CapsProm: a capsule network for promoter prediction.

Locating the promoter region in DNA sequences is of paramount importance in bioinformatics. This problem has been widely studied in the literature, but it has not yet been fully resolved. Some researchers have shown remarkable results using convolutional networks that allowed the automatic extraction of features from a DNA chain. However, a single architecture schema that could learn the promoter prediction task competitively for several organisms has not yet been achieved. Thus, researchers must seek new architectures by hand-designing or by Neural Architecture Search for each new evaluated organism dataset. This work proposes a versatile architecture based on a capsule network that can accurately identify promoter sequences in raw DNA data from five different organisms, eukaryotic and prokaryotic. Our architecture, the CapsProm, could help create models with minimum effort to learn the promoter identification task between different datasets. Furthermore, the CapsProm showed competitive results, overcoming the baseline method in five out of seven tested datasets (F1-score). The models and source code are made available at https://github.com/lauromoraes/CapsNet-promoter.

Dataset for Hop varieties classification.

Humulus lupulus L., also known as hops, is a vine whose flowers are a major component in brewing. It delivers flavor, bitterness, and aroma to beer and also aids in foam stabilization. Furthermore, it plays an important role in beer conservation due to its antimicrobial and antioxidant properties, which have recently been studied for food preservation. Hops can also be found in the production of cosmetics and is considered healthy food. There are more than 250 cataloged varieties of hops, and among the main attributes that differ from each other are alpha-acids, beta-acids, and essential oils. Those components give the beer a unique combination of characteristics, and may even influence its category. There are many ways to identify the hop variety from its acids and essential oils using methods such as chromatography, mass spectrometry, capillary electrophoresis, and nuclear magnetic resonance. However, these methods demand expensive and complex equipment, inaccessible or unavailable to most beer producers. In this work, we present a database that includes 1592 images of hop leaves, from 12 popular hop varieties in southeastern Brazil. From these images, it is possible to explore methods of pattern recognition and machine learning to classify hop varieties.

A deep descriptor for cross-tasking EEG-based recognition.

Due to the application of vital signs in expert systems, new approaches have emerged, and vital signals have been gaining space in biometrics. One of these signals is the electroencephalogram (EEG). The motor task in which a subject is doing, or even thinking, influences the pattern of brain waves and disturb the signal acquired. In this work, biometrics with the EEG signal from a cross-task perspective are explored. Based on deep convolutional networks (CNN) and Squeeze-and-Excitation Blocks, a novel method is developed to produce a deep EEG signal descriptor to assess the impact of the motor task in EEG signal on biometric verification. The Physionet EEG Motor Movement/Imagery Dataset is used here for method evaluation, which has 64 EEG channels from 109 subjects performing different tasks. Since the volume of data provided by the dataset is not large enough to effectively train a Deep CNN model, it is also proposed a data augmentation technique to achieve better performance. An evaluation protocol is proposed to assess the robustness regarding the number of EEG channels and also to enforce train and test sets without individual overlapping. A new state-of-the-art result is achieved for the cross-task scenario (EER of 0.1%) and the Squeeze-and-Excitation based networks overcome the simple CNN architecture in three out of four cross-individual scenarios.

Robustness analysis in an inter-cities mobility network: modeling municipal, state and federal initiatives as failures and attacks toward SARS-CoV-2 containment.

We present a robustness analysis of an inter-cities mobility complex network, motivated by the challenge of the COVID-19 pandemic and the seek for proper containment strategies. Brazilian data from 2016 are used to build a network with more than five thousand cities (nodes) and twenty-seven states with the edges representing the weekly flow of people between cities via terrestrial transports. Nodes are systematically isolated (removed from the network) either at random (failures) or guided by specific strategies (targeted attacks), and the impacts are assessed with three metrics: the number of components, the size of the giant component, and the total remaining flow of people. We propose strategies to identify which regions should be isolated first and their impact on people mobility. The results are compared with the so-called reactive strategy, which consists of isolating regions ordered by the date the first case of COVID-19 appeared. We assume that the nodes' failures abstract individual municipal and state initiatives that are independent and possess a certain level of unpredictability. Differently, the targeted attacks are related to centralized strategies led by the federal government in agreement with municipalities and states. Removing a node means completely restricting the mobility of people between the referred city/state and the rest of the network. Results reveal that random failures do not cause a high impact on mobility restraint, but the coordinated isolation of specific cities with targeted attacks is crucial to detach entire network areas and thus prevent spreading. Moreover, the targeted attacks perform better than the reactive strategy for the three analyzed robustness metrics.

Towards better heartbeat segmentation with deep learning classification.

