Gladston Moreira

Lauro Moraes, Pedro Silva, Eduardo Luz et al.

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.

Arthur Negrão, Pedro Silva, Vander L. S. Freitas et al.

The rapid growth of Large Language Models (LLMs) intensifies the need for effective compression, with weight quantization being the most widely adopted technique. Standard uniform quantizers assume that parameters are evenly distributed, an assumption at odds with the highly skewed distributions observed in practice. We propose Benford-Quant, a simple, data-free non-uniform quantizer inspired by Benford's Law, which predicts that leading digits follow a logarithmic distribution. Benford-Quant replaces the uniform grid with a log-spaced codebook, dedicating more resolution to the frequent small-magnitude weights. We provide both theoretical intuition and empirical evidence: (i) weights in transformer transformational layers adhere closely to Benford statistics, while normalization layers systematically deviate; (ii) on Small Language Models (SLMs), Benford-Quant consistently improves perplexity, reducing 4-bit perplexity on Gemma-270M by more than 10%; and (iii) on larger LLMs, it remains competitive, with differences explained by over-parameterization effects. Our results indicate that incorporating a Benford-inspired prior into quantization grids is a low-cost modification that yields accuracy gains in aggressive few-bit regimes. Although it is not able to surpass the state of the art in tasks such as perplexity and LAMBADA, the Benford-Quant approach can be hybridized with other quantization methods-such as SmoothQuant and Activation-Aware Quantization-without major pipeline modification, potentially improving their performance.

Guilherme Silva, Pedro Silva, Gladston Moreira et al.

The classification of electrocardiogram (ECG) signals is crucial for early detection of arrhythmias and other cardiac conditions. However, despite advances in machine learning, many studies fail to follow standardization protocols, leading to inconsistencies in performance evaluation and real-world applicability. Additionally, hardware constraints essential for practical deployment, such as in pacemakers, Holter monitors, and wearable ECG patches, are often overlooked. Since real-world impact depends on feasibility in resource-constrained devices, ensuring efficient deployment is critical for continuous monitoring. This review systematically analyzes ECG classification studies published between 2017 and 2024, focusing on those adhering to the E3C (Embedded, Clinical, and Comparative Criteria), which include inter-patient paradigm implementation, compliance with Association for the Advancement of Medical Instrumentation (AAMI) recommendations, and model feasibility for embedded systems. While many studies report high accuracy, few properly consider patient-independent partitioning and hardware limitations. We identify state-of-the-art methods meeting E3C criteria and conduct a comparative analysis of accuracy, inference time, energy consumption, and memory usage. Finally, we propose standardized reporting practices to ensure fair comparisons and practical applicability of ECG classification models. By addressing these gaps, this study aims to guide future research toward more robust and clinically viable ECG classification systems.

Sara Câmara, Eduardo Luz, Valéria Carvalho et al.

Prompt engineering is crucial for unlocking the potential of Large Language Models (LLMs). Still, since manual prompt design is often complex, non-intuitive, and time-consuming, automatic prompt optimization has emerged as a research area. However, a significant challenge in prompt optimization is managing the inherent trade-off between task performance, such as accuracy, and context size. Most existing automated methods focus on a single objective, typically performance, thereby failing to explore the critical spectrum of efficiency and effectiveness. This paper introduces the MOPrompt, a novel Multi-objective Evolutionary Optimization (EMO) framework designed to optimize prompts for both accuracy and context size (measured in tokens) simultaneously. Our framework maps the Pareto front of prompt solutions, presenting practitioners with a set of trade-offs between context size and performance, a crucial tool for deploying Large Language Models (LLMs) in real-world applications. We evaluate MOPrompt on a sentiment analysis task in Portuguese, using Gemma-2B and Sabiazinho-3 as evaluation models. Our findings show that MOPrompt substantially outperforms the baseline framework. For the Sabiazinho model, MOPrompt identifies a prompt that achieves the same peak accuracy (0.97) as the best baseline solution, but with a 31% reduction in token length.

Pedro Silva, Guilherme A. L. Silva, Pablo Coelho et al.

Deep Metric Learning (DML) aims to learn embedding functions that map semantically similar inputs to proximate points in a metric space while separating dissimilar ones. Existing methods, such as pairwise losses, are hindered by complex sampling requirements and slow convergence. In contrast, proxy-based losses, despite their improved scalability, often fail to optimize global distribution properties. The Decidability-based Loss (D-Loss) addresses this by targeting the decidability index (d') to enhance distribution separability, but its reliance on large mini-batches imposes significant computational constraints. We introduce Proxy-Decidability Loss (PD-Loss), a novel objective that integrates learnable proxies with the statistical framework of d' to optimize embedding spaces efficiently. By estimating genuine and impostor distributions through proxies, PD-Loss combines the computational efficiency of proxy-based methods with the principled separability of D-Loss, offering a scalable approach to distribution-aware DML. Experiments across various tasks, including fine-grained classification and face verification, demonstrate that PD-Loss achieves performance comparable to that of state-of-the-art methods while introducing a new perspective on embedding optimization, with potential for broader applications.

Pablo G. Almeida, Guilherme A. L. Silva, Valéria Santos et al.

