Abstract
An early diagnosis of cancer is essential for a good prognosis, and the identification of differentially expressed genes can enable a better personalization of the treatment plan that can target those genes in therapy. This work proposes a pipeline that predicts the presence of lung cancer and the subtype allowing the identification of differentially expressed genes for lung cancer adenocarcinoma and squamous cell carcinoma subtypes. A gradient boosted tree model is used for the classification tasks based on RNA-seq data. The analysis of gene expressions that better differentiate cancerous from normal tissue, and features that distinguish between lung subtypes is the main focus of the present work. Differential expressed genes are analyzed by performing hierarchical clustering in order to identify gene signatures that are commonly regulated and biological signatures associated with a specific subtype. This analysis highlighted patterns of commonly regulated genes already known in the literature as cancer or subtype-specific genes, and others that are not yet documented in the literature.

Abstract
Echocardiography-based cardiac boundary tracking provides valuable information about the heart condition for interventional procedures and intensive care applications. Nevertheless, echocardiographic images come with several issues, making it a challenging task to develop a tracking and segmentation algorithm that is robust to shadows, occlusions, and heart rate changes. We propose an autonomous tracking method to improve the robustness and efficiency of echocardiographic tracking. A method denoted by hybrid Condensation and adaptive Kalman filter (HCAKF) is proposed to overcome tracking challenges of echocardiograms, such as variable heart rate and sensitivity to the initialization stage. The tracking process is initiated by utilizing active shape model, which provides the tracking methods with a number of tracking features. The procedure tracks the endocardium borders, and it is able to adapt to changes in the cardiac boundaries velocity and visibility. HCAKF enables one to use a much smaller number of samples that is used in Condensation without sacrificing tracking accuracy. Furthermore, despite combining the two methods, our complexity analysis shows that HCAKF can produce results in real-time. The obtained results demonstrate the robustness of the proposed method to the changes in the heart rate, yielding an Hausdorff distance of 1.032 +/- 0.375 while providing adequate efficiency for real-time operations.

Abstract
Microscopy images have been increasingly analyzed quantitatively in biomedical research. Segmenting individual cell nucleus is an important step as many research studies involve counting cell nuclei and analysing their shape. We propose a novel weakly supervised instance segmentation method trained with image segmentation masks only. Our system comprises two models: an implicit shape Multi-Layer Perceptron (MLP) that learns the shape of the nuclei in canonical coordinates; and 2) an encoder that predicts the parameters of the affine transformation to deform the canonical shape into the correct location, scale, and orientation in the image. To further improve the performance of the model, we propose a loss that uses the total number of nuclei in an image as supervision. Our system is explainable, as the implicit shape MLP learns that the canonical shape of the cell nuclei is a circle, and interpretable as the output of the encoder are parameters of affine transformations. We obtain image segmentation performance close to DeepLabV3 and, additionally, obtain an F1-scoreIoU=0.5 of 68.47% at the instance segmentation task, even though the system was trained with image segmentations. © 2022 P. Costa, A. Gaudio, A. Campilho & J.S. Cardoso.

Abstract
Is there an initialization for deep networks that requires no learning? ExplainFix adopts two design principles: the fixed filters principle that all spatial filter weights of convolutional neural networks can be fixed at initialization and never learned, and the nimbleness principle that only few network parameters suffice. We contribute (a) visual model-based explanations, (b) speed and accuracy gains, and (c) novel tools for deep convolutional neural networks. ExplainFix gives key insights that spatially fixed networks should have a steered initialization, that spatial convolution layers tend to prioritize low frequencies, and that most network parameters are not necessary in spatially fixed models. ExplainFix models have up to x100 fewer spatial filter kernels than fully learned models and matching or improved accuracy. Our extensive empirical analysis confirms that ExplainFix guarantees nimbler models (train up to 17% faster with channel pruning), matching or improved predictive performance (spanning 13 distinct baseline models, four architectures and two medical image datasets), improved robustness to larger learning rate, and robustness to varying model size. We are first to demonstrate that all spatial filters in state-of-the-art convolutional deep networks can be fixed at initialization, not learned.This article is categorized under:Technologies > Machine LearningFundamental Concepts of Data and Knowledge > Explainable AIFundamental Concepts of Data and Knowledge > Key Design Issues in Data Mining

