Deep Learning-based Computer-Aided Diagnosis systems: a contribution to prostate cancer detection in histopathological images

In this work, novel computer-aided diagnosis systems for medical image analysis focusing on prostate cancer are proposed and implemented. First, the histopathology of prostate cancer was studied, along with the Gleason Grading System, which measures the aggressiveness of a tumor through different patterns with the purpose of driving therapies dealing with this disease. Furthermore, a study of Deep Learning techniques, particularly focusing on neural networks applied to medical image analysis, was conducted. Based on these studies, a Deep Learning-based system to detect malignant regions in gigapixel-size whole-slide prostate cancer tissue images was proposed and developed, which is able to report spatial information of the malignant areas. This solution was evaluated in terms of performance and execution time, obtaining promising results when compared to other state-of-the-art methods. Since the implemented system locates malignant regions within the image without providing a global class, a customWide & Deep network was developed to report a slide-level label per image. The proposed system provides a fast screening method for analyzing histopathological images. Next, a neural network was proposed to assign a specific Gleason pattern to the malignant areas of the tissue. Finally, with the purpose of developing a global computeraided diagnosis system for prostate cancer detection and classification, the three aforementioned subsystems were combined, allowing a complete analysis of histopathological images by reporting whether the sample is normal or malignant, and, in the last case, a heatmap of the malignant areas with their corresponding Gleason pattern. The studied algorithms were also used for other medical image analysis tasks. The performance of these systems were evaluated, discussing the obtained results, presenting conclusions and proposing improvements for future works

An Automated Fall Detection System Using Recurrent Neural Networks

Falls are the most common cause of fatal injuries in elderly people, causing even death if there is no immediate assistance. Fall detection systems can be used to alert and request help when this type of accident happens. Certain types of these systems include wearable devices that analyze bio-medical signals from the person carrying it in real time. In this way, Deep Learning algorithms could automate and improve the detection of unintentional falls by analyzing these signals. These algorithms have proven to achieve high effectiveness with competitive performances in many classification problems. This work aims to study 16 Recurrent Neural Networks architectures (using Long Short-Term Memory and Gated Recurrent Units) for falls detection based on accelerometer data, reducing computational requirements of previous research. The architectures have been tested on a labeled version of the publicly available SisFall dataset, achieving a mean F1-score above 0.73 and improving state-of-the-art solutions in terms of network complexity.Ministerio de Economía y Competitivida TEC2016-77785-

Breast Cancer Automatic Diagnosis System using Faster Regional Convolutional Neural Networks

Breast cancer is one of the most frequent causes of mortality in women. For the early detection of breast cancer, the mammography is used as the most efficient technique to identify abnormalities such as tumors. Automatic detection of tumors in mammograms has become a big challenge and can play a crucial role to assist doctors in order to achieve an accurate diagnosis. State-of-the-art Deep Learning algorithms such as Faster Regional Convolutional Neural Networks are able to determine the presence of an object and also its position inside the image in a reduced computation time. In this work, we evaluate these algorithms to detect tumors in mammogram images and propose a detection system that contains: (1) a preprocessing step performed on mammograms taken from the Digital Database for Screening Mammography (DDSM) and (2) the Neural Network model, which performs feature extraction over the mammograms in order to locate tumors within each image and classify them as malignant or benign. The results obtained show that the proposed algorithm has an accuracy of 97.375%. These results show that the system could be very useful for aiding physicians when detecting tumors from mammogram images.Ministerio de Economía y Competitividad TEC2016-77785-

Multi-dataset Training for Medical Image Segmentation as a Service

Deep Learning tools are widely used for medical image segmentation. The results produced by these techniques depend to a great extent on the data sets used to train the used network. Nowadays many cloud service providers offer the required resources to train networks and deploy deep learning networks. This makes the idea of segmentation as a cloud-based service attractive. In this paper we study the possibility of training, a generalized configurable, Keras U-Net to test the feasibility of training with images acquired, with specific instruments, to perform predictions on data from other instruments. We use, as our application example, the segmentation of Optic Disc and Cup which can be applied to glaucoma detection. We use two publicly available data sets (RIM-One V3 and DRISHTI) to train either independently or combining their data.Ministerio de Economía y Competitividad TEC2016-77785-

COVID-XNet: a custom Deep Learning system to diagnose and locate COVID-19 in chest X-ray images

The COVID-19 pandemic caused by the new coronavirus SARS-CoV-2 has changed the world as we know it. An early diagnosis is crucial in order to prevent new outbreaks and control its rapid spread. Medical imaging techniques, such as X-ray or chest computed tomography, are commonly used for this purpose due to their reliability for COVID-19 diagnosis. Computer-aided diagnosis systems could play an essential role in aiding radiologists in the screening process. In this work, a novel Deep Learning-based system, called COVID-XNet, is presented for COVID-19 diagnosis in chest X-ray images. The proposed system performs a set of preprocessing algorithms to the input images for variability reduction and contrast enhancement, which are then fed to a custom Convolutional Neural Network in order to extract relevant features and perform the classification between COVID-19 and normal cases. The system is trained and validated using a 5-fold cross-validation scheme, achieving an average accuracy of 94.43% and an AUC of 0.988. The output of the system can be visualized using Class Activation Maps, highlighting the main findings for COVID-19 in X-ray images. These promising results indicate that COVID-XNet could be used as a tool to aid radiologists and contribute to the fight against COVID-19.European Regional Development Fund COFNET TEC2016-77785-PAndalusian Regional (Spain) / FEDER Project PAIDI2020Andalusian Regional /FEDER PROMETEO AT17-5410-US