Student dropout is a significant challenge in educational systems worldwide, leading to substantial social and economic costs. Predicting students at risk of dropout allows for timely interventions. While traditional Machine Learning (ML) models operating on tabular data have shown promise, Graph Neural Networks (GNNs) offer a potential advantage by capturing complex relationships inherent in student data if structured as graphs. This paper investigates whether transforming tabular student data into graph structures, primarily using clustering techniques, enhances dropout prediction accuracy. We compare the performance of GNNs (a custom Graph Convolutional Network (GCN) and GraphSAGE) on these generated graphs against established tabular models (Random Forest (RF), XGBoost, and TabNet) using a real-world student dataset. Our experiments explore various graph construction strategies based on different clustering algorithms (K-Means, HDBSCAN) and dimensionality reduction techniques (Principal Component Analysis (PCA), Uniform Manifold Approximation and Projection (UMAP)). Our findings demonstrate that a specific GNN configuration, GraphSAGE on a graph derived from PCA-KMeans clustering, achieved superior performance, notably improving the macro F1-score by approximately 7 percentage points and accuracy by nearly 2 percentage points over the strongest tabular baseline (XGBoost). However, other GNN configurations and graph construction methods did not consistently surpass tabular models, emphasizing the critical role of the graph generation strategy and GNN architecture selection. This highlights both the potential of GNNs and the challenges in optimally transforming tabular data for graph-based learning in this domain.

Michele Andrade, Guilherme A. L. Silva, Valéria Santos et al.

Estimating the nutritional content of food from images is a critical task with significant implications for health and dietary monitoring. This is challenging, especially when relying solely on 2D images, due to the variability in food presentation, lighting, and the inherent difficulty in inferring volume and mass without depth information. Furthermore, reproducibility in this domain is hampered by the reliance of state-of-the-art methods on proprietary datasets for large-scale pre-training. In this paper, we investigate the impact of large-scale pre-training datasets on the performance of deep learning models for nutritional estimation using only 2D images. We fine-tune and evaluate Vision Transformer (ViT) models pre-trained on two large public datasets, ImageNet and COYO, comparing their performance against baseline CNN models (InceptionV2 and ResNet-50) and a state-of-the-art method pre-trained on the proprietary JFT-300M dataset. We conduct extensive experiments on the Nutrition5k dataset, a large-scale collection of real-world food plates with high-precision nutritional annotations. Our evaluation using Mean Absolute Error (MAE) and Mean Absolute Percentage Error (MAE%) reveals that models pre-trained on JFT-300M significantly outperform those pre-trained on public datasets. Unexpectedly, the model pre-trained on the massive COYO dataset performs worse than the model pre-trained on ImageNet for this specific regression task, refuting our initial hypothesis. Our analysis provides quantitative evidence highlighting the critical role of pre-training dataset characteristics, including scale, domain relevance, and curation quality, for effective transfer learning in 2D nutritional estimation.

Gladston Moreira, Ivan Meneghini, Elizabeth Wanner

Multi-objective optimization problems (MOPs) often require a trade-off between conflicting objectives, maximizing diversity and convergence in the objective space. This study presents an approach to improve the quality of MOP solutions by optimizing the dispersion in the decision space and the convergence in a specific region of the objective space. Our approach defines a Region of Interest (ROI) based on a cone representing the decision maker's preferences in the objective space, while enhancing the dispersion of solutions in the decision space using a uniformity measure. Combining solution concentration in the objective space with dispersion in the decision space intensifies the search for Pareto-optimal solutions while increasing solution diversity. When combined, these characteristics improve the quality of solutions and avoid the bias caused by clustering solutions in a specific region of the decision space. Preliminary experiments suggest that this method enhances multi-objective optimization by generating solutions that effectively balance dispersion and concentration, thereby mitigating bias in the decision space.

Pedro Silva, Gladston Moreira, Vander Freitas et al.

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.

Eduardo Luz, Pedro Lopes Silva, Rodrigo Silva et al.

Confronting the pandemic of COVID-19, 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. The standard method for COVID-19 identification, the Reverse transcription polymerase chain reaction method, is time-consuming and in short supply due to the pandemic. Thus, researchers have been looking for alternative screening methods and deep learning applied to chest X-rays of patients has been showing promising results. Despite their success, the computational cost of these methods remains high, which imposes difficulties to their accessibility and availability. Thus, the main goal of this work is to propose an accurate yet efficient method in terms of memory and processing time for the problem of COVID-19 screening in chest X-rays. Methods: To achieve the defined objective we exploit and extend the EfficientNet family of deep artificial neural networks which are known for their high accuracy and low footprints in other applications. We also exploit the underlying taxonomy of the problem with a hierarchical classifier. A dataset of 13,569 X-ray images divided into healthy, non-COVID-19 pneumonia, and COVID-19 patients is used to train the proposed approaches and other 5 competing architectures. Finally, 231 images of the three classes were used to assess the quality of the methods. Results: The results show that the proposed approach was able to 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 from 5 to 30 times fewer parameters than other than the other tested architectures. Larger and more heterogeneous databases are still needed for validation before claiming that deep learning can assist physicians in the task of detecting COVID-19 in X-ray images.

Diego R. Lucio, Rayson Laroca, Luiz A. Zanlorensi et al.

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.

Evair Severo, Rayson Laroca, Cides S. Bezerra et al.

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.