José Miranda

Elena Espinosa, Rubén Rodríguez Álvarez, José Miranda et al.

The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic data volume and diversity. This volume of workloads places genomics among the top four big data challenges anticipated for this decade. In this context, pairwise sequence alignment represents a very time- and energy-intensive step in common bioinformatics pipelines. Speeding up this step requires the implementation of heuristic approaches, optimized algorithms, and/or hardware acceleration. Although state-of-the-art CPU and GPU implementations have demonstrated significant performance gains, recent FPGA implementations have shown improved energy efficiency. However, the latter often suffer from limited read-length scalability due to constraints on hardware resources when aligning longer sequences. In this work, we present a flexible FPGA-based accelerator template scalable up to 1000 bp that implements Myers's algorithm to compute exact unit-cost edit-distance using high-level synthesis and a worker-based architecture. GeneTEK, a set of instances of this accelerator template in a Xilinx Zynq UltraScale+ FPGA, achieves up to 113% increase in execution speed and up to 111x reduction in energy consumption compared to leading CPU and GPU solutions, while fitting comparison matrices up to 13x larger than previous FPGA-based systolic-array solutions. By following a SW-HW co-design approach, GeneTEK exploits parallelization at multiple levels and efficient memory use to deliver a scalable and accurate FPGA-based accelerator. These results reaffirm the potential of FPGAs as an energy-efficient platform for pairwise alignment of read-lengths up to 1000 bp.

Jose A. Miranda, Celia López-Ongil, Javier Andreu-Perez

Most of today's wearable technology provides seamless cardiac activity monitoring. Specifically, the vast majority employ Photoplethysmography (PPG) sensors to acquire blood volume pulse information, which is further analysed to extract useful and physiologically related features. Nevertheless, PPG-based signal reliability presents different challenges that strongly affect such data processing. This is mainly related to the fact of PPG morphological wave distortion due to motion artefacts, which can lead to erroneous interpretation of the extracted cardiac-related features. On this basis, in this paper, we propose a novel personalised and adjustable Interval Type-2 Fuzzy Logic System (IT2FLS) for assessing the quality of PPG signals. The proposed system employs a personalised approach to adapt the IT2FLS parameters to the unique characteristics of each individual's PPG signals.Additionally, the system provides adjustable levels of personalisation, allowing healthcare providers to adjust the system to meet specific requirements for different applications. The proposed system obtained up to 93.72\% for average accuracy during validation. The presented system has the potential to enable ultra-low complexity and real-time PPG quality assessment, improving the accuracy and reliability of PPG-based health monitoring systems at the edge.

Laura Gutierrez-Martin, Celia Lopez Ongil, Jose M. Lanza-Gutierrez et al.

Emotion recognition through artificial intelligence and smart sensing of physical and physiological signals (Affective Computing) is achieving very interesting results in terms of accuracy, inference times, and user-independent models. In this sense, there are applications related to the safety and well-being of people (sexual aggressions, gender-based violence, children and elderly abuse, mental health, etc.) that require even more improvements. Emotion detection should be done with fast, discrete, and non-luxurious systems working in real-time and real life (wearable devices, wireless communications, battery-powered). Furthermore, emotional reactions to violence are not equal in all people. Then, large general models cannot be applied to a multiuser system for people protection, and customized and simple AI models would be welcomed by health and social workers and law enforcement agents. These customized models will be applicable to clusters of subjects sharing similarities in their emotional reactions to external stimuli. This customization requires several steps: creating clusters of subjects with similar behaviors, creating AI models for every cluster, continually updating these models with new data, and enrolling new subjects in clusters when required. A methodology for clustering data compiled (physical and physiological data, together with emotional labels) is presented in this work, as well as the method for including new subjects once the AI model is generated. Experimental results demonstrate an improvement of 4% in accuracy and 3% in f1-score w.r.t. the general model, along with a 14% reduction in variability.

Christodoulos Kechris, Jonathan Dan, Jose Miranda et al.

Non-linear activation functions are crucial in Convolutional Neural Networks. However, until now they have not been well described in the frequency domain. In this work, we study the spectral behavior of ReLU, a popular activation function. We use the ReLU's Taylor expansion to derive its frequency domain behavior. We demonstrate that ReLU introduces higher frequency oscillations in the signal and a constant DC component. Furthermore, we investigate the importance of this DC component, where we demonstrate that it helps the model extract meaningful features related to the input frequency content. We accompany our theoretical derivations with experiments and real-world examples. First, we numerically validate our frequency response model. Then we observe ReLU's spectral behavior on two example models and a real-world one. Finally, we experimentally investigate the role of the DC component introduced by ReLU in the CNN's representations. Our results indicate that the DC helps to converge to a weight configuration that is close to the initial random weights.

Christodoulos Kechris, Jonathan Dan, Jose Miranda et al.