Abstract
Optical Fiber Tweezers (OFT) can be used to study manifestations of light-matter interactions and deduce properties of micron-sized bioparticles trapped within its laser focal point. Our group has previously co-invented an innovative approach for this purpose based on advanced optical signal processing named iLoF-intelligent Lab on Fiber- with very relevant results revealing it is possible to create a variety of time and frequency magnitude features for label-free and non-invasive optical fiber sensing technologies. Nevertheless, phase spectra has been neglected in these photonics approaches. In this context, we present an exploratory study on informative content extraction from phase of OFT back-scattering signals. Furthermore, we analyze if these phase features provide better discriminative performance when compared spectrum magnitude ones previously used by the iLoF technology. The phase spectrum of back-scattering signals showed to retain patterns related to the intrinsic properties of each particle and the derived set of features proved to be robust to detect and discriminate from synthetic microparticles to highly similar cancer-derived mammalian cells, with better discriminative potential than their previous magnitude spectral counterparts. Such results introduce phase as a potential new domain to obtain discriminative light pattern features from OFT systems applied to micron-sized particles detection. The high sensitivity of the analyzed phase features to different micron-sized bioparticles, namely cancer-associated glycoforms, presents great potential for future applications in point-of-care diagnosis, such as detection and identification of molecules circulating in the blood or its derivatives with important clinical outcomes.

Abstract
Purpose This study aims to investigate retinal and choroidal vascular reactivity to carbogen in central serous chorioretinopathy (CSC) patients. Methods An experimental pilot study including 68 eyes from 20 CSC patients and 14 age and sex-matched controls was performed. The participants inhaled carbogen (5% CO2 + 95% O-2) for 2 min through a high-concentration disposable mask. A 30 degrees disc-centered fundus imaging using infra-red (IR) and macular spectral domain optical coherence tomography (SD-OCT) using the enhanced depth imaging (EDI) technique was performed, both at baseline and after a 2-min gas exposure. A parametric model fitting-based approach for automatic retinal blood vessel caliber estimation was used to assess the mean variation in both arterial and venous vasculature. Choroidal thickness was measured in two different ways: the subfoveal choroidal thickness (SFCT) was calculated using a manual caliper and the mean central choroidal thickness (MCCT) was assessed using an automatic software. Results No significant differences were detected in baseline hemodynamic parameters between both groups. A significant positive correlation was found between the participants' age and arterial diameter variation (p < 0.001, r= 0.447), meaning that younger participants presented a more vasoconstrictive response (negative variation) than older ones. No significant differences were detected in the vasoreactive response between CSC and controls for both arterial and venous vessels (p = 0.63 and p = 0.85, respectively). Although the vascular reactivity was not related to the activity of CSC, it was related to the time of disease, for both the arterial (p = 0.02, r = 0.381) and venous (p = 0.001, r= 0.530) beds. SFCT and MCCT were highly correlated (r= 0.830, p < 0.001). Both SFCT and MCCT significantly increased in CSC patients (p < 0.001 and p < 0.001) but not in controls (p = 0.059 and 0.247). A significant negative correlation between CSC patients' age and MCCT variation (r = - 0.340, p = 0.049) was detected. In CSC patients, the choroidal thickness variation was not related to the activity state, time of disease, or previous photodynamic treatment. Conclusion Vasoreactivity to carbogen was similar in the retinal vessels but significantly higher in the choroidal vessels of CSC patients when compared to controls, strengthening the hypothesis of a choroidal regulation dysfunction in this pathology.