Clinician-driven automated classification of limb fractures from free-text radiology reports

The aim of this research is to report initial experimental results and evaluation of a clinician-driven automated method that can address the issue of misdiagnosis from unstructured radiology reports. Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to disperse information resources and vast amounts of manual processing of unstructured information, a point-of-care accurate diagnosis is often difficult. A rule-based method that considers the occurrence of clinician specified keywords related to radiological findings was developed to identify limb abnormalities, such as fractures. A dataset containing 99 narrative reports of radiological findings was sourced from a tertiary hospital. The rule-based method achieved an F-measure of 0.80 and an accuracy of 0.80. While our method achieves promising performance, a number of avenues for improvement were identified using advanced natural language processing (NLP) techniques.

Automatic classification of free-text radiology reports to identify limb fractures using machine learning and the SNOMED CT ontology

Objective To develop and evaluate machine learning techniques that identify limb fractures and other abnormalities (e.g. dislocations) from radiology reports. Materials and Methods 99 free-text reports of limb radiology examinations were acquired from an Australian public hospital. Two clinicians were employed to identify fractures and abnormalities from the reports; a third senior clinician resolved disagreements. These assessors found that, of the 99 reports, 48 referred to fractures or abnormalities of limb structures. Automated methods were then used to extract features from these reports that could be useful for their automatic classification. The Naive Bayes classification algorithm and two implementations of the support vector machine algorithm were formally evaluated using cross-fold validation over the 99 reports. Result Results show that the Naive Bayes classifier accurately identifies fractures and other abnormalities from the radiology reports. These results were achieved when extracting stemmed token bigram and negation features, as well as using these features in combination with SNOMED CT concepts related to abnormalities and disorders. The latter feature has not been used in previous works that attempted classifying free-text radiology reports. Discussion Automated classification methods have proven effective at identifying fractures and other abnormalities from radiology reports (F-Measure up to 92.31%). Key to the success of these techniques are features such as stemmed token bigrams, negations, and SNOMED CT concepts associated with morphologic abnormalities and disorders. Conclusion This investigation shows early promising results and future work will further validate and strengthen the proposed approaches.

Spatially-explicit modelling of grassland classes - an improved method of integrating a climate-based classification model with interpolated climate surfaces

Spatially-explicit modelling of grassland classes is important to site-specific planning for improving grassland and environmental management over large areas. In this study, a climate-based grassland classification model, the Comprehensive and Sequential Classification System (CSCS) was integrated with spatially interpolated climate data to classify grassland in Gansu province, China. The study area is characterized by complex topographic features imposed by plateaus, high mountains, basins and deserts. To improve the quality of the interpolated climate data and the quality of the spatial classification over this complex topography, three linear regression methods, namely an analytic method based on multiple regression and residues (AMMRR), a modification of the AMMRR method through adding the effect of slope and aspect to the interpolation analysis (M-AMMRR) and a method which replaces the IDW approach for residue interpolation in M-AMMRR with an ordinary kriging approach (I-AMMRR), for interpolating climate variables were evaluated. The interpolation outcomes from the best interpolation method were then used in the CSCS model to classify the grassland in the study area. Climate variables interpolated included the annual cumulative temperature and annual total precipitation. The results indicated that the AMMRR and M-AMMRR methods generated acceptable climate surfaces but the best model fit and cross validation result were achieved by the I-AMMRR method. Twenty-six grassland classes were classified for the study area. The four grassland vegetation classes that covered more than half of the total study area were "cool temperate-arid temperate zonal semi-desert", "cool temperate-humid forest steppe and deciduous broad-leaved forest", "temperate-extra-arid temperate zonal desert", and "frigid per-humid rain tundra and alpine meadow". The vegetation classification map generated in this study provides spatial information on the locations and extents of the different grassland classes. This information can be used to facilitate government agencies' decision-making in land-use planning and environmental management, and for vegetation and biodiversity conservation. The information can also be used to assist land managers in the estimation of safe carrying capacities which will help to prevent overgrazing and land degradation.

Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor 1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

Supplementary material : large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

Binary image steganographic techniques classification based on multi-class steganalysis

In this paper, we propose a new multi-class steganalysis for binary image. The proposed method can identify the type of steganographic technique used by examining on the given binary image. In addition, our proposed method is also capable of differentiating an image with hidden message from the one without hidden message. In order to do that, we will extract some features from the binary image. The feature extraction method used is a combination of the method extended from our previous work and some new methods proposed in this paper. Based on the extracted feature sets, we construct our multi-class steganalysis from the SVM classifier. We also present the empirical works to demonstrate that the proposed method can effectively identify five different types of steganography.

Automated classification of limb fractures from free-text radiology reports using a clinician-informed gazetteer methodology

Background Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to dispersed information resources and a vast amount of manual processing of unstructured information, accurate point-of-care diagnosis is often difficult. Aims The aim of this research is to report initial experimental evaluation of a clinician-informed automated method for the issue of initial misdiagnoses associated with delayed receipt of unstructured radiology reports. Method A method was developed that resembles clinical reasoning for identifying limb abnormalities. The method consists of a gazetteer of keywords related to radiological findings; the method classifies an X-ray report as abnormal if it contains evidence contained in the gazetteer. A set of 99 narrative reports of radiological findings was sourced from a tertiary hospital. Reports were manually assessed by two clinicians and discrepancies were validated by a third expert ED clinician; the final manual classification generated by the expert ED clinician was used as ground truth to empirically evaluate the approach. Results The automated method that attempts to individuate limb abnormalities by searching for keywords expressed by clinicians achieved an F-measure of 0.80 and an accuracy of 0.80. Conclusion While the automated clinician-driven method achieved promising performances, a number of avenues for improvement were identified using advanced natural language processing (NLP) and machine learning techniques.

Classification of cancer-related death certificates using machine learning

Background Cancer monitoring and prevention relies on the critical aspect of timely notification of cancer cases. However, the abstraction and classification of cancer from the free-text of pathology reports and other relevant documents, such as death certificates, exist as complex and time-consuming activities. Aims In this paper, approaches for the automatic detection of notifiable cancer cases as the cause of death from free-text death certificates supplied to Cancer Registries are investigated. Method A number of machine learning classifiers were studied. Features were extracted using natural language techniques and the Medtex toolkit. The numerous features encompassed stemmed words, bi-grams, and concepts from the SNOMED CT medical terminology. The baseline consisted of a keyword spotter using keywords extracted from the long description of ICD-10 cancer related codes. Results Death certificates with notifiable cancer listed as the cause of death can be effectively identified with the methods studied in this paper. A Support Vector Machine (SVM) classifier achieved best performance with an overall F-measure of 0.9866 when evaluated on a set of 5,000 free-text death certificates using the token stem feature set. The SNOMED CT concept plus token stem feature set reached the lowest variance (0.0032) and false negative rate (0.0297) while achieving an F-measure of 0.9864. The SVM classifier accounts for the first 18 of the top 40 evaluated runs, and entails the most robust classifier with a variance of 0.001141, half the variance of the other classifiers. Conclusion The selection of features significantly produced the most influences on the performance of the classifiers, although the type of classifier employed also affects performance. In contrast, the feature weighting schema created a negligible effect on performance. Specifically, it is found that stemmed tokens with or without SNOMED CT concepts create the most effective feature when combined with an SVM classifier.

Random projections on manifolds of symmetric positive definite matrices for image classification

Recent advances suggest that encoding images through Symmetric Positive Definite (SPD) matrices and then interpreting such matrices as points on Riemannian manifolds can lead to increased classification performance. Taking into account manifold geometry is typically done via (1) embedding the manifolds in tangent spaces, or (2) embedding into Reproducing Kernel Hilbert Spaces (RKHS). While embedding into tangent spaces allows the use of existing Euclidean-based learning algorithms, manifold shape is only approximated which can cause loss of discriminatory information. The RKHS approach retains more of the manifold structure, but may require non-trivial effort to kernelise Euclidean-based learning algorithms. In contrast to the above approaches, in this paper we offer a novel solution that allows SPD matrices to be used with unmodified Euclidean-based learning algorithms, with the true manifold shape well-preserved. Specifically, we propose to project SPD matrices using a set of random projection hyperplanes over RKHS into a random projection space, which leads to representing each matrix as a vector of projection coefficients. Experiments on face recognition, person re-identification and texture classification show that the proposed approach outperforms several recent methods, such as Tensor Sparse Coding, Histogram Plus Epitome, Riemannian Locality Preserving Projection and Relational Divergence Classification.

