CapsProm: A Capsule Network For Promoter Prediction

Locating the promoter region in DNA sequences is of paramount importance in the field of bioinformatics. This is a problem widely studied in the literature, however, not yet fully resolved. Some researchers have presented remarkable results using convolution networks, that allowed the automatic extraction of features from a DNA chain. However, a universal architecture that could generalize to several organisms has not yet been achieved, and thus, requiring researchers to seek new architectures and hyperparameters for each new organism evaluated. In this work, we propose a versatile architecture, based on capsule network, that can accurately identify promoter sequences in raw DNA data from seven different organisms, eukaryotic, and prokaryotic. Our model, the CapsProm, could assist in the transfer of learning between organisms and expand its applicability. Furthermore the CapsProm showed competitive results, overcoming the baseline method in five out of seven of the tested datasets (F1-score). The models and source code are made available at https://github.com/lauromoraes/CapsNet-promoter.

A Decidability-Based Loss Function

Nowadays, deep learning is the standard approach for a wide range of problems, including biometrics, such as face recognition and speech recognition, etc. Biometric problems often use deep learning models to extract features from images, also known as embeddings. Moreover, the loss function used during training strongly influences the quality of the generated embeddings. In this work, a loss function based on the decidability index is proposed to improve the quality of embeddings for the verification routine. Our proposal, the D-loss, avoids some Triplet-based loss disadvantages such as the use of hard samples and tricky parameter tuning, which can lead to slow convergence. The proposed approach is compared against the Softmax (cross-entropy), Triplets Soft-Hard, and the Multi Similarity losses in four different benchmarks: MNIST, Fashion-MNIST, CIFAR10 and CASIA-IrisV4. The achieved results show the efficacy of the proposal when compared to other popular metrics in the literature. The D-loss computation, besides being simple, non-parametric and easy to implement, favors both the inter-class and intra-class scenarios.

Towards an Effective and Efficient Deep Learning Model for COVID-19 Patterns Detection in X-ray Images

Confronting the pandemic of COVID-19 caused by the new coronavirus, the SARS-CoV-2, is nowadays one of the most prominent challenges of the human species. A key factor in slowing down the virus propagation is the rapid diagnosis and isolation of infected patients. Nevertheless, the standard method for COVID-19 identification, the Reverse transcription polymerase chain reaction (RT-PCR) method, is time-consuming and in short supply due to the pandemic. Researchers around the world have been looking for alternative screening methods. In this context, deep learning applied to chest X-rays of patients has been showing promising results in the identification of COVID-19. Despite their success, the computational cost of these methods remains high, which imposes difficulties in their accessibility and availability. Thus, in this work, we propose to explore and extend the EfficientNet family of models using chest X-rays images to perform COVID-19 detection. As a result, we can produce a high-quality model with an overall accuracy of 93.9%, COVID-19, sensitivity of 96.8% and positive prediction of 100% while having about 30 times fewer parameters than the baseline literature model, 28 and 5 times fewer parameters than the popular VGG16 and ResNet50 architectures, respectively. We believe the reported figures represent state-of-the-art results, both in terms of efficiency and effectiveness, for the COVIDx database, a database comprised of 13,800 X-ray images, 183 of which are from patients affected by COVID-19.

Towards an Efficient Deep Learning Model for COVID-19 Patterns Detection in X-ray Images

Confronting the pandemic of COVID-19 caused by the new coronavirus, the SARS-CoV-2, is nowadays one of the most prominent challenges of the human species. A key factor in slowing down the virus propagation is rapid diagnosis and isolation of infected patients. Nevertheless, the standard method for COVID-19 identification, the RT-PCR, is time-consuming and in short supply due to the pandemic. Researchers around the world have been trying to find alternative screening methods. In this context, deep learning applied to chest X-rays of patients has been showing a lot of promise for the identification of COVID-19. Despite their success, the computational cost of these methods remains high, which imposes difficulties in their accessibility and availability. Thus, in this work, we address the hypothesis that better performance in terms of overall accuracy and COVID-19 sensitivity can be achieved with much more compact models. In order to test this hypothesis, we propose a modification of the EfficientNet family of models. By doing this we were able to produce a high-quality model with an overall accuracy of 91.4%, COVID-19, sensitivity of 90% and positive prediction of 100% while having about 30 times fewer parameters than the baseline model, 28 and 5 times fewer parameters than the popular VGG16 and ResNet50 architectures, respectively.

Simultaneous Iris and Periocular Region Detection Using Coarse Annotations

In this work, we propose to detect the iris and periocular regions simultaneously using coarse annotations and two well-known object detectors: YOLOv2 and Faster R-CNN. We believe coarse annotations can be used in recognition systems based on the iris and periocular regions, given the much smaller engineering effort required to manually annotate the training images. We manually made coarse annotations of the iris and periocular regions (122K images from the visible (VIS) spectrum and 38K images from the near-infrared (NIR) spectrum). The iris annotations in the NIR databases were generated semi-automatically by first applying an iris segmentation CNN and then performing a manual inspection. These annotations were made for 11 well-known public databases (3 NIR and 8 VIS) designed for the iris-based recognition problem and are publicly available to the research community. Experimenting our proposal on these databases, we highlight two results. First, the Faster R-CNN + Feature Pyramid Network (FPN) model reported an Intersection over Union (IoU) higher than YOLOv2 (91.86% vs 85.30%). Second, the detection of the iris and periocular regions being performed simultaneously is as accurate as performed separately, but with a lower computational cost, i.e., two tasks were carried out at the cost of one.

A Benchmark for Iris Location and a Deep Learning Detector Evaluation

The iris is considered as the biometric trait with the highest unique probability. The iris location is an important task for biometrics systems, affecting directly the results obtained in specific applications such as iris recognition, spoofing and contact lenses detection, among others. This work defines the iris location problem as the delimitation of the smallest squared window that encompasses the iris region. In order to build a benchmark for iris location we annotate (iris squared bounding boxes) four databases from different biometric applications and make them publicly available to the community. Besides these 4 annotated databases, we include 2 others from the literature. We perform experiments on these six databases, five obtained with near infra-red sensors and one with visible light sensor. We compare the classical and outstanding Daugman iris location approach with two window based detectors: 1) a sliding window detector based on features from Histogram of Oriented Gradients (HOG) and a linear Support Vector Machines (SVM) classifier; 2) a deep learning based detector fine-tuned from YOLO object detector. Experimental results showed that the deep learning based detector outperforms the other ones in terms of accuracy and runtime (GPUs version) and should be chosen whenever possible.