Deep learning time-series processing often relies on convolutional neural networks with overlapping windows. This overlap allows the network to produce an output faster than the window length. However, it introduces additional computations. This work explores the potential to optimize computational efficiency during inference by exploiting convolution's shift-invariance properties to skip the calculation of layer activations between successive overlapping windows. Although convolutions are shift-invariant, zero-padding and pooling operations, widely used in such networks, are not efficient and complicate efficient streaming inference. We introduce StreamiNNC, a strategy to deploy Convolutional Neural Networks for online streaming inference. We explore the adverse effects of zero padding and pooling on the accuracy of streaming inference, deriving theoretical error upper bounds for pooling during streaming. We address these limitations by proposing signal padding and pooling alignment and provide guidelines for designing and deploying models for StreamiNNC. We validate our method in simulated data and on three real-world biomedical signal processing applications. StreamiNNC achieves a low deviation between streaming output and normal inference for all three networks (2.03 - 3.55% NRMSE). This work demonstrates that it is possible to linearly speed up the inference of streaming CNNs processing overlapping windows, negating the additional computation typically incurred by overlapping windows.

Christodoulos Kechris, Jonathan Dan, Jose Miranda et al.

Accurate extraction of heart rate from photoplethysmography (PPG) signals remains challenging due to motion artifacts and signal degradation. Although deep learning methods trained as a data-driven inference problem offer promising solutions, they often underutilize existing knowledge from the medical and signal processing community. In this paper, we address three shortcomings of deep learning models: motion artifact removal, degradation assessment, and physiologically plausible analysis of the PPG signal. We propose KID-PPG, a knowledge-informed deep learning model that integrates expert knowledge through adaptive linear filtering, deep probabilistic inference, and data augmentation. We evaluate KID-PPG on the PPGDalia dataset, achieving an average mean absolute error of 2.85 beats per minute, surpassing existing reproducible methods. Our results demonstrate a significant performance improvement in heart rate tracking through the incorporation of prior knowledge into deep learning models. This approach shows promise in enhancing various biomedical applications by incorporating existing expert knowledge in deep learning models.

Paula Ruiz-Barroso, Francisco M. Castro, José Miranda et al.

Cardiovascular diseases, a leading cause of noncommunicable disease-related deaths, require early and accurate detection to improve patient outcomes. Taking advantage of advances in machine learning and deep learning, multiple approaches have been proposed in the literature to address the challenge of detecting ECG anomalies. Typically, these methods are based on the manual interpretation of ECG signals, which is time consuming and depends on the expertise of healthcare professionals. The objective of this work is to propose a deep learning system, FADE, designed for normal ECG forecasting and anomaly detection, which reduces the need for extensive labeled datasets and manual interpretation. FADE has been trained in a self-supervised manner with a novel morphological inspired loss function. Unlike conventional models that learn from labeled anomalous ECG waveforms, our approach predicts the future of normal ECG signals, thus avoiding the need for extensive labeled datasets. Using a novel distance function to compare forecasted ECG signals with actual sensor data, our method effectively identifies cardiac anomalies. Additionally, this approach can be adapted to new contexts through domain adaptation techniques. To evaluate our proposal, we performed a set of experiments using two publicly available datasets: MIT-BIH NSR and MIT-BIH Arrythmia. The results demonstrate that our system achieves an average accuracy of 83.84% in anomaly detection, while correctly classifying normal ECG signals with an accuracy of 85.46%. Our proposed approach exhibited superior performance in the early detection of cardiac anomalies in ECG signals, surpassing previous methods that predominantly identify a limited range of anomalies. FADE effectively detects both abnormal heartbeats and arrhythmias, offering significant advantages in healthcare through cost reduction or processing of large-scale ECG data.

Amirhossein Shahbazinia, Jonathan Dan, Jose A. Miranda et al.

Objective: Epilepsy, a prevalent neurological disease, demands careful diagnosis and continuous care. Seizure detection remains challenging, as current clinical practice relies on expert analysis of electroencephalography, which is a time-consuming process and requires specialized knowledge. Addressing this challenge, this paper explores automated epileptic seizure detection using deep learning, focusing on personalized continual learning models that adapt to each patient's unique electroencephalography signal features, which evolve over time. Methods: In this context, our approach addresses the challenge of integrating new data into existing models without catastrophic forgetting, a common issue in static deep learning models. We propose EpiSMART, a continual learning framework for seizure detection that uses a size-constrained replay buffer and an informed sample selection strategy to incrementally adapt to patient-specific electroencephalography signals. By selectively retaining high-entropy and seizure-predicted samples, our method preserves critical past information while maintaining high performance with minimal memory and computational requirements. Results: Validation on the CHB-MIT dataset, shows that EpiSMART achieves a 21% improvement in the F1 score over a trained baseline without updates in all other patients. On average, EpiSMART requires only 6.46 minutes of labeled data and 6.28 updates per day, making it suitable for real-time deployment in wearable systems. Conclusion:EpiSMART enables robust and personalized seizure detection under realistic and resource-constrained conditions by effectively integrating new data into existing models without degrading past knowledge. Significance: This framework advances automated seizure detection by providing a continual learning approach that supports patient-specific adaptation and practical deployment in wearable healthcare systems.