The confidence of medical equipment is intimately related to false alarms. The higher the number of false events occurs, the less truthful is the equipment. In this sense, reducing (or suppressing) false positive alarms is hugely desirable. In this work, we propose a feasible and real-time approach that works as a validation method for a heartbeat segmentation third-party algorithm. The approach is based on convolutional neural networks (CNNs), which may be embedded in dedicated hardware. Our proposal aims to detect the pattern of a single heartbeat and classifies them into two classes: a heartbeat and not a heartbeat. For this, a seven-layer convolution network is employed for both data representation and classification. We evaluate our approach in two well-settled databases in the literature on the raw heartbeat signal. The first database is a conventional on-the-person database called MIT-BIH, and the second is one less uncontrolled off-the-person type database known as CYBHi. To evaluate the feasibility and the performance of the proposed approach, we use as a baseline the Pam-Tompkins algorithm, which is a well-known method in the literature and still used in the industry. We compare the baseline against the proposed approach: a CNN model validating the heartbeats detected by a third-party algorithm. In this work, the third-party algorithm is the same as the baseline for comparison purposes. The results support the feasibility of our approach showing that our method can enhance the positive prediction of the Pan-Tompkins algorithm from [Formula: see text]/[Formula: see text] to [Formula: see text]/[Formula: see text] by slightly decreasing the sensitivity from [Formula: see text]/[Formula: see text] to [Formula: see text] [Formula: see text] on the MIT-BIH/CYBHi databases.

COVID-19 detection in CT images with deep learning: A voting-based scheme and cross-datasets analysis.

Early detection and diagnosis are critical factors to control the COVID-19 spreading. A number of deep learning-based methodologies have been recently proposed for COVID-19 screening in CT scans as a tool to automate and help with the diagnosis. These approaches, however, suffer from at least one of the following problems: (i) they treat each CT scan slice independently and (ii) the methods are trained and tested with sets of images from the same dataset. Treating the slices independently means that the same patient may appear in the training and test sets at the same time which may produce misleading results. It also raises the question of whether the scans from the same patient should be evaluated as a group or not. Moreover, using a single dataset raises concerns about the generalization of the methods. Different datasets tend to present images of varying quality which may come from different types of CT machines reflecting the conditions of the countries and cities from where they come from. In order to address these two problems, in this work, we propose an Efficient Deep Learning Technique for the screening of COVID-19 with a voting-based approach. In this approach, the images from a given patient are classified as group in a voting system. The approach is tested in the two biggest datasets of COVID-19 CT analysis with a patient-based split. A cross dataset study is also presented to assess the robustness of the models in a more realistic scenario in which data comes from different distributions. The cross-dataset analysis has shown that the generalization power of deep learning models is far from acceptable for the task since accuracy drops from 87.68% to 56.16% on the best evaluation scenario. These results highlighted that the methods that aim at COVID-19 detection in CT-images have to improve significantly to be considered as a clinical option and larger and more diverse datasets are needed to evaluate the methods in a realistic scenario.

ChimericalDataset Creation Protocol Based on Doddington Zoo: A Biometric Application with Face, Eye, and ECG.

Multimodal systems are a workaround to enhance the robustness and effectiveness of biometric systems. A proper multimodal dataset is of the utmost importance to build such systems. The literature presents some multimodal datasets, although, to the best of our knowledge, there are no previous studies combining face, iris/eye, and vital signals such as the Electrocardiogram (ECG). Moreover, there is no methodology to guide the construction and evaluation of a chimeric dataset. Taking that fact into account, we propose to create a chimeric dataset from three modalities in this work: ECG, eye, and face. Based on the Doddington Zoo criteria, we also propose a generic and systematic protocol imposing constraints for the creation of homogeneous chimeric individuals, which allow us to perform a fair and reproducible benchmark. Moreover, we have proposed a multimodal approach for these modalities based on state-of-the-art deep representations built by convolutional neural networks. We conduct the experiments in the open-world verification mode and on two different scenarios (intra-session and inter-session), using three modalities from two datasets: CYBHi (ECG) and FRGC (eye and face). Our multimodal approach achieves impressive decidability of 7.20 ± 0.18, yielding an almost perfect verification system (i.e., Equal Error Rate (EER) of 0.20% ± 0.06) on the intra-session scenario with unknown data. On the inter-session scenario, we achieve a decidability of 7.78 ± 0.78 and an EER of 0.06% ± 0.06. In summary, these figures represent a gain of over 28% in decidability and a reduction over 11% of the EER on the intra-session scenario for unknown data compared to the best-known unimodal approach. Besides, we achieve an improvement greater than 22% in decidability and an EER reduction over 6% in the inter-session scenario.

Border analysis for spatial clusters.