Automatic classification of human epithelial type 2 cell indirect immunofluorescence images using cell pyramid matching

This paper describes a novel system for automatic classification of images obtained from Anti-Nuclear Antibody (ANA) pathology tests on Human Epithelial type 2 (HEp-2) cells using the Indirect Immunofluorescence (IIF) protocol. The IIF protocol on HEp-2 cells has been the hallmark method to identify the presence of ANAs, due to its high sensitivity and the large range of antigens that can be detected. However, it suffers from numerous shortcomings, such as being subjective as well as time and labour intensive. Computer Aided Diagnostic (CAD) systems have been developed to address these problems, which automatically classify a HEp-2 cell image into one of its known patterns (eg. speckled, homogeneous). Most of the existing CAD systems use handpicked features to represent a HEp-2 cell image, which may only work in limited scenarios. We propose a novel automatic cell image classification method termed Cell Pyramid Matching (CPM), which is comprised of regional histograms of visual words coupled with the Multiple Kernel Learning framework. We present a study of several variations of generating histograms and show the efficacy of the system on two publicly available datasets: the ICPR HEp-2 cell classification contest dataset and the SNPHEp-2 dataset.

Improved image set classification via joint sparse approximated nearest subspaces

Existing multi-model approaches for image set classification extract local models by clustering each image set individually only once, with fixed clusters used for matching with other image sets. However, this may result in the two closest clusters to represent different characteristics of an object, due to different undesirable environmental conditions (such as variations in illumination and pose). To address this problem, we propose to constrain the clustering of each query image set by forcing the clusters to have resemblance to the clusters in the gallery image sets. We first define a Frobenius norm distance between subspaces over Grassmann manifolds based on reconstruction error. We then extract local linear subspaces from a gallery image set via sparse representation. For each local linear subspace, we adaptively construct the corresponding closest subspace from the samples of a probe image set by joint sparse representation. We show that by minimising the sparse representation reconstruction error, we approach the nearest point on a Grassmann manifold. Experiments on Honda, ETH-80 and Cambridge-Gesture datasets show that the proposed method consistently outperforms several other recent techniques, such as Affine Hull based Image Set Distance (AHISD), Sparse Approximated Nearest Points (SANP) and Manifold Discriminant Analysis (MDA).

Polarization of forecast densities : a new approach to time series classification

Time series classification has been extensively explored in many fields of study. Most methods are based on the historical or current information extracted from data. However, if interest is in a specific future time period, methods that directly relate to forecasts of time series are much more appropriate. An approach to time series classification is proposed based on a polarization measure of forecast densities of time series. By fitting autoregressive models, forecast replicates of each time series are obtained via the bias-corrected bootstrap, and a stationarity correction is considered when necessary. Kernel estimators are then employed to approximate forecast densities, and discrepancies of forecast densities of pairs of time series are estimated by a polarization measure, which evaluates the extent to which two densities overlap. Following the distributional properties of the polarization measure, a discriminant rule and a clustering method are proposed to conduct the supervised and unsupervised classification, respectively. The proposed methodology is applied to both simulated and real data sets, and the results show desirable properties.

A pilot study on affective classification of facial images for emerging news topics

The proliferation of news reports published in online websites and news information sharing among social media users necessitates effective techniques for analysing the image, text and video data related to news topics. This paper presents the first study to classify affective facial images on emerging news topics. The proposed system dynamically monitors and selects the current hot (of great interest) news topics with strong affective interestingness using textual keywords in news articles and social media discussions. Images from the selected hot topics are extracted and classified into three categorized emotions, positive, neutral and negative, based on facial expressions of subjects in the images. Performance evaluations on two facial image datasets collected from real-world resources demonstrate the applicability and effectiveness of the proposed system in affective classification of facial images in news reports. Facial expression shows high consistency with the affective textual content in news reports for positive emotion, while only low correlation has been observed for neutral and negative. The system can be directly used for applications, such as assisting editors in choosing photos with a proper affective semantic for a certain topic during news report preparation.

Large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.