Use of Convolutional Neural Networks for the Detection of u-Serrated Patterns in Direct Immunofluorescence Images to Facilitate the Diagnosis of Epidermolysis Bullosa Acquisita.

The u-serrated immunodeposition pattern in direct immunofluorescence (DIF) microscopy is a recognizable feature and confirmative for the diagnosis of epidermolysis bullosa acquisita (EBA). Due to unfamiliarity with serrated patterns, serration pattern recognition is still of limited use in routine DIF microscopy. The objective of this study was to investigate the feasibility of using convolutional neural networks (CNNs) for the recognition of u-serrated patterns that can assist in the diagnosis of EBA. The nine most commonly used CNNs were trained and validated by using 220,800 manually delineated DIF image patches from 106 images of 46 different patients. The data set was split into 10 subsets: nine training subsets from 42 patients to train CNNs and the last subset from the remaining four patients for a validation data set of diagnostic accuracy. This process was repeated 10 times with a different subset used for validation. The best-performing CNN achieved a specificity of 89.3% and a corresponding sensitivity of 89.3% in the classification of u-serrated DIF image patches, an expert level of diagnostic accuracy. Experiments and results show the effectiveness of CNN approaches for u-serrated pattern recognition with a high accuracy. The proposed approach can assist clinicians and pathologists in recognition of u-serrated patterns in DIF images and facilitate the diagnosis of EBA.

LTC-Mapping, Enhancing Long-Term Consistency of Object-Oriented Semantic Maps in Robotics.

This paper proposes LTC-Mapping, a method for building object-oriented semantic maps that remain consistent in the long-term operation of mobile robots. Among the different challenges that compromise this aim, LTC-Mapping focuses on two of the more relevant ones: preventing duplicate instances of objects (instance duplication) and handling dynamic scenes. The former refers to creating multiple instances of the same physical object in the map, usually as a consequence of partial views or occlusions. The latter deals with the typical assumption made by object-oriented mapping methods that the world is static, resulting in outdated representations when the objects change their positions. To face these issues, we model the detected objects with 3D bounding boxes, and analyze the visibility of their vertices to detect occlusions and partial views. Besides this geometric modeling, the boxes are augmented with semantic information regarding the categories of the objects they represent. Both the geometric entities (bounding boxes) and their semantic content are propagated over time through data association and a fusion technique. In addition, in order to keep the map curated, the non-detection of objects in the areas where they should appear is also considered, proposing a mechanism that removes them from the map once there is evidence that they have been moved (i.e., multiple non-detections occur). To validate our proposal, a number of experiments have been carried out using the Robot@VirtualHome ecosystem, comparing its performance with a state-of-the-art alternative. The results report a superior performance of LTC-Mapping when modeling both geometric and semantic information of objects, and also support its online execution.

Discriminative power of visual attributes in dermatology.

BACKGROUND/PURPOSE: Visual characteristics such as color and shape of skin lesions play an important role in the diagnostic process. In this contribution, we quantify the discriminative power of such attributes using an information theoretical approach. METHODS: We estimate the probability of occurrence of each attribute as a function of the skin diseases. We use the distribution of this probability across the studied diseases and its entropy to define the discriminative power of the attribute. The discriminative power has a maximum value for attributes that occur (or do not occur) for only one disease and a minimum value for those which are equally likely to be observed among all diseases. RESULTS: Verrucous surface, red and brown colors, and the presence of more than 10 lesions are among the most informative attributes. A ranking of attributes is also carried out and used together with a naive Bayesian classifier, yielding results that confirm the soundness of the proposed method. CONCLUSION: proposed measure is proven to be a reliable way of assessing the discriminative power of dermatological attributes, and it also helps generate a condensed dermatological lexicon. Therefore, it can be of added value to the manual or computer-aided diagnostic process.

Survey of feature selection and extraction techniques for stock market prediction.

