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.

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.

Rafael F. Oliveira, Gladston J. P. Moreira, Vander L. S. Freitas et al.

Arrhythmias, detectable through electrocardiograms (ECGs), pose significant health risks, underscoring the need for accurate and efficient automated detection techniques. While recent advancements in graph-based methods have demonstrated potential to enhance arrhythmia classification, the challenge lies in effectively representing ECG signals as graphs. This study investigates the use of Visibility Graph (VG) and Vector Visibility Graph (VVG) representations combined with Graph Convolutional Networks (GCNs) for arrhythmia classification under the ANSI/AAMI standard, ensuring reproducibility and fair comparison with other techniques. Through extensive experiments on the MIT-BIH dataset, we evaluate various GCN architectures and preprocessing parameters. Our findings demonstrate that VG and VVG mappings enable GCNs to classify arrhythmias directly from raw ECG signals, without the need for preprocessing or noise removal. Notably, VG offers superior computational efficiency, while VVG delivers enhanced classification performance by leveraging additional lead features. The proposed approach outperforms baseline methods in several metrics, although challenges persist in classifying the supraventricular ectopic beat (S) class, particularly under the inter-patient paradigm.

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 Henrique Nascimento Castro, Gabriel Cássia Fortuna, Rafael Alves Bonfim de Queiroz et al.

In response to the prevalent challenge of overfitting in deep neural networks, this paper introduces Simultaneous Learning, a regularization approach drawing on principles of Transfer Learning and Multi-task Learning. We leverage auxiliary datasets with the target dataset, the UFOP-HVD, to facilitate simultaneous classification guided by a customized loss function featuring an inter-group penalty. This experimental configuration allows for a detailed examination of model performance across similar (PlantNet) and dissimilar (ImageNet) domains, thereby enriching the generalizability of Convolutional Neural Network models. Remarkably, our approach demonstrates superior performance over models without regularization and those applying dropout regularization exclusively, enhancing accuracy by 5 to 22 percentage points. Moreover, when combined with dropout, the proposed approach improves generalization, securing state-of-the-art results for the UFOP-HVD challenge. The method also showcases efficiency with significantly smaller sample sizes, suggesting its broad applicability across a spectrum of related tasks. In addition, an interpretability approach is deployed to evaluate feature quality by analyzing class feature correlations within the network's convolutional layers. The findings of this study provide deeper insights into the efficacy of Simultaneous Learning, particularly concerning its interaction with the auxiliary and target datasets.

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.