cover a large spectrum of natural images and object categories, making them not only useful as a testbed for comparing machine learning approaches, but also a great resource for bootstrapping different domain-specific perception and robotic systems. One such domain is domestic environments, where an autonomous robot has to recognize a large variety of everyday objects such as groceries. This is a challenging task due to the large variety of objects and products, and where there is great need for real-world training data that goes beyond product images available online. In this paper, we address this issue and present a dataset consisting of 5,000 images covering 25 different classes of groceries, with at least 97 images per class. We collected all images from real-world settings at different stores and apartments. In contrast to existing groceries datasets, our dataset includes a large variety of perspectives, lighting conditions, and degrees of clutter. Overall, our images contain thousands of different object instances. It is our hope that machine learning and robotics researchers find this dataset of use for training, testing, and bootstrapping their approaches. As a baseline classifier to facilitate comparison, we re-trained the CaffeNet architecture (an adaptation of the well-known AlexNet) on our dataset and achieved a mean accuracy of 78.9 . We release this trained model along with the code and data splits we used in our experiments. Similarity-preserving hashing is a commonly used method for nearest neighbor search in large-scale image retrieval. For image retrieval, deep-network-based hashing methods are appealing, since they can simultaneously learn effective image representations and compact hash codes. This paper focuses on deep-network-based hashing for multi-label images, each of which may contain objects of multiple categories. In most existing hashing methods, each image is represented by one piece of hash code, which is referred to as semantic hashing. This setting may be suboptimal for multi-label image retrieval. To solve this problem, we propose a deep architecture that learns instance-aware image representations for multi-label image data, which are organized in multiple groups, with each group containing the features for one category. The instance-aware representations not only bring advantages to semantic hashing but also can be used in category-aware hashing, in which an image is represented by multiple pieces of hash codes and each piece of code corresponds to a category. Extensive evaluations conducted on several benchmark data sets demonstrate that for both the semantic hashing and the category-aware hashing, the proposed method shows substantial improvement over the state-of-the-art supervised and unsupervised hashing methods. Most state-of-the-art named entity recognition (NER) systems rely on handcrafted features and on the output of other NLP tasks such as part-of-speech (POS) tagging and text chunking. In this work we propose a language-independent NER system that uses automatically learned features only. Our approach is based on the CharWNN deep neural network, which uses word-level and character-level representations (embeddings) to perform sequential classification. We perform an extensive number of experiments using two annotated corpora in two different languages: HAREM I corpus, which contains texts in Portuguese; and the SPA CoNLL-2002 corpus, which contains texts in Spanish. Our experimental results shade light on the contribution of neural character embeddings for NER. Moreover, we demonstrate that the same neural network which has been successfully applied to POS tagging can also achieve state-of-the-art results for language-independet NER, using the same hyperparameters, and without any handcrafted features. For the HAREM I corpus, CharWNN outperforms the state-of-the-art system by 7.9 points in the F1-score for the total scenario (ten NE classes), and by 7.2 points in the F1 for the selective scenario (five NE classes). The field of medical diagnostics contains a wealth of challenges which closely resemble classical machine learning problems; practical constraints, however, complicate the translation of these endpoints naively into classical architectures. Many tasks in radiology, for example, are largely problems of multi-label classification wherein medical images are interpreted to indicate multiple present or suspected pathologies. Clinical settings drive the necessity for high accuracy simultaneously across a multitude of pathological outcomes and greatly limit the utility of tools which consider only a subset. This issue is exacerbated by a general scarcity of training data and maximizes the need to extract clinically relevant features from available samples -- ideally without the use of pre-trained models which may carry forward undesirable biases from tangentially related tasks. We present and evaluate a partial solution to these constraints in using LSTMs to leverage interdependencies among target labels in predicting 14 pathologic patterns from chest x-rays and establish state of the art results on the largest publicly available chest x-ray dataset from the NIH without pre-training. Furthermore, we propose and discuss alternative evaluation metrics and their relevance in clinical practice. What happens if one pushes a cup sitting on a table toward the edge of the table? How about pushing a desk against a wall? In this paper, we study the problem of understanding the movements of objects as a result of applying external forces to