In stock market forecasting, the identification of critical features that affect the performance of machine learning (ML) models is crucial to achieve accurate stock price predictions. Several review papers in the literature have focused on various ML, statistical, and deep learning-based methods used in stock market forecasting. However, no survey study has explored feature selection and extraction techniques for stock market forecasting. This survey presents a detailed analysis of 32 research works that use a combination of feature study and ML approaches in various stock market applications. We conduct a systematic search for articles in the Scopus and Web of Science databases for the years 2011-2022. We review a variety of feature selection and feature extraction approaches that have been successfully applied in the stock market analyses presented in the articles. We also describe the combination of feature analysis techniques and ML methods and evaluate their performance. Moreover, we present other survey articles, stock market input and output data, and analyses based on various factors. We find that correlation criteria, random forest, principal component analysis, and autoencoder are the most widely used feature selection and extraction techniques with the best prediction accuracy for various stock market applications.

Pre-insemination prediction of dystocia in dairy cattle.

Dystocia or difficult calving in cattle is detrimental to the health of the afflicted cows and has a negative economic impact on the dairy industry. The goal of this study was to create a data-driven tool for predicting the calving difficulty of non-heifer cows using input variables that are known prior to the moment of insemination. Compared to past studies, we excluded input variables that can only be known during or after insemination, such as birth weight and gestation length. This makes the model suitable for informing mating decisions that could reduce the incidence of difficult calvings or mitigate their consequences. We used a dataset consisting of 131,527 calving records of Holstein cattle, from which we derived a total of 274 phenotypic features and estimated breeding values. The distribution of classes in the dataset was 96.7 % normal calvings, and 3.3 % difficult calvings. We used a gradient boosted trees (XGBoost) as the learning model and a bagging ensemble approach to deal with the extreme class imbalance. The model achieved an average area under the ROC curve of 0.73 on unseen test data. Using feature importance analysis, we identified a number of features that have a high discriminatory value for calving difficulty, including maternal and paternal breeding values, and past phenotypic measurements of the cow.

A CORF computational model of a simple cell that relies on LGN input outperforms the Gabor function model.

Simple cells in primary visual cortex are believed to extract local contour information from a visual scene. The 2D Gabor function (GF) model has gained particular popularity as a computational model of a simple cell. However, it short-cuts the LGN, it cannot reproduce a number of properties of real simple cells, and its effectiveness in contour detection tasks has never been compared with the effectiveness of alternative models. We propose a computational model that uses as afferent inputs the responses of model LGN cells with center-surround receptive fields (RFs) and we refer to it as a Combination of Receptive Fields (CORF) model. We use shifted gratings as test stimuli and simulated reverse correlation to explore the nature of the proposed model. We study its behavior regarding the effect of contrast on its response and orientation bandwidth as well as the effect of an orthogonal mask on the response to an optimally oriented stimulus. We also evaluate and compare the performances of the CORF and GF models regarding contour detection, using two public data sets of images of natural scenes with associated contour ground truths. The RF map of the proposed CORF model, determined with simulated reverse correlation, can be divided in elongated excitatory and inhibitory regions typical of simple cells. The modulated response to shifted gratings that this model shows is also characteristic of a simple cell. Furthermore, the CORF model exhibits cross orientation suppression, contrast invariant orientation tuning and response saturation. These properties are observed in real simple cells, but are not possessed by the GF model. The proposed CORF model outperforms the GF model in contour detection with high statistical confidence (RuG data set: p<10(-4), and Berkeley data set: p<10(-4)). The proposed CORF model is more realistic than the GF model and is more effective in contour detection, which is assumed to be the primary biological role of simple cells.

Comparison of color representations for content-based image retrieval in dermatology.

BACKGROUND/PURPOSE: We compare the effectiveness of 10 different color representations in a content-based image retrieval task for dermatology. METHODS: As features, we use the average colors of healthy and lesion skin in an image. The extracted features are used to retrieve similar images from a database using a k-nearest-neighbor search and Euclidean distance. The images in the database are divided into four different color categories. We measure the effectiveness of retrieval by the average percentage of retrieved images that belong to the same category as a query image. RESULTS: We found that the difference of the colors of lesion and healthy skin is a better color descriptor than the pair of these colors. We obtained the best results with the CIE-Lab color representation [75+/-3.8% (95% confidence interval) correct retrieval rate for k=11], followed by CIE-Luv and CIE-Lch. CONCLUSION: CIE-Lab is the most effective color space for content-based image retrieval of dermatological images. The difference of the colors of lesion and healthy skin in an image is a better color descriptor than the pair of these colors.