Glioma Diagnosis Aid through CNNs and Fuzzy-C Means for MRI

Glioma is a type of brain tumor that causes mortality in many cases. Early diagnosis is an important factor. Typically, it is detected through MRI and then either a treatment is applied, or it is removed through surgery. Deep-learning techniques are becoming popular in medical applications and image-based diagnosis. Convolutional Neural Networks are the preferred architecture for object detection and classification in images. In this paper, we present a study to evaluate the efficiency of using CNNs for diagnosis aids in glioma detection and the improvement of the method when using a clustering method (Fuzzy C-means) for preprocessing the input MRI dataset. Results offered an accuracy improvement from 0.77 to 0.81 when using Fuzzy C-Means.Ministerio de Economía y Competitividad TEC2016-77785-

Sampling Frequency Evaluation on Recurrent Neural Networks Architectures for IoT Real-time Fall Detection Devices

Falls are one of the most frequent causes of injuries in elderly people. Wearable Fall Detection Systems provided a ubiquitous tool for monitoring and alert when these events happen. Recurrent Neural Networks (RNN) are algorithms that demonstrates a great accuracy in some problems analyzing sequential inputs, such as temporal signal values. However, their computational complexity are an obstacle for the implementation in IoT devices. This work shows a performance analysis of a set of RNN architectures when trained with data obtained using different sampling frequencies. These architectures were trained to detect both fall and fall hazards by using accelerometers and were tested with 10-fold cross validation, using the F1-score metric. The results obtained show that sampling with a frequency of 25Hz does not affect the effectiveness, based on the F1-score, which implies a substantial increase in the performance in terms of computational cost. The architectures with two RNN layers and without a first dense layer had slightly better results than the smallest architectures. In future works, the best architectures obtained will be integrated in an IoT solution to determine the effectiveness empirically.Ministerio de Economía y Competitividad TEC2016-77785-

Implementing a Distance Estimator for a Wildlife Tracking System Based on 802.15.4

In this work, a novel distance estimation mechanism using received signal strength indication (RSSI) signals with ZigBee modules is designed, implemented and tested in several scenarios. This estimator was used for a research project focused on a wildlife behavioral classification system deployed in Doñana’s National Park. As a supporting feature for that project, this work was implemented for locating animal’s collars acting as wireless nodes in order to find those who went outside of the coverage area of the network or that were accidentally detached from animals. This work describes the system architecture and the implementation of a mobile assistant capable of recovering devices located beyond the coverage of the network. The analytical model needed for distance estimation and the signal filtering are described, as well as the difficulties that the researchers must deal when building robust location estimators. This theoretical model was applied to three different scenarios and tested with two validation experiments.Junta de Andalucía P12-TIC-130

Interfacing PDM MEMS Microphones with PFM Spiking Systems: Application for Neuromorphic Auditory Sensors

Neuromorphic computation processes sensors output in the spiking domain, which presents constraints in many cases when converting information to spikes, loosing, as example, temporal accuracy. This paper presents a spike-based system to adapt audio information from low-power pulse-density modulation (PDM) microelectromechanical systems microphones into rate coded spike frequencies. These spikes could be directly used by the neuromorphic auditory sensor (NAS) for frequency decomposition in different bands, avoiding the analog or digital conversion to spike streams. This improves the time response of the NAS, allowing its use in more time restrictive applications. This adaptation was conducted in VHDL as an interface for PDM microphones, converting their pulses into temporal distributed spikes following a pulse-frequency modulation scheme with an accurate inter-spike-interval, known as PDM to spikes interface (PSI). We introduce a new architecture of spike-based band-pass filter to reject DC components and distribute spikes in time. This was tested in two scenarios, first as a stand-alone circuit for its characterization, and then integrated with a NAS for verification. The PSI achieves a total harmonic distortion of −46.18 dB and a signal-to-noise ratio of 63.47 dB, demands less than 1% of the resources of a Spartan-6 FPGA and its power consumption is around 7 mW.Agencia Estatal de Investigación PID2019-105556GB-C33/AEI/10.13039/501100011033 (MINDROB)Ministerio de Ciencia, Innovación y Universidades PCI2019-111841-2 (CHIST-ERA SMALL

Performance Evaluation of Deep Learning-Based Prostate Cancer Screening Methods in Histopathological Images: Measuring the Impact of the Model’s Complexity on Its Processing Speed

Prostate cancer (PCa) is the second most frequently diagnosed cancer among men worldwide, with almost 1.3 million new cases and 360,000 deaths in 2018. As it has been estimated, its mortality will double by 2040, mostly in countries with limited resources. These numbers suggest that recent trends in deep learning-based computer-aided diagnosis could play an important role, serving as screening methods for PCa detection. These algorithms have already been used with histopathological images in many works, in which authors tend to focus on achieving high accuracy results for classifying between malignant and normal cases. These results are commonly obtained by training very deep and complex convolutional neural networks, which require high computing power and resources not only in this process, but also in the inference step. As the number of cases rises in regions with limited resources, reducing prediction time becomes more important. In this work, we measured the performance of current state-of-the-art models for PCa detection with a novel benchmark and compared the results with PROMETEO, a custom architecture that we proposed. The results of the comprehensive comparison show that using dedicated models for specific applications could be of great importance in the future.Spanish grant and the European Regional Development Fund MIND-ROB PID2019-105556GB-C33EU H2020 project CHISTERA SMALL PCI2019-111841-2Andalusian Regional Project PAIDI2020 with FEDER support PROMETEO AT17-5410-US