2025
Authors
Montrezol, J; Oliveira, HS; Araujo, J; Oliveira, HP;
Publication
2025 47TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC)
Abstract
The Vision Transformer (ViT) architecture has emerged as a potential game-changer in computer vision, offering scalability and global attention that have generated considerable interest in recent years. Its adaptability has fueled enthusiasm for its application. This work investigates the boundaries of the architecture, focusing on developing new techniques targeting explicitly complex tasks, such as medical imaging datasets, which often exhibit high variability, class imbalance, and limited sample sizes. We propose a set of mixed regularisation and augmentation techniques to enhance the performance of models. These include a novel loss function and a smoothly differentiable activation function, leading to more stable training and model performance. The results show that incorporating these techniques improves model performance and training convergence.
2025
Authors
Pereira, M; Mendes, T; Hespanhol, V; Oliveira, P; Pereira, T;
Publication
Proceedings - 2025 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2025
Abstract
Epidermal Growth Factor Receptor (EGFR) is one of the most frequently mutated genes in lung cancer. Its mutation status characterization is crucial for personalized treatment in Non-Small-Cell Lung Cancer (NSCLC). Biopsy is the gold standard for characterizing the EGFR mutation status. However, it is an invasive time-consuming method and is often burdensome or even impractical for some patients. Therefore, it is of utmost importance to identify alternative non-invasive methods for classifying this mutation. Computed Tomography (CT) images represent a non-invasive, safer and faster method to directly characterize lung cancer. This study developed a comprehensive radiomic approach for EGFR mutation classification using CT images, in which two preprocessing strategies were compared and five machine learning algorithms were evaluated across different datasets. We analyzed two independent datasets individually and combined, implementing lung containing nodule versus bounding box around nodule preprocessing approaches. Radiomic features were extracted using PyRadiomics and selected through Principal Component Analysis (PCA) (65-95% variance thresholds) and pairwise correlation filtering. The results demonstrated that the lung with nodule strategy achieved better and more consistent performance compared to the bounding box around the nodule method. The best performance (AUC=0.780) was achieved using Random Forest with correlation filtering. The results suggest that radiomics may be a potential support tool for EGFR classification when biopsy is not feasible or recommended. This would enable safer and more efficient personalized treatment. Nevertheless, the results underscore the need for larger, diverse datasets to improve model robustness for characterizing such complex and variable information before clinical integration. © 2025 IEEE.
2025
Authors
Carvalho, MI; Facao, M; Descalzi, O;
Publication
CHAOS
Abstract
Modulation instability (MI) of the continuous wave (cw) has been associated with the onset of stable solitons in conservative and dissipative systems. The cubic complex Ginzburg-Landau equation (CGLE) is a prototype of a damped, driven, nonlinear, and dispersive system. The inclusion of nonlinear gradients is essential to stabilize pulses whether stationary or oscillatory. The soliton solutions of this model have been reasonably studied; however, its cw solution characteristics and stability have not been reported yet. Here, we obtain the cw solutions of the cubic CGLE with nonlinear gradient terms and study its short- and long-term evolution under the effect of small perturbations. We have found that, for each admissible amplitude, there are two branches of cw solutions, and all of them are unstable. Then, through direct integration of the evolution equation, we study the evolution of those cw solutions, observing the emergence of plain and oscillatory solitons. Depending on whether the cw and/or its perturbation are sinusoidal, we can obtain a train of a finite number of pulses or bound states.
2025
Authors
Guerra, AR; Oliveira, LR; Rodrigues, GO; Pinheiro, MR; Carvalho, MI; Tuchin, VV; Oliveira, LM;
Publication
JOURNAL OF BIOPHOTONICS
Abstract
Measuring the density of tartrazine (TZ) powder allowed to develop a protocol for fast preparation of aqueous solutions with a desired concentration. The stability time of these solutions decreases exponentially with the increase of TZ concentration: solutions with TZ concentrations below 25% remain stable for more than 24 h, while the solution with 60% TZ remains stable only for 35 min. To validate the developed protocol, muscle samples were immersed in the 40% TZ solution and, as expected, the tissue transparency increased smoothly and exponentially during the whole treatment of 30 min. The diffusion time of TZ in ex vivo skeletal muscle was quantitatively determined with high accuracy as tau TZ = 5.39 +/- 0.49 min for sample thickness of 0.5 mm. By measuring the refractive index of TZ solutions during preparation, it will be easier to prepare such solutions in a fast manner for future research on tissue optical clearing.
2025
Authors
Facao, M; Malheiro, D; Carvalho, MI;
Publication
PHYSICAL REVIEW A
Abstract
We studied the characteristics, regions of existence, and stability of different types of solitons for a distributed model of a mode-locked laser whose dispersion is purely quartic and normal. Among the different types of solitons, we identified three main branches that are named according to their different amplitude: low, medium, and high amplitude solitons. It was found that the first solitons are always unstable while the latter two exist and are stable in relatively large regions of the parameter space. Moreover, the stability regions of medium and high amplitude solitons overlap over a certain range of parameters, manifesting effects of bistability. The energy of high amplitude solitons increases quadratically with their width, whereas the energy of medium amplitude solitons may decrease or increase with the width depending on the parameter region. Furthermore, we have investigated the long term evolution of the continuous-wave solutions under modulational instability, showing that medium amplitude solitons can arise in this scenario. Additionally, we assessed the effects of second- and third-order dispersion on medium and high amplitude solitons and found that both remain stable in the presence of these terms.
2025
Authors
Descalzi, O; Facao, M; Carvalho, MI; Cartes, C; Brand, HR;
Publication
PHYSICA D-NONLINEAR PHENOMENA
Abstract
We study the dynamics as well as the interaction of stable dissipative solitons (DSs) of the cubic complex Ginzburg-Landau equation which are stabilized only by nonlinear gradient (NLG) terms. First we review stationary, periodic, quasi-periodic, and chaotic solutions. Then we investigate sudden transitions to chaotic from periodic and vice versa as a function of one parameter, as well as different outcomes, for fixed parameters, when varying the initial condition. In addition, we present a quasi-analytic approach to evaluate the separation of nearby trajectories for the case of stationary DSs as well as for periodic DSs, both stabilized by nonlinear gradient terms. In a separate section collisions between different types of DSs are reviewed. First we present a concise review of collisions of DSs without NLG terms and then the results of collisions between stationary DSs stabilized by NLG terms are summarized focusing on the influence of the nonlinear gradient term associated with the Raman effect. We point out that both, meandering oscillatory bound states as well as bound states with large amplitude oscillations appear to be specific for coupled cubic complex Ginzburg-Landau equations with a stabilizing cubic nonlinear gradient term.
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