Hierarchical Approach to Classify Food Scenes in Egocentric Photo-Streams.

Recent studies have shown that the environment where people eat can affect their nutritional behavior [1]. In this paper, we provide automatic tools for personalized analysis of a person's health habits by the examination of daily recorded egocentric photo-streams. Specifically, we propose a new automatic approach for the classification of food-related environments, that is able to classify up to 15 such scenes. In this way, people can monitor the context around their food intake in order to get an objective insight into their daily eating routine. We propose a model that classifies food-related scenes organized in a semantic hierarchy. Additionally, we present and make available a new egocentric dataset composed of more than 33 000 images recorded by a wearable camera, over which our proposed model has been tested. Our approach obtains an accuracy and F-score of 56% and 65%, respectively, clearly outperforming the baseline methods.

Continuous glass patterns for painterly rendering.

Glass patterns have been exhaustively studied both in the vision literature and from a purely mathematical point of view. We extend the related formalism to the continuous case and we show that continuous Glass patterns can be used for artistic imaging applications. The general idea is to replace natural texture present in an input image with synthetic painterly texture that is generated by means of a continuous Glass pattern, whose geometrical structure is controlled by the gradient orientation of the input image. The behavior of the proposed algorithm is analytically interpreted in terms of the theory of dynamical systems. Experimental results on a broad range of input images validate the effectiveness of the proposed method in terms of lack of undesired artifacts, which are present with other existing methods, and easy interpretability of the input parameters.

Robust Inhibition-Augmented Operator for Delineation of Curvilinear Structures.

Delineation of curvilinear structures in images is an important basic step of several image processing applications, such as segmentation of roads or rivers in aerial images, vessels or staining membranes in medical images, and cracks in pavements and roads, among others. Existing methods suffer from insufficient robustness to noise. In this paper, we propose a novel operator for the detection of curvilinear structures in images, which we demonstrate to be robust to various types of noise and effective in several applications. We call it RUSTICO, which stands for RobUST Inhibition-augmented Curvilinear Operator. It is inspired by the push-pull inhibition in visual cortex and takes as input the responses of two trainable B-COSFIRE filters of opposite polarity. The output of RUSTICO consists of a magnitude map and an orientation map. We carried out experiments on a data set of synthetic stimuli with noise drawn from different distributions, as well as on several benchmark data sets of retinal fundus images, crack pavements, and aerial images and a new data set of rose bushes used for automatic gardening. We evaluated the performance of RUSTICO by a metric that considers the structural properties of line networks (connectivity, area, and length) and demonstrated that RUSTICO outperforms many existing methods with high statistical significance. RUSTICO exhibits high robustness to noise and texture.

Proposal for an eHealth Based Ecosystem Serving National Healthcare.

The European Union (EU)'s keen concern about citizens' health and well-being advancement has been expressed at all levels. It has been understood that at present, these can only be achieved through coordinated actions at the individual member states' level based on EU directives, as well as through promoting and funding R&D and expanding the use of eHealth technologies. Despite the diversities and particularities among member states, common values such as universal access to good quality healthcare, equity, and solidarity have been widely accepted across EU. That demanded the adoption of policies and follow directives, which streamlined actions to bridge healthcare gaps, and facilitate cross-border healthcare. This paper articulates a framework for deriving a national healthcare system, based on interoperable Electronic Health Record (EHR) with safeguarding healthcare quality, enabling quadruple helix (Public, Academia, Industry, NGOs) driven R&D and guided by a patient-centered approach. A methodology to develop an integrated EHR at National level is proposed as a prerequisite for eHealth and put into perspective. Recommendations are given for the steps needed, from the managerial, legal, technical, and financial concerns in developing an open access, patient-centered national healthcare system based on the context and constraints of a country. The example of a small country to apply the proposed methodology is demonstrated. Stakeholders, including citizens, healthcare professionals, academia, and the industry are mobilized, enabled, and incentivized for implementing the methodology. Experiences are aspired to be offered as lessons learned for other countries to adapt on their environment.