BACKGROUND: The spatial scan statistic is widely used by public health professionals in the detection of spatial clusters in inhomogeneous point process. The most popular version of the spatial scan statistic uses a circular-shaped scanning window. Several other variants, using other parametric or non-parametric shapes, are also available. However, none of them offer information about the uncertainty on the borders of the detected clusters. METHOD: We propose a new method to evaluate uncertainty on the boundaries of spatial clusters identified through the spatial scan statistic for Poisson data. For each spatial data location i, a function F(i) is calculated. While not a probability, this function takes values in the [0, 1] interval, with a higher value indicating more evidence that the location belongs to the true cluster. RESULTS: Through a set of simulation studies, we show that the F function provides a way to define, measure and visualize the certainty or uncertainty of each specific location belonging to the true cluster. The method can be applied whether there are one or multiple detected clusters on the map. We illustrate the new method on a data set concerning Chagas disease in Minas Gerais, Brazil. CONCLUSIONS: The higher the intensity given to an area, the higher the plausibility of that particular area to belong to the true cluster in case it exists. This way, the F function provides information from which the public health practitioner can perform a border analysis of the detected spatial scan statistic clusters. We have implemented and illustrated the border analysis F function in the context of the circular spatial scan statistic for spatially aggregated Poisson data. The definition is clearly independent of both the shape of the scanning window and the probability model under which the data is generated. To make the new method widely available to users, it has been implemented in the freely available SaTScan[Formula: see text] software www.satscan.org .

Inter-Patient ECG Heartbeat Classification with Temporal VCG Optimized by PSO.

Classifying arrhythmias can be a tough task for a human being and automating this task is highly desirable. Nevertheless fully automatic arrhythmia classification through Electrocardiogram (ECG) signals is a challenging task when the inter-patient paradigm is considered. For the inter-patient paradigm, classifiers are evaluated on signals of unknown subjects, resembling the real world scenario. In this work, we explore a novel ECG representation based on vectorcardiogram (VCG), called temporal vectorcardiogram (TVCG), along with a complex network for feature extraction. We also fine-tune the SVM classifier and perform feature selection with a particle swarm optimization (PSO) algorithm. Results for the inter-patient paradigm show that the proposed method achieves the results comparable to state-of-the-art in MIT-BIH database (53% of Positive predictive (+P) for the Supraventricular ectopic beat (S) class and 87.3% of Sensitivity (Se) for the Ventricular ectopic beat (V) class) that TVCG is a richer representation of the heartbeat and that it could be useful for problems involving the cardiac signal and pattern recognition.

Automatic cardiac arrhythmia detection and classification using vectorcardiograms and complex networks.

This paper intends to bring new insights in the methods for extracting features for cardiac arrhythmia detection and classification systems. We explore the possibility for utilizing vectorcardiograms (VCG) along with electrocardiograms (ECG) to get relevant informations from the heartbeats on the MIT-BIH database. For this purpose, we apply complex networks to extract features from the VCG. We follow the ANSI/AAMI EC57:1998 standard, for classifying the beats into 5 classes (N, V, S, F and Q), and de Chazal's scheme for dataset division into training and test set, with 22 folds validation setup for each set. We used the Support Vector Machinhe (SVM) classifier and the best result we chose had a global accuracy of 84.1%, while still obtaining relatively high Sensitivities and Positive Predictive Value and low False Positive Rates, when compared to other papers that follows the same evaluation methodology that we do.

Voronoi distance based prospective space-time scans for point data sets: a dengue fever cluster analysis in a southeast Brazilian town.

BACKGROUND: The Prospective Space-Time scan statistic (PST) is widely used for the evaluation of space-time clusters of point event data. Usually a window of cylindrical shape is employed, with a circular or elliptical base in the space domain. Recently, the concept of Minimum Spanning Tree (MST) was applied to specify the set of potential clusters, through the Density-Equalizing Euclidean MST (DEEMST) method, for the detection of arbitrarily shaped clusters. The original map is cartogram transformed, such that the control points are spread uniformly. That method is quite effective, but the cartogram construction is computationally expensive and complicated. RESULTS: A fast method for the detection and inference of point data set space-time disease clusters is presented, the Voronoi Based Scan (VBScan). A Voronoi diagram is built for points representing population individuals (cases and controls). The number of Voronoi cells boundaries intercepted by the line segment joining two cases points defines the Voronoi distance between those points. That distance is used to approximate the density of the heterogeneous population and build the Voronoi distance MST linking the cases. The successive removal of edges from the Voronoi distance MST generates sub-trees which are the potential space-time clusters. Finally, those clusters are evaluated through the scan statistic. Monte Carlo replications of the original data are used to evaluate the significance of the clusters. An application for dengue fever in a small Brazilian city is presented. CONCLUSIONS: The ability to promptly detect space-time clusters of disease outbreaks, when the number of individuals is large, was shown to be feasible, due to the reduced computational load of VBScan. Instead of changing the map, VBScan modifies the metric used to define the distance between cases, without requiring the cartogram construction. Numerical simulations showed that VBScan has higher power of detection, sensitivity and positive predicted value than the Elliptic PST. Furthermore, as VBScan also incorporates topological information from the point neighborhood structure, in addition to the usual geometric information, it is more robust than purely geometric methods such as the elliptic scan. Those advantages were illustrated in a real setting for dengue fever space-time clusters.