them. For a given force vector applied to a specific location in an image, our goal is to predict long-term sequential movements caused by that force. Doing so entails reasoning about scene geometry, objects, their attributes, and the physical rules that govern the movements of objects. We design a deep neural network model that learns long-term sequential dependencies of object movements while taking into account the geometry and appearance of the scene by combining Convolutional and Recurrent Neural Networks. Training our model requires a large-scale dataset of object movements caused by external forces. To build a dataset of forces in scenes, we reconstructed all images in SUN RGB-D dataset in a physics simulator to estimate the physical movements of objects caused by external forces applied to them. Our Forces in Scenes (ForScene) dataset contains 65,000 object movements in 3D which represent a variety of external forces applied to different types of objects. Our experimental evaluations show that the challenging task of predicting long-term movements of objects as their reaction to external forces is possible from a single image. The code and dataset are available at: http: allenai.org plato forces. Urban planning applications (energy audits, investment, etc.) require an understanding of built infrastructure and its environment, i.e., both low-level, physical features (amount of vegetation, building area and geometry etc.), as well as higher-level concepts such as land use classes (which encode expert understanding of socio-economic end uses). This kind of data is expensive and labor-intensive to obtain, which limits its availability (particularly in developing countries). We analyze patterns in land use in urban neighborhoods using large-scale satellite imagery data (which is available worldwide from third-party providers) and state-of-the-art computer vision techniques based on deep convolutional neural networks. For supervision, given the limited availability of standard benchmarks for remote-sensing data, we obtain ground truth land use class labels carefully sampled from open-source surveys, in particular the Urban Atlas land classification dataset of @math land use classes across @math European cities. We use this data to train and compare deep architectures which have recently shown good performance on standard computer vision tasks (image classification and segmentation), including on geospatial data. Furthermore, we show that the deep representations extracted from satellite imagery of urban environments can be used to compare neighborhoods across several cities. We make our dataset available for other machine learning researchers to use for remote-sensing applications. In recent years, deep neural networks have emerged as a dominant machine learning tool for a wide variety of application domains. However, training a deep neural network requires a large amount of labeled data, which is an expensive process in terms of time, labor and human expertise. Domain adaptation or transfer learning algorithms address this challenge by leveraging labeled data in a different, but related source domain, to develop a model for the target domain. Further, the explosive growth of digital data has posed a fundamental challenge concerning its storage and retrieval. Due to its storage and retrieval efficiency, recent years have witnessed a wide application of hashing in a variety of computer vision applications. In this paper, we first introduce a new dataset, Office-Home, to evaluate domain adaptation algorithms. The dataset contains images of a variety of everyday objects from multiple domains. We then propose a novel deep learning framework that can exploit labeled source data and unlabeled target data to learn informative hash codes, to accurately classify unseen target data. To the best of our knowledge, this is the first research effort to exploit the feature learning capabilities of deep neural networks to learn representative hash codes to address the domain adaptation problem. Our extensive empirical studies on multiple transfer tasks corroborate the usefulness of the framework in learning efficient hash codes which outperform existing competitive baselines for unsupervised domain adaptation. Deep learning for human action recognition in videos is making significant progress, but is slowed down by its dependency on expensive manual labeling of large video collections. In this work, we investigate the generation of synthetic training data for action recognition, as it has recently shown promising results for a variety of other computer vision tasks. We propose an interpretable parametric generative model of human action videos that relies on procedural generation and other computer graphics techniques of modern game engines. We generate a diverse, realistic, and physically plausible dataset of human action videos, called PHAV for Procedural Human Action Videos. It contains a total of 39,982 videos, with more than 1,000 examples for each action of 35 categories. Our approach is not limited to existing motion capture sequences, and we procedurally define 14 synthetic actions. We introduce a deep multi-task representation learning architecture to mix synthetic and real videos, even if the action categories differ. Our experiments on the UCF101 and HMDB51 benchmarks suggest that combining our large set of synthetic videos with small real-world datasets can boost recognition performance, significantly outperforming fine-tuning state-of-the-art unsupervised generative models of videos.