Detection of u-serrated patterns in direct immunofluorescence images of autoimmune bullous diseases by inhibition-augmented COSFIRE filters.

Direct immunofluorescence (DIF) microscopy of a skin biopsy is used by physicians and pathologists to diagnose autoimmune bullous dermatoses (AIBD). This technique is the reference standard for diagnosis of AIBD, which is used worldwide in medical laboratories. For diagnosis of subepidermal AIBD (sAIBD), two different types of serrated pattern of immunodepositions can be recognized from DIF images, namely n- and u-serrated patterns. The n-serrated pattern is typically found in the most common sAIBD bullous pemphigoid. Presence of the u-serrated pattern indicates the sAIBD subtype epidermolysis bullosa acquisita (EBA), which has a different prognosis and requires a different treatment. The manual identification of these serrated patterns is learnable but challenging. We propose an automatic technique that is able to localize u-serrated patterns for automated computer-assisted diagnosis of EBA. The distinctive feature of u-serrated patterns as compared to n-serrated patterns is the presence of ridge-endings. We introduce a novel ridge-ending detector which uses inhibition-augmented trainable COSFIRE filters. Then, we apply a hierarchical clustering approach to detect the suspicious u-serrated patterns from the detected ridge-endings. For each detected u-serrated pattern we provide a score that indicates the reliability of its detection. In order to evaluate the proposed approach, we created a data set with 180 DIF images for serration pattern analysis. This data set consists of seven subsets which were obtained from various biopsy samples under different conditions. We achieve an average recognition rate of 82.2% of the u-serrated pattern on these 180 DIF images, which is comparable to the recognition rate achieved by experienced medical doctors and pathologists.

Adaptive pseudo dilation for gestalt edge grouping and contour detection.

We consider the problem of detecting object contours in natural images. In many cases, local luminance changes turn out to be stronger in textured areas than on object contours. Therefore, local edge features, which only look at a small neighborhood of each pixel, cannot be reliable indicators of the presence of a contour, and some global analysis is needed. We introduce a new morphological operator, called adaptive pseudo-dilation (APD), which uses context dependent structuring elements in order to identify long curvilinear structure in the edge map. We show that grouping edge pixels as the connected components of the output of APD results in a good agreement with the gestalt law of good continuation. The novelty of this operator is that dilation is limited to the Voronoi cell of each edge pixel. An efficient implementation of APD is presented. The grouping algorithm is then embedded in a multithreshold contour detector. At each threshold level, small groups of edges are removed, and contours are completed by means of a generalized reconstruction from markers. The use of different thresholds makes the algorithm much less sensitive to the values of the input parameters. Both qualitative and quantitative comparison with existing approaches prove the superiority of the proposed contour detector in terms of larger amount of suppressed texture and more effective detection of low-contrast contours.

Automatic classification of the acrosome status of boar spermatozoa using digital image processing and LVQ.

We consider images of boar spermatozoa obtained with an optical phase-contrast microscope. Our goal is to automatically classify single sperm cells as acrosome-intact (class 1) or acrosome-damaged (class 2). Such classification is important for the estimation of the fertilization potential of a sperm sample for artificial insemination. We segment the sperm heads and compute a feature vector for each head. As a feature vector we use the gradient magnitude along the contour of the sperm head. We apply learning vector quantization (LVQ) to the feature vectors obtained for 320 heads that were labelled as intact or damaged using stains. A LVQ system with four prototypes (two for each class) allows us to classify cells with an overall test error of 6.8%. This is considered to be sufficient for semen quality control in an artificial insemination center.

Prediction of slaughter age in pigs and assessment of the predictive value of phenotypic and genetic information using random forest.

The weight of a pig and the rate of its growth are key elements in pig production. In particular, predicting future growth is extremely useful, since it can help in determining feed costs, pen space requirements, and the age at which a pig reaches a desired slaughter weight. However, making these predictions is challenging, due to the natural variation in how individual pigs grow, and the different causes of this variation. In this paper, we used machine learning, namely random forest (RF) regression, for predicting the age at which the slaughter weight of 120 kg is reached. Additionally, we used the variable importance score from RF to quantify the importance of different types of input data for that prediction. Data of 32,979 purebred Large White pigs were provided by Topigs Norsvin, consisting of phenotypic data, estimated breeding values (EBVs), along with pedigree and pedigree-genetic relationships. Moreover, we presented a 2-step data reduction procedure, based on random projections (RPs) and principal component analysis (PCA), to extract features from the pedigree and genetic similarity matrices for use as inputs in the prediction models. Our results showed that relevant phenotypic features were the most effective in predicting the output (age at 120 kg), explaining approximately 62% of its variance (i.e., R2 = 0.62). Estimated breeding value, pedigree, or pedigree-genetic features interchangeably explain 2% of additional variance when added to the phenotypic features, while explaining, respectively, 38%, 39%, and 34% of the variance when used separately.

Using Neural Networks with Routine Health Records to Identify Suicide Risk: Feasibility Study.

BACKGROUND: Each year, approximately 800,000 people die by suicide worldwide, accounting for 1-2 in every 100 deaths. It is always a tragic event with a huge impact on family, friends, the community and health professionals. Unfortunately, suicide prevention and the development of risk assessment tools have been hindered by the complexity of the underlying mechanisms and the dynamic nature of a person's motivation and intent. Many of those who die by suicide had contact with health services in the preceding year but identifying those most at risk remains a challenge. OBJECTIVE: To explore the feasibility of using artificial neural networks with routinely collected electronic health records to support the identification of those at high risk of suicide when in contact with health services. METHODS: Using the Secure Anonymised Information Linkage Databank UK, we extracted the data of those who died by suicide between 2001 and 2015 and paired controls. Looking at primary (general practice) and secondary (hospital admissions) electronic health records, we built a binary feature vector coding the presence of risk factors at different times prior to death. Risk factors included: general practice contact and hospital admission; diagnosis of mental health issues; injury and poisoning; substance misuse; maltreatment; sleep disorders; and the prescription of opiates and psychotropics. Basic artificial neural networks were trained to differentiate between the suicide cases and paired controls. We interpreted the output score as the estimated suicide risk. System performance was assessed with 10x10-fold repeated cross-validation, and its behavior was studied by representing the distribution of estimated risk across the cases and controls, and the distribution of factors across estimated risks. RESULTS: We extracted a total of 2604 suicide cases and 20 paired controls per case. Our best system attained a mean error rate of 26.78% (SD 1.46; 64.57% of sensitivity and 81.86% of specificity). While the distribution of controls was concentrated around estimated risks < 0.5, cases were almost uniformly distributed between 0 and 1. Prescription of psychotropics, depression and anxiety, and self-harm increased the estimated risk by ~0.4. At least 95% of those presenting these factors were identified as suicide cases. CONCLUSIONS: Despite the simplicity of the implemented system, the proposed methodology obtained an accuracy like other published methods based on specialized questionnaire generated data. Most of the errors came from the heterogeneity of patterns shown by suicide cases, some of which were identical to those of the paired controls. Prescription of psychotropics, depression and anxiety, and self-harm were strongly linked with higher estimated risk scores, followed by hospital admission and long-term drug and alcohol misuse. Other risk factors like sleep disorders and maltreatment had more complex effects.

Artistic edge and corner enhancing smoothing.

Two important visual properties of paintings and painting-like images are the absence of texture details and the increased sharpness of edges as compared to photographic images. Painting-like artistic effects can be achieved from photographic images by filters that smooth out texture details, while preserving or enhancing edges and corners. However, not all edge preserving smoothers are suitable for this purpose. We present a simple nonlinear local operator that generalizes both the well known Kuwahara filter and the more general class of filters known in the literature as "criterion and value filter structure." This class of operators suffers from intrinsic theoretical limitations which give rise to a dramatic instability in presence of noise, especially on shadowed areas. Such limitations are discussed in the paper and overcome by the proposed operator. A large variety of experimental results shows that the output of the proposed operator is visually similar to a painting. Comparisons with existing techniques on a large set of natural images highlight conditions on which traditional edge preserving smoothers fail, whereas our approach produces good results. In particular, unlike many other well established approaches, the proposed operator is robust to degradations of the input image such as blurring and noise contamination.

Automating Vector Autoregression on Electronic Patient Diary Data.

Finding the best vector autoregression model for any dataset, medical or otherwise, is a process that, to this day, is frequently performed manually in an iterative manner requiring a statistical expertize and time. Very few software solutions for automating this process exist, and they still require statistical expertize to operate. We propose a new application called Autovar, for the automation of finding vector autoregression models for time series data. The approach closely resembles the way in which experts work manually. Our proposal offers improvements over the manual approach by leveraging computing power, e.g., by considering multiple alternatives instead of choosing just one. In this paper, we describe the design and implementation of Autovar, we compare its performance against experts working manually, and we compare its features to those of the most used commercial solution available today. The main contribution of Autovar is to show that vector autoregression on a large scale is feasible. We show that an exhaustive approach for model selection can be relatively safe to use. This study forms an important step toward making adaptive, personalized treatment available and affordable for all branches of healthcare.

Robustness of shape descriptors to incomplete contour representations.

With inspiration from psychophysical researches of the human visual system, we propose a novel aspect and a method for performance evaluation of contour-based shape recognition algorithms regarding their robustness to incompleteness of contours. We use complete contour representations of objects as a reference (training) set. Incomplete contour representations of the same objects are used as a test set. The performance of an algorithm is reported using the recognition rate as a function of the percentage of contour retained. We call this evaluation procedure the ICR test. We consider three types of contour incompleteness, viz. segment-wise contour deletion, occlusion, and random pixel depletion. As an illustration, the robustness of two shape recognition algorithms to contour incompleteness is evaluated. These algorithms use a shape context and a distance multiset as local shape descriptors. Qualitatively, both algorithms mimic human visual perception in the sense that recognition performance monotonously increases with the degree of completeness and that they perform best in the case of random depletion and worst in the case of occluded contours. The distance multiset method performs better than the shape context method in this test framework.

Trainable COSFIRE filters for vessel delineation with application to retinal images.

Retinal imaging provides a non-invasive opportunity for the diagnosis of several medical pathologies. The automatic segmentation of the vessel tree is an important pre-processing step which facilitates subsequent automatic processes that contribute to such diagnosis. We introduce a novel method for the automatic segmentation of vessel trees in retinal fundus images. We propose a filter that selectively responds to vessels and that we call B-COSFIRE with B standing for bar which is an abstraction for a vessel. It is based on the existing COSFIRE (Combination Of Shifted Filter Responses) approach. A B-COSFIRE filter achieves orientation selectivity by computing the weighted geometric mean of the output of a pool of Difference-of-Gaussians filters, whose supports are aligned in a collinear manner. It achieves rotation invariance efficiently by simple shifting operations. The proposed filter is versatile as its selectivity is determined from any given vessel-like prototype pattern in an automatic configuration process. We configure two B-COSFIRE filters, namely symmetric and asymmetric, that are selective for bars and bar-endings, respectively. We achieve vessel segmentation by summing up the responses of the two rotation-invariant B-COSFIRE filters followed by thresholding. The results that we achieve on three publicly available data sets (DRIVE: Se=0.7655, Sp=0.9704; STARE: Se=0.7716, Sp=0.9701; CHASE_DB1: Se=0.7585, Sp=0.9587) are higher than many of the state-of-the-art methods. The proposed segmentation approach is also very efficient with a time complexity that is significantly lower